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Diff for /imach/src/imach.c between versions 1.234 and 1.333

-version 1.234, 2016/08/23 16:51:20
+version 1.333, 2022/08/21 09:10:30
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.333  2022/08/21 09:10:30  brouard
+   * src/imach.c (Module): Version 0.99r33 A lot of changes in
+   reassigning covariates: my first idea was that people will always
+   use the first covariate V1 into the model but in fact they are
+   producing data with many covariates and can use an equation model
+   with some of the covariate; it means that in a model V2+V3 instead
+   of codtabm(k,Tvaraff[j]) which calculates for combination k, for
+   three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
+   the equation model is restricted to two variables only (V2, V3)
+   and the combination for V2 should be codtabm(k,1) instead of
+   (codtabm(k,2), and the code should be
+   codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
+   made. All of these should be simplified once a day like we did in
+   hpxij() for example by using precov[nres] which is computed in
+   decoderesult for each nres of each resultline. Loop should be done
+   on the equation model globally by distinguishing only product with
+   age (which are changing with age) and no more on type of
+   covariates, single dummies, single covariates.
+   Revision 1.332  2022/08/21 09:06:25  brouard
+   Summary: Version 0.99r33
+   * src/imach.c (Module): Version 0.99r33 A lot of changes in
+   reassigning covariates: my first idea was that people will always
+   use the first covariate V1 into the model but in fact they are
+   producing data with many covariates and can use an equation model
+   with some of the covariate; it means that in a model V2+V3 instead
+   of codtabm(k,Tvaraff[j]) which calculates for combination k, for
+   three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
+   the equation model is restricted to two variables only (V2, V3)
+   and the combination for V2 should be codtabm(k,1) instead of
+   (codtabm(k,2), and the code should be
+   codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
+   made. All of these should be simplified once a day like we did in
+   hpxij() for example by using precov[nres] which is computed in
+   decoderesult for each nres of each resultline. Loop should be done
+   on the equation model globally by distinguishing only product with
+   age (which are changing with age) and no more on type of
+   covariates, single dummies, single covariates.
+   Revision 1.331  2022/08/07 05:40:09  brouard
+   *** empty log message ***
+   Revision 1.330  2022/08/06 07:18:25  brouard
+   Summary: last 0.99r31
+   *  imach.c (Module): Version of imach using partly decoderesult to rebuild xpxij function
+   Revision 1.329  2022/08/03 17:29:54  brouard
+   *  imach.c (Module): Many errors in graphs fixed with Vn*age covariates.
+   Revision 1.328  2022/07/27 17:40:48  brouard
+   Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage
+   Revision 1.327  2022/07/27 14:47:35  brouard
+   Summary: Still a problem for one-step probabilities in case of quantitative variables
+   Revision 1.326  2022/07/26 17:33:55  brouard
+   Summary: some test with nres=1
+   Revision 1.325  2022/07/25 14:27:23  brouard
+   Summary: r30
+   * imach.c (Module): Error cptcovn instead of nsd in bmij (was
+   coredumped, revealed by Feiuno, thank you.
+   Revision 1.324  2022/07/23 17:44:26  brouard
+   *** empty log message ***
+   Revision 1.323  2022/07/22 12:30:08  brouard
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.322  2022/07/22 12:27:48  brouard
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.321  2022/07/22 12:04:24  brouard
+   Summary: r28
+   *  imach.c (Module): Output of Wald test in the htm file and not only in the log.
+   Revision 1.320  2022/06/02 05:10:11  brouard
+   *** empty log message ***
+   Revision 1.319  2022/06/02 04:45:11  brouard
+   * imach.c (Module): Adding the Wald tests from the log to the main
+   htm for better display of the maximum likelihood estimators.
+   Revision 1.318  2022/05/24 08:10:59  brouard
+   * imach.c (Module): Some attempts to find a bug of wrong estimates
+   of confidencce intervals with product in the equation modelC
+   Revision 1.317  2022/05/15 15:06:23  brouard
+   * imach.c (Module):  Some minor improvements
+   Revision 1.316  2022/05/11 15:11:31  brouard
+   Summary: r27
+   Revision 1.315  2022/05/11 15:06:32  brouard
+   *** empty log message ***
+   Revision 1.314  2022/04/13 17:43:09  brouard
+   * imach.c (Module): Adding link to text data files
+   Revision 1.313  2022/04/11 15:57:42  brouard
+   * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
+   Revision 1.312  2022/04/05 21:24:39  brouard
+   *** empty log message ***
+   Revision 1.311  2022/04/05 21:03:51  brouard
+   Summary: Fixed quantitative covariates
+           Fixed covariates (dummy or quantitative)
+         with missing values have never been allowed but are ERRORS and
+         program quits. Standard deviations of fixed covariates were
+         wrongly computed. Mean and standard deviations of time varying
+         covariates are still not computed.
+   Revision 1.310  2022/03/17 08:45:53  brouard
+   Summary: 99r25
+   Improving detection of errors: result lines should be compatible with
+   the model.
+   Revision 1.309  2021/05/20 12:39:14  brouard
+   Summary: Version 0.99r24
+   Revision 1.308  2021/03/31 13:11:57  brouard
+   Summary: Version 0.99r23
+   * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
+   Revision 1.307  2021/03/08 18:11:32  brouard
+   Summary: 0.99r22 fixed bug on result:
+   Revision 1.306  2021/02/20 15:44:02  brouard
+   Summary: Version 0.99r21
+   * imach.c (Module): Fix bug on quitting after result lines!
+   (Module): Version 0.99r21
+   Revision 1.305  2021/02/20 15:28:30  brouard
+   * imach.c (Module): Fix bug on quitting after result lines!
+   Revision 1.304  2021/02/12 11:34:20  brouard
+   * imach.c (Module): The use of a Windows BOM (huge) file is now an error
+   Revision 1.303  2021/02/11 19:50:15  brouard
+   *  (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
+   Revision 1.302  2020/02/22 21:00:05  brouard
+   *  (Module): imach.c Update mle=-3 (for computing Life expectancy
+   and life table from the data without any state)
+   Revision 1.301  2019/06/04 13:51:20  brouard
+   Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
+   Revision 1.300  2019/05/22 19:09:45  brouard
+   Summary: version 0.99r19 of May 2019
+   Revision 1.299  2019/05/22 18:37:08  brouard
+   Summary: Cleaned 0.99r19
+   Revision 1.298  2019/05/22 18:19:56  brouard
+   *** empty log message ***
+   Revision 1.297  2019/05/22 17:56:10  brouard
+   Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
+   Revision 1.296  2019/05/20 13:03:18  brouard
+   Summary: Projection syntax simplified
+   We can now start projections, forward or backward, from the mean date
+   of inteviews up to or down to a number of years of projection:
+   prevforecast=1 yearsfproj=15.3 mobil_average=0
+   or
+   prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
+   or
+   prevbackcast=1 yearsbproj=12.3 mobil_average=1
+   or
+   prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
+   Revision 1.295  2019/05/18 09:52:50  brouard
+   Summary: doxygen tex bug
+   Revision 1.294  2019/05/16 14:54:33  brouard
+   Summary: There was some wrong lines added
+   Revision 1.293  2019/05/09 15:17:34  brouard
+   *** empty log message ***
+   Revision 1.292  2019/05/09 14:17:20  brouard
+   Summary: Some updates
+   Revision 1.291  2019/05/09 13:44:18  brouard
+   Summary: Before ncovmax
+   Revision 1.290  2019/05/09 13:39:37  brouard
+   Summary: 0.99r18 unlimited number of individuals
+   The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
+   Revision 1.289  2018/12/13 09:16:26  brouard
+   Summary: Bug for young ages (<-30) will be in r17
+   Revision 1.288  2018/05/02 20:58:27  brouard
+   Summary: Some bugs fixed
+   Revision 1.287  2018/05/01 17:57:25  brouard
+   Summary: Bug fixed by providing frequencies only for non missing covariates
+   Revision 1.286  2018/04/27 14:27:04  brouard
+   Summary: some minor bugs
+   Revision 1.285  2018/04/21 21:02:16  brouard
+   Summary: Some bugs fixed, valgrind tested
+   Revision 1.284  2018/04/20 05:22:13  brouard
+   Summary: Computing mean and stdeviation of fixed quantitative variables
+   Revision 1.283  2018/04/19 14:49:16  brouard
+   Summary: Some minor bugs fixed
+   Revision 1.282  2018/02/27 22:50:02  brouard
+   *** empty log message ***
+   Revision 1.281  2018/02/27 19:25:23  brouard
+   Summary: Adding second argument for quitting
+   Revision 1.280  2018/02/21 07:58:13  brouard
+   Summary: 0.99r15
+   New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
+   Revision 1.279  2017/07/20 13:35:01  brouard
+   Summary: temporary working
+   Revision 1.278  2017/07/19 14:09:02  brouard
+   Summary: Bug for mobil_average=0 and prevforecast fixed(?)
+   Revision 1.277  2017/07/17 08:53:49  brouard
+   Summary: BOM files can be read now
+   Revision 1.276  2017/06/30 15:48:31  brouard
+   Summary: Graphs improvements
+   Revision 1.275  2017/06/30 13:39:33  brouard
+   Summary: Saito's color
+   Revision 1.274  2017/06/29 09:47:08  brouard
+   Summary: Version 0.99r14
+   Revision 1.273  2017/06/27 11:06:02  brouard
+   Summary: More documentation on projections
+   Revision 1.272  2017/06/27 10:22:40  brouard
+   Summary: Color of backprojection changed from 6 to 5(yellow)
+   Revision 1.271  2017/06/27 10:17:50  brouard
+   Summary: Some bug with rint
+   Revision 1.270  2017/05/24 05:45:29  brouard
+   *** empty log message ***
+   Revision 1.269  2017/05/23 08:39:25  brouard
+   Summary: Code into subroutine, cleanings
+   Revision 1.268  2017/05/18 20:09:32  brouard
+   Summary: backprojection and confidence intervals of backprevalence
+   Revision 1.267  2017/05/13 10:25:05  brouard
+   Summary: temporary save for backprojection
+   Revision 1.266  2017/05/13 07:26:12  brouard
+   Summary: Version 0.99r13 (improvements and bugs fixed)
+   Revision 1.265  2017/04/26 16:22:11  brouard
+   Summary: imach 0.99r13 Some bugs fixed
+   Revision 1.264  2017/04/26 06:01:29  brouard
+   Summary: Labels in graphs
+   Revision 1.263  2017/04/24 15:23:15  brouard
+   Summary: to save
+   Revision 1.262  2017/04/18 16:48:12  brouard
+   *** empty log message ***
+   Revision 1.261  2017/04/05 10:14:09  brouard
+   Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
+   Revision 1.260  2017/04/04 17:46:59  brouard
+   Summary: Gnuplot indexations fixed (humm)
+   Revision 1.259  2017/04/04 13:01:16  brouard
+   Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
+   Revision 1.258  2017/04/03 10:17:47  brouard
+   Summary: Version 0.99r12
+   Some cleanings, conformed with updated documentation.
+   Revision 1.257  2017/03/29 16:53:30  brouard
+   Summary: Temp
+   Revision 1.256  2017/03/27 05:50:23  brouard
+   Summary: Temporary
+   Revision 1.255  2017/03/08 16:02:28  brouard
+   Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
+   Revision 1.254  2017/03/08 07:13:00  brouard
+   Summary: Fixing data parameter line
+   Revision 1.253  2016/12/15 11:59:41  brouard
+   Summary: 0.99 in progress
+   Revision 1.252  2016/09/15 21:15:37  brouard
+   *** empty log message ***
+   Revision 1.251  2016/09/15 15:01:13  brouard
+   Summary: not working
+   Revision 1.250  2016/09/08 16:07:27  brouard
+   Summary: continue
+   Revision 1.249  2016/09/07 17:14:18  brouard
+   Summary: Starting values from frequencies
+   Revision 1.248  2016/09/07 14:10:18  brouard
+   *** empty log message ***
+   Revision 1.247  2016/09/02 11:11:21  brouard
+   *** empty log message ***
+   Revision 1.246  2016/09/02 08:49:22  brouard
+   *** empty log message ***
+   Revision 1.245  2016/09/02 07:25:01  brouard
+   *** empty log message ***
+   Revision 1.244  2016/09/02 07:17:34  brouard
+   *** empty log message ***
+   Revision 1.243  2016/09/02 06:45:35  brouard
+   *** empty log message ***
+   Revision 1.242  2016/08/30 15:01:20  brouard
+   Summary: Fixing a lots
+   Revision 1.241  2016/08/29 17:17:25  brouard
+   Summary: gnuplot problem in Back projection to fix
+   Revision 1.240  2016/08/29 07:53:18  brouard
+   Summary: Better
+   Revision 1.239  2016/08/26 15:51:03  brouard
+   Summary: Improvement in Powell output in order to copy and paste
+   Author:
+   Revision 1.238  2016/08/26 14:23:35  brouard
+   Summary: Starting tests of 0.99
+   Revision 1.237  2016/08/26 09:20:19  brouard
+   Summary: to valgrind
+   Revision 1.236  2016/08/25 10:50:18  brouard
+   *** empty log message ***
+   Revision 1.235  2016/08/25 06:59:23  brouard
+   *** empty log message ***
    Revision 1.234  2016/08/23 16:51:20  brouard
    *** empty log message ***
- Line 75
+ Line 450
    Author: Nicolas Brouard
    Revision 1.210  2015/11/18 17:41:20  brouard
-   Summary: Start working on projected prevalences
+   Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
-   Revision 1.209  2015/11/17 22:12:03  brouard
    Summary: Adding ftolpl parameter
    Author: N Brouard
- Line 565
+ Line 938
    The same imach parameter file can be used but the option for mle should be -3.
-   Agnès, who wrote this part of the code, tried to keep most of the
+   Agnès, who wrote this part of the code, tried to keep most of the
    former routines in order to include the new code within the former code.
    The output is very simple: only an estimate of the intercept and of
- Line 720  Back prevalence and projections:
+ Line 1093  Back prevalence and projections:
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                          oldm=oldms;savm=savms;
-    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
       Computes the transition matrix starting at age 'age' over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
- Line 744  Important routines
+ Line 1117  Important routines
  - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
    and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
  - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
-   o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
+   o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
      race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
-   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
+   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
-            Institut national d'études démographiques, Paris.
+            Institut national d'études démographiques, Paris.
    This software have been partly granted by Euro-REVES, a concerted action
    from the European Union.
    It is copyrighted identically to a GNU software product, ie programme and
- Line 814  Important routines
+ Line 1187  Important routines
  #define POWELLNOF3INFF1TEST /* Skip test */
  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
+ /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
  #include <math.h>
  #include <stdio.h>
- Line 865  typedef struct {
+ Line 1239  typedef struct {
  /* #include <libintl.h> */
  /* #define _(String) gettext (String) */
- #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
+ #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
  #define GNUPLOTPROGRAM "gnuplot"
  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
- #define FILENAMELENGTH 132
+ #define FILENAMELENGTH 256
  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
- Line 880  typedef struct {
+ Line 1254  typedef struct {
  #define NINTERVMAX 8
  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
+ #define NCOVMAX 30  /**< Maximum number of covariates used in the model, including generated covariates V1*V2 or V1*age */
  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
  #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
- #define MAXN 20000
+ /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
  #define YEARM 12. /**< Number of months per year */
  /* #define AGESUP 130 */
- #define AGESUP 150
+ /* #define AGESUP 150 */
+ #define AGESUP 200
+ #define AGEINF 0
  #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
  #define AGEBASE 40
  #define AGEOVERFLOW 1.e20
- Line 906  typedef struct {
+ Line 1282  typedef struct {
  /* $State$ */
  #include "version.h"
  char version[]=__IMACH_VERSION__;
- char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
+ char copyright[]="August 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";
  char fullversion[]="$Revision$ $Date$";
  char strstart[80];
  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
- /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
+ /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */
- int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
+ /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
- int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
+ int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age */
- int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
+ int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
+ int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
  int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
  int cptcovprodnoage=0; /**< Number of covariate products without age */
- int cptcoveff=0; /* Total number of covariates to vary for printing results */
+ int cptcoveff=0; /* Total number of covariates to vary for printing results (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */
  int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
  int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
  int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
- Line 930  int nqfveff=0; /**< nqfveff Number of Qu
+ Line 1307  int nqfveff=0; /**< nqfveff Number of Qu
  int ntveff=0; /**< ntveff number of effective time varying variables */
  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
  int cptcov=0; /* Working variable */
+ int nobs=10;  /* Number of observations in the data lastobs-firstobs */
  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
- int npar=NPARMAX;
+ int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
  int nlstate=2; /* Number of live states */
  int ndeath=1; /* Number of dead states */
  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
- Line 979  FILE *ficrescveij;
+ Line 1357  FILE *ficrescveij;
  char filerescve[FILENAMELENGTH];
  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
- FILE  *ficresvpl;
- char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char model[MAXLINE]; /**< The model line */
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
- Line 1020  double dval;
+ Line 1397  double dval;
  #define FTOL 1.0e-10
  #define NRANSI
  #define ITMAX 200
+ #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
  #define TOL 2.0e-4
- Line 1068  int *ncodemaxwundef;  /* ncodemax[j]= Nu
+ Line 1446  int *ncodemaxwundef;  /* ncodemax[j]= Nu
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
  double **pmmij, ***probs; /* Global pointer */
  double ***mobaverage, ***mobaverages; /* New global variable */
+ double **precov; /* New global variable to store for each resultline, values of model covariates given by the resultlines (in order to speed up)  */
  double *ageexmed,*agecens;
  double dateintmean=0;
+   double anprojd, mprojd, jprojd; /* For eventual projections */
+   double anprojf, mprojf, jprojf;
+   double anbackd, mbackd, jbackd; /* For eventual backprojections */
+   double anbackf, mbackf, jbackf;
+   double jintmean,mintmean,aintmean;
  double *weight;
  int **s; /* Status */
  double *agedc;
  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                    * covar=matrix(0,NCOVMAX,1,n);
                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
- double **coqvar; /* Fixed quantitative covariate iqv */
+ double **coqvar; /* Fixed quantitative covariate nqv */
- double ***cotvar; /* Time varying covariate itv */
+ double ***cotvar; /* Time varying covariate ntv */
  double ***cotqvar; /* Time varying quantitative covariate itqv */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
- /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ /* Some documentation */
- /*k          1  2   3   4     5    6    7     8    9 */
+       /*   Design original data
- /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
+        *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12
- /* Tndvar[k]    1   2   3               4          5 */
+        *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
- /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
+        *                                                             ntv=3     nqtv=1
- /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
+        *  cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
- /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
+        * For time varying covariate, quanti or dummies
- /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
+        *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
- /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
+        *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
- /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
+        *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
- /* Tprod[i]=k           4               7            */
+        *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
- /* Tage[i]=k                  5               8      */
+        *       covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
- /* */
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
+        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
+        *   k=  1    2      3       4     5       6      7        8   9     10       11
+        */
+ /* According to the model, more columns can be added to covar by the product of covariates */
+ /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
+   # States 1=Coresidence, 2 Living alone, 3 Institution
+   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
+ */
+ /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ /*    k        1  2   3   4     5    6    7     8    9 */
+ /*Typevar[k]=  0  0   0   2     1    0    2     1    0 *//*0 for simple covariate (dummy, quantitative,*/
+                                                          /* fixed or varying), 1 for age product, 2 for*/
+                                                          /* product */
+ /*Dummy[k]=    1  0   0   1     3    1    1     2    0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
+                                                          /*(single or product without age), 2 dummy*/
+                                                          /* with age product, 3 quant with age product*/
+ /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
+ /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
+ /*TnsdVar[Tvar]   1   2                              3 */
+ /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
+ /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */
+ /*    nsq      1                     2                 */ /* Counting single quantit tv */
+ /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */
+ /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */
+ /* Tprod[i]=k             1               2            */ /* Position in model of the ith prod without age */
+ /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */
+ /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */
+ /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */
+ /* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/
+ /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
+ /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
  /* Type                    */
  /* V         1  2  3  4  5 */
  /*           F  F  V  V  V */
  /*           D  Q  D  D  Q */
  /*                         */
  int *TvarsD;
+ int *TnsdVar;
  int *TvarsDind;
  int *TvarsQ;
  int *TvarsQind;
+ #define MAXRESULTLINESPONE 10+1
+ int nresult=0;
+ int parameterline=0; /* # of the parameter (type) line */
+ int TKresult[MAXRESULTLINESPONE];
+ int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model correspond to the k3 position in the resultline */
+ int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
+ int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line  */
+ double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
+ int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */
+ double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
+ double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
+ int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
+ /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
+   # States 1=Coresidence, 2 Living alone, 3 Institution
+   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
+ */
  /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
  int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
  int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
- Line 1126  double *Tvalsel; /**< Selected modality
+ Line 1559  double *Tvalsel; /**< Selected modality
  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
  int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
  int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
+ int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
  int *Tage;
  int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
  int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
- Line 1134  int *TmodelInvQind; /** Tmodelqind[1]=1
+ Line 1569  int *TmodelInvQind; /** Tmodelqind[1]=1
  int *Ndum; /** Freq of modality (tricode */
  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
  int **Tvard;
+ int **Tvardk;
  int *Tprod;/**< Gives the k position of the k1 product */
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
  int *Tposprod; /**< Gives the k1 product from the k position */
- /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
-    if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
-    Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
- */
  int cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
- Line 1305  char *cutl(char *blocc, char *alocc, cha
+ Line 1740  char *cutl(char *blocc, char *alocc, cha
  {
    /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
-      gives blocc="abcdef" and alocc="ghi2j".
+      gives alocc="abcdef" and blocc="ghi2j".
       If occ is not found blocc is null and alocc is equal to in. Returns blocc
    */
    char *s, *t;
- Line 1587  char *subdirf(char fileres[])
+ Line 2022  char *subdirf(char fileres[])
  /*************** function subdirf2 ***********/
  char *subdirf2(char fileres[], char *preop)
  {
+   /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
+  Errors in subdirf, 2, 3 while printing tmpout is
+  rewritten within the same printf. Workaround: many printfs */
    /* Caution optionfilefiname is hidden */
    strcpy(tmpout,optionfilefiname);
    strcat(tmpout,"/");
- Line 1958  void linmin(double p[], double xi[], int
+ Line 2395  void linmin(double p[], double xi[], int
  #endif
  #ifdef LINMINORIGINAL
  #else
-         if(fb == fx){ /* Flat function in the direction */
+   if(fb == fx){ /* Flat function in the direction */
-                 xmin=xx;
+     xmin=xx;
      *flat=1;
-         }else{
+   }else{
      *flat=0;
  #endif
                  /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
- Line 2019  void linmin(double p[], double xi[], int
+ Line 2456  void linmin(double p[], double xi[], int
  /*************** powell ************************/
  /*
- Minimization of a function func of n variables. Input consists of an initial starting point
+ Minimization of a function func of n variables. Input consists in an initial starting point
- p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
+ p[1..n] ; an initial matrix xi[1..n][1..n]  whose columns contain the initial set of di-
- rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
+ rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
- such that failure to decrease by more than this amount on one iteration signals doneness. On
+ such that failure to decrease by more than this amount in one iteration signals doneness. On
  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
  function value at p , and iter is the number of iterations taken. The routine linmin is used.
   */
- Line 2038  void powell(double p[], double **xi, int
+ Line 2475  void powell(double p[], double **xi, int
   void linmin(double p[], double xi[], int n, double *fret,
                double (*func)(double []));
  #else
   void linmin(double p[], double xi[], int n, double *fret,
-                                                  double (*func)(double []),int *flat);
+              double (*func)(double []),int *flat);
  #endif
-   int i,ibig,j;
+  int i,ibig,j,jk,k;
    double del,t,*pt,*ptt,*xit;
    double directest;
    double fp,fptt;
    double *xits;
    int niterf, itmp;
- #ifdef LINMINORIGINAL
- #else
-   flatdir=ivector(1,n);
-   for (j=1;j<=n;j++) flatdir[j]=0;
- #endif
    pt=vector(1,n);
    ptt=vector(1,n);
- Line 2062  void powell(double p[], double **xi, int
+ Line 2493  void powell(double p[], double **xi, int
    for (j=1;j<=n;j++) pt[j]=p[j];
    rcurr_time = time(NULL);
    for (*iter=1;;++(*iter)) {
-     fp=(*fret); /* From former iteration or initial value */
      ibig=0;
      del=0.0;
      rlast_time=rcurr_time;
      /* (void) gettimeofday(&curr_time,&tzp); */
      rcurr_time = time(NULL);
      curr_time = *localtime(&rcurr_time);
-     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
+     printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
-     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
+     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
+     fp=(*fret); /* From former iteration or initial value */
      for (i=1;i<=n;i++) {
-       printf(" %d %.12f",i, p[i]);
-       fprintf(ficlog," %d %.12lf",i, p[i]);
        fprintf(ficrespow," %.12lf", p[i]);
      }
+     fprintf(ficrespow,"\n");fflush(ficrespow);
+     printf("\n#model=  1      +     age ");
+     fprintf(ficlog,"\n#model=  1      +     age ");
+     if(nagesqr==1){
+         printf("  + age*age  ");
+         fprintf(ficlog,"  + age*age  ");
+     }
+     for(j=1;j <=ncovmodel-2;j++){
+       if(Typevar[j]==0) {
+         printf("  +      V%d  ",Tvar[j]);
+         fprintf(ficlog,"  +      V%d  ",Tvar[j]);
+       }else if(Typevar[j]==1) {
+         printf("  +    V%d*age ",Tvar[j]);
+         fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
+       }else if(Typevar[j]==2) {
+         printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+       }
+     }
      printf("\n");
+ /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
+ /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
      fprintf(ficlog,"\n");
-     fprintf(ficrespow,"\n");fflush(ficrespow);
+     for(i=1,jk=1; i <=nlstate; i++){
-     if(*iter <=3){
+       for(k=1; k <=(nlstate+ndeath); k++){
+         if (k != i) {
+           printf("%d%d ",i,k);
+           fprintf(ficlog,"%d%d ",i,k);
+           for(j=1; j <=ncovmodel; j++){
+             printf("%12.7f ",p[jk]);
+             fprintf(ficlog,"%12.7f ",p[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+         }
+       }
+     }
+     if(*iter <=3 && *iter >1){
        tml = *localtime(&rcurr_time);
        strcpy(strcurr,asctime(&tml));
        rforecast_time=rcurr_time;
        itmp = strlen(strcurr);
        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-                                 strcurr[itmp-1]='\0';
+         strcurr[itmp-1]='\0';
        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
        for(niterf=10;niterf<=30;niterf+=10){
-                                 rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-                                 forecast_time = *localtime(&rforecast_time);
+         forecast_time = *localtime(&rforecast_time);
-                                 strcpy(strfor,asctime(&forecast_time));
+         strcpy(strfor,asctime(&forecast_time));
-                                 itmp = strlen(strfor);
+         itmp = strlen(strfor);
-                                 if(strfor[itmp-1]=='\n')
+         if(strfor[itmp-1]=='\n')
-                                         strfor[itmp-1]='\0';
+           strfor[itmp-1]='\0';
-                                 printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-                                 fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
        }
      }
      for (i=1;i<=n;i++) { /* For each direction i */
- Line 2143  void powell(double p[], double **xi, int
+ Line 2607  void powell(double p[], double **xi, int
      /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
      /* New value of last point Pn is not computed, P(n-1) */
-       for(j=1;j<=n;j++) {
+     for(j=1;j<=n;j++) {
-                                 if(flatdir[j] >0){
+       if(flatdir[j] >0){
-                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
-                                 }
+       }
-                                 /* printf("\n"); */
+       /* printf("\n"); */
-                                 /* fprintf(ficlog,"\n"); */
+       /* fprintf(ficlog,"\n"); */
-                         }
+     }
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
+     /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
+     if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
- Line 2187  void powell(double p[], double **xi, int
+ Line 2652  void powell(double p[], double **xi, int
        }
  #endif
- #ifdef LINMINORIGINAL
- #else
-       free_ivector(flatdir,1,n);
- #endif
        free_vector(xit,1,n);
        free_vector(xits,1,n);
        free_vector(ptt,1,n);
        free_vector(pt,1,n);
        return;
      } /* enough precision */
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
        ptt[j]=2.0*p[j]-pt[j];
        xit[j]=p[j]-pt[j];
- Line 2294  void powell(double p[], double **xi, int
+ Line 2755  void powell(double p[], double **xi, int
              flatd++;
          }
          if(flatd >0){
-           printf("%d flat directions\n",flatd);
+           printf("%d flat directions: ",flatd);
-           fprintf(ficlog,"%d flat directions\n",flatd);
+           fprintf(ficlog,"%d flat directions :",flatd);
            for (j=1;j<=n;j++) {
              if(flatdir[j]>0){
                printf("%d ",j);
- Line 2304  void powell(double p[], double **xi, int
+ Line 2765  void powell(double p[], double **xi, int
            }
            printf("\n");
            fprintf(ficlog,"\n");
+ #ifdef FLATSUP
+           free_vector(xit,1,n);
+           free_vector(xits,1,n);
+           free_vector(ptt,1,n);
+           free_vector(pt,1,n);
+           return;
+ #endif
          }
  #endif
          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
- Line 2333  void powell(double p[], double **xi, int
+ Line 2801  void powell(double p[], double **xi, int
  /**** Prevalence limit (stable or period prevalence)  ****************/
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
+   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
    {
-     /* Computes the prevalence limit in each live state at age x and for covariate combiation ij by left multiplying the unit
+     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
-        matrix by transitions matrix until convergence is reached with precision ftolpl */
+      *   (and selected quantitative values in nres)
-   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
+      *  by left multiplying the unit
-   /* Wx is row vector: population in state 1, population in state 2, population dead */
+      *  matrix by transitions matrix until convergence is reached with precision ftolpl
-   /* or prevalence in state 1, prevalence in state 2, 0 */
+      * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
-   /* newm is the matrix after multiplications, its rows are identical at a factor */
+      * Wx is row vector: population in state 1, population in state 2, population dead
-   /* Initial matrix pimij */
+      * or prevalence in state 1, prevalence in state 2, 0
+      * newm is the matrix after multiplications, its rows are identical at a factor.
+      * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
+      * Output is prlim.
+      * Initial matrix pimij
+      */
    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
    /*  0,                   0                  , 1} */
- Line 2355  double **prevalim(double **prlim, int nl
+ Line 2828  double **prevalim(double **prlim, int nl
    /*  0.51326036147820708, 0.48673963852179264} */
    /* If we start from prlim again, prlim tends to a constant matrix */
-   int i, ii,j,k;
+     int i, ii,j,k, k1;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
    double **newm;
    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
    int ncvloop=0;
+   int first=0;
    min=vector(1,nlstate);
    max=vector(1,nlstate);
- Line 2382  double **prevalim(double **prlim, int nl
+ Line 2856  double **prevalim(double **prlim, int nl
      newm=savm;
      /* Covariates have to be included here again */
      cov[2]=agefin;
-     if(nagesqr==1)
+      if(nagesqr==1){
-       cov[3]= agefin*agefin;;
+       cov[3]= agefin*agefin;
-     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
+      }
-                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
+      /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
-       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
+      /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
-       printf("prevalim ij=%d k=%d TvarsD[%d]=%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k));
+      for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-     }
+        if(Typevar[k1]==1){ /* A product with age */
-     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
+          cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+        }else{
-       /* cov[2+nagesqr+TvarsQind[k]]=qselvar[k]; */
+          cov[2+nagesqr+k1]=precov[nres][k1];
-       printf("prevalim ij=%d k=%d  TvarsQind[%d]=%d \n",ij,k,k,TvarsQind[k]);
+        }
-     }
+      }/* End of loop on model equation */
-     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
+ /* Start of old code (replaced by a loop on position in the model equation */
-     for (k=1; k<=cptcovage;k++){
+     /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only of the model *\/ */
-       if(Dummy[Tvar[Tage[k]]]){
+     /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
-         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+     /*   /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; *\/ */
-       } else{
+     /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])]; */
-         ;
+     /*   /\* model = 1 +age + V1*V3 + age*V1 + V2 + V1 + age*V2 + V3 + V3*age + V1*V2  */
-         /* cov[2+nagesqr+Tage[k]]=qselvar[k]; */
+     /*    * k                  1        2      3    4      5      6     7        8 */
-       }
+     /*    *cov[]   1    2      3        4      5    6      7      8     9       10 */
-       printf("prevalim Age ij=%d k=%d  Tage[%d]=%d \n",ij,k,k,Tage[k]);
+     /*    *TypeVar[k]          2        1      0    0      1      0     1        2 */
-     }
+     /*    *Dummy[k]            0        2      0    0      2      0     2        0 */
-     for (k=1; k<=cptcovprod;k++){ /*  */
+     /*    *Tvar[k]             4        1      2    1      2      3     3        5 */
-       printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=%d, Tvard[%d][2]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]);
+     /*    *nsd=3                              (1)  (2)           (3) */
-       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+     /*    *TvarsD[nsd]                      [1]=2    1             3 */
-     }
+     /*    *TnsdVar                          [2]=2 [1]=1         [3]=3 */
+     /*    *TvarsDind[nsd](=k)               [1]=3 [2]=4         [3]=6 */
+     /*    *Tage[]                  [1]=1                  [2]=2      [3]=3 */
+     /*    *Tvard[]       [1][1]=1                                           [2][1]=1 */
+     /*    *                   [1][2]=3                                           [2][2]=2 */
+     /*    *Tprod[](=k)     [1]=1                                              [2]=8 */
+     /*    *TvarsDp(=Tvar)   [1]=1            [2]=2             [3]=3          [4]=5 */
+     /*    *TvarD (=k)       [1]=1            [2]=3 [3]=4       [3]=6          [4]=6 */
+     /*    *TvarsDpType */
+     /*    *si model= 1 + age + V3 + V2*age + V2 + V3*age */
+     /*    * nsd=1              (1)           (2) */
+     /*    *TvarsD[nsd]          3             2 */
+     /*    *TnsdVar           (3)=1          (2)=2 */
+     /*    *TvarsDind[nsd](=k)  [1]=1        [2]=3 */
+     /*    *Tage[]                  [1]=2           [2]= 3    */
+     /*    *\/ */
+     /*   /\* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; *\/ */
+     /*   /\* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
+     /* } */
+     /* for (k=1; k<=nsq;k++) { /\* For single quantitative varying covariates only of the model *\/ */
+     /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
+     /*   /\* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 *\/ */
+     /*   /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
+     /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][resultmodel[nres][k1]] */
+     /*   /\* cov[++k1]=Tqresult[nres][k];  *\/ */
+     /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
+     /*   if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+     /*  /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
+     /*   } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
+     /*  /\* cov[++k1]=Tqresult[nres][k];  *\/ */
+     /*   } */
+     /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
+     /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
+     /*   if(Dummy[Tvard[k][1]]==0){ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+     /*    /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+     /*    /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; *\/ */
+     /*  } */
+     /*   }else{ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+     /*    /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; *\/ */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+     /*    /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
+     /*  } */
+     /*   } */
+     /* } /\* End product without age *\/ */
+ /* ENd of old code */
      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
-                 /* age and covariate values of ij are in 'cov' */
+     /* age and covariate values of ij are in 'cov' */
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
- Line 2449  double **prevalim(double **prlim, int nl
+ Line 2980  double **prevalim(double **prlim, int nl
        free_vector(meandiff,1,nlstate);
        return prlim;
      }
-   } /* age loop */
+   } /* agefin loop */
      /* After some age loop it doesn't converge */
-   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+   if(!first){
- Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+     first=1;
+     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+   }else if (first >=1 && first <10){
+     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+     first++;
+   }else if (first ==10){
+     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+     printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
+     fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
+     first++;
+   }
    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
    free_vector(min,1,nlstate);
    free_vector(max,1,nlstate);
- Line 2466  Earliest age to start was %d-%d=%d, ncvl
+ Line 3009  Earliest age to start was %d-%d=%d, ncvl
   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
-  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
+   double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
  {
-   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
+   /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
       matrix by transitions matrix until convergence is reached with precision ftolpl */
    /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
    /* Wx is row vector: population in state 1, population in state 2, population dead */
- Line 2488  Earliest age to start was %d-%d=%d, ncvl
+ Line 3031  Earliest age to start was %d-%d=%d, ncvl
    /*  0.51326036147820708, 0.48673963852179264} */
    /* If we start from prlim again, prlim tends to a constant matrix */
-   int i, ii,j,k;
+   int i, ii,j,k, k1;
+   int first=0;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
    double **out, cov[NCOVMAX+1], **bmij();
- Line 2503  Earliest age to start was %d-%d=%d, ncvl
+ Line 3047  Earliest age to start was %d-%d=%d, ncvl
    max=vector(1,nlstate);
    meandiff=vector(1,nlstate);
-         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
+   dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
-         oldm=oldms; savm=savms;
+   oldm=oldms; savm=savms;
-         /* Starting with matrix unity */
+   /* Starting with matrix unity */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-                 for (j=1;j<=nlstate+ndeath;j++){
+     for (j=1;j<=nlstate+ndeath;j++){
        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      }
- Line 2517  Earliest age to start was %d-%d=%d, ncvl
+ Line 3061  Earliest age to start was %d-%d=%d, ncvl
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
    /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
+   /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
+   for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
      ncvloop++;
      newm=savm; /* oldm should be kept from previous iteration or unity at start */
                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
      /* Covariates have to be included here again */
      cov[2]=agefin;
-     if(nagesqr==1)
+     if(nagesqr==1){
        cov[3]= agefin*agefin;;
-     for (k=1; k<=cptcovn;k++) {
+     }
-       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+     for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       if(Typevar[k1]==1){ /* A product with age */
-       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
+         cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-     }
+       }else{
-     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+         cov[2+nagesqr+k1]=precov[nres][k1];
-     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
+       }
-     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
+     }/* End of loop on model equation */
-     for (k=1; k<=cptcovprod;k++) /* Useless */
-       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+ /* Old code */
-       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+     /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
+     /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
+     /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; */
+     /*   /\* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
+     /* } */
+     /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
+     /* /\*   /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
+     /* /\*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
+     /* /\*   /\\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\\/ *\/ */
+     /* /\* } *\/ */
+     /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
+     /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
+     /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
+     /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* /\* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; *\/ */
+     /* /\* for (k=1; k<=cptcovprod;k++) /\\* Useless *\\/ *\/ */
+     /* /\*   /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\\/ *\/ */
+     /* /\*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+     /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
+     /*   /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age *\\/ ERROR ???*\/ */
+     /*   if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+     /*   } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
+     /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
+     /*   } */
+     /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+     /* } */
+     /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
+     /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
+     /*   if(Dummy[Tvard[k][1]]==0){ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+     /*  } */
+     /*   }else{ */
+     /*  if(Dummy[Tvard[k][2]]==0){ */
+     /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+     /*  }else{ */
+     /*    cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+     /*  } */
+     /*   } */
+     /* } */
      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- Line 2550  Earliest age to start was %d-%d=%d, ncvl
+ Line 3139  Earliest age to start was %d-%d=%d, ncvl
      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
+     /* if((int)age == 86 || (int)age == 87){ */
+     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
+     /*   for(i=1; i<=nlstate+ndeath; i++) { */
+     /*  printf("%d newm= ",i); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",newm[i][j]); */
+     /*  } */
+     /*  printf("oldm * "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",oldm[i][j]); */
+     /*  } */
+     /*  printf(" bmmij "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",pmmij[i][j]); */
+     /*  } */
+     /*  printf("\n"); */
+     /*   } */
+     /* } */
      savm=oldm;
      oldm=newm;
      for(j=1; j<=nlstate; j++){
        max[j]=0.;
        min[j]=1.;
- Line 2567  Earliest age to start was %d-%d=%d, ncvl
+ Line 3175  Earliest age to start was %d-%d=%d, ncvl
      maxmax=0.;
      for(i=1; i<=nlstate; i++){
-       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column, could be nan! */
        maxmax=FMAX(maxmax,meandiff[i]);
        /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
-     } /* j loop */
+     } /* i loop */
      *ncvyear= -( (int)age- (int)agefin);
-     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
      if(maxmax < ftolpl){
        /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
        free_vector(min,1,nlstate);
- Line 2580  Earliest age to start was %d-%d=%d, ncvl
+ Line 3188  Earliest age to start was %d-%d=%d, ncvl
        free_vector(meandiff,1,nlstate);
        return bprlim;
      }
-   } /* age loop */
+   } /* agefin loop */
      /* After some age loop it doesn't converge */
-   printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+   if(!first){
+     first=1;
+     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
+ Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+   }
+   fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
    free_vector(min,1,nlstate);
- Line 2597  Oldest age to start was %d-%d=%d, ncvloo
+ Line 3210  Oldest age to start was %d-%d=%d, ncvloo
  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
    /* According to parameters values stored in x and the covariate's values stored in cov,
-      computes the probability to be observed in state j being in state i by appying the
+      computes the probability to be observed in state j (after stepm years) being in state i by appying the
       model to the ncovmodel covariates (including constant and age).
       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
- Line 2606  double **pmij(double **ps, double *cov,
+ Line 3219  double **pmij(double **ps, double *cov,
       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-      Outputs ps[i][j] the probability to be observed in j being in j according to
+      Outputs ps[i][j] or probability to be observed in j being in i according to
       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+      Sum on j ps[i][j] should equal to 1.
    */
    double s1, lnpijopii;
    /*double t34;*/
- Line 2621  double **pmij(double **ps, double *cov,
+ Line 3235  double **pmij(double **ps, double *cov,
          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
        }
        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
      }
      for(j=i+1; j<=nlstate+ndeath;j++){
        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
- Line 2630  double **pmij(double **ps, double *cov,
+ Line 3244  double **pmij(double **ps, double *cov,
          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
        }
        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
      }
    }
- Line 2637  double **pmij(double **ps, double *cov,
+ Line 3252  double **pmij(double **ps, double *cov,
      s1=0;
      for(j=1; j<i; j++){
        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       /* printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
      }
      for(j=i+1; j<=nlstate+ndeath; j++){
        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       /* printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
      }
      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
      ps[i][i]=1./(s1+1.);
      /* Computing other pijs */
      for(j=1; j<i; j++)
-       ps[i][j]= exp(ps[i][j])*ps[i][i];
+       ps[i][j]= exp(ps[i][j])*ps[i][i];/* Bug valgrind */
      for(j=i+1; j<=nlstate+ndeath; j++)
        ps[i][j]= exp(ps[i][j])*ps[i][i];
      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
- Line 2659  double **pmij(double **ps, double *cov,
+ Line 3274  double **pmij(double **ps, double *cov,
        ps[ii][ii]=1;
      }
    }
    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
- Line 2671  double **pmij(double **ps, double *cov,
+ Line 3286  double **pmij(double **ps, double *cov,
    /*
      for(i=1; i<= npar; i++) printf("%f ",x[i]);
                  goto end;*/
-   return ps;
+   return ps; /* Pointer is unchanged since its call */
  }
  /*************** backward transition probabilities ***************/
- Line 2680  double **pmij(double **ps, double *cov,
+ Line 3295  double **pmij(double **ps, double *cov,
  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
  {
-   /* Computes the backward probability at age agefin and covariate ij
+   /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
-    * and returns in **ps as well as **bmij.
+    * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
     */
    int i, ii, j,k;
    double **out, **pmij();
    double sumnew=0.;
    double agefin;
+   double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
    double **dnewm, **dsavm, **doldm;
    double **bbmij;
    doldm=ddoldms; /* global pointers */
    dnewm=ddnewms;
    dsavm=ddsavms;
+   /* Debug */
+   /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
    agefin=cov[2];
+   /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
    /* bmij *//* age is cov[2], ij is included in cov, but we need for
-      the observed prevalence (with this covariate ij) */
+      the observed prevalence (with this covariate ij) at beginning of transition */
-   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
+   /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-   /* We do have the matrix Px in savm  and we need pij */
+   /* P_x */
+   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm *//* Bug valgrind */
+   /* outputs pmmij which is a stochastic matrix in row */
+   /* Diag(w_x) */
+   /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
+   sumnew=0.;
+   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
+   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
+     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
+     sumnew+=prevacurrent[(int)agefin][ii][ij];
+   }
+   if(sumnew >0.01){  /* At least some value in the prevalence */
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       for (j=1;j<=nlstate+ndeath;j++)
+         doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
+     }
+   }else{
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       for (j=1;j<=nlstate+ndeath;j++)
+       doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
+     }
+     /* if(sumnew <0.9){ */
+     /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
+     /* } */
+   }
+   k3=0.0;  /* We put the last diagonal to 0 */
+   for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
+       doldm[ii][ii]= k3;
+   }
+   /* End doldm, At the end doldm is diag[(w_i)] */
+   /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
+   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
+   /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
+   /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
    for (j=1;j<=nlstate+ndeath;j++){
-     sumnew=0.; /* w1 p11 + w2 p21 only on live states */
+     sumnew=0.;
      for (ii=1;ii<=nlstate;ii++){
-       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
+       /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
+       sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
      } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
      for (ii=1;ii<=nlstate+ndeath;ii++){
-       if(sumnew >= 1.e-10){
          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
-         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
          /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
-         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
          /* }else */
-         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
+       dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
-       }else{
-         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
-       }
      } /*End ii */
-   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
+   } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
-   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
-   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
+   ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
-   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
+   /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
-   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-   /* left Product of this matrix by diag matrix of prevalences (savm) */
-   for (j=1;j<=nlstate+ndeath;j++){
-     for (ii=1;ii<=nlstate+ndeath;ii++){
-       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
-     }
-   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
-   ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
-   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
    /* end bmij */
-   return ps;
+   return ps; /*pointer is unchanged */
  }
  /*************** transition probabilities ***************/
- Line 2802  double **bpmij(double **ps, double *cov,
+ Line 3444  double **bpmij(double **ps, double *cov,
        ps[ii][ii]=1;
      }
    }
-   /* Added for backcast */ /* Transposed matrix too */
+   /* Added for prevbcast */ /* Transposed matrix too */
    for(jj=1; jj<= nlstate+ndeath; jj++){
      s1=0.;
      for(ii=1; ii<= nlstate+ndeath; ii++){
- Line 2856  double **matprod2(double **out, double *
+ Line 3498  double **matprod2(double **out, double *
  /************* Higher Matrix Product ***************/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
  {
-   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
+   /* Computes the transition matrix starting at age 'age' and dummies values in each resultline (loop on ij to find the corresponding combination) to over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 2870  double ***hpxij(double ***po, int nhstep
+ Line 3512  double ***hpxij(double ***po, int nhstep
       */
-   int i, j, d, h, k;
+   int i, j, d, h, k, k1;
    double **out, cov[NCOVMAX+1];
    double **newm;
    double agexact;
- Line 2890  double ***hpxij(double ***po, int nhstep
+ Line 3532  double ***hpxij(double ***po, int nhstep
        cov[1]=1.;
        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
        cov[2]=agexact;
-       if(nagesqr==1)
+       if(nagesqr==1){
          cov[3]= agexact*agexact;
-       for (k=1; k<=cptcovn;k++)
+       }
-         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
-       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
-       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
+       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+         if(Typevar[k1]==1){ /* A product with age */
-         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+         }else{
-       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+           cov[2+nagesqr+k1]=precov[nres][k1];
-         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+         }
-       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       }/* End of loop on model equation */
+         /* Old code */
+ /*      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy  *\/ */
+ /* /\*     V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) *\/ */
+ /* /\*       for (k=1; k<=nsd;k++) { /\\* For single dummy covariates only *\\/ *\/ */
+ /* /\* /\\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\\/ *\/ */
+ /*      /\* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 *\/ */
+ /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
+ /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
+ /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
+ /* /\*    nsd         1   2                              3 *\/ /\* Counting single dummies covar fixed or tv *\/ */
+ /* /\*TvarsD[nsd]     4   3                              1 *\/ /\* ID of single dummy cova fixed or timevary*\/ */
+ /* /\*TvarsDind[k]    2   3                              9 *\/ /\* position K of single dummy cova *\/ */
+ /*        /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] *\/ */
+ /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
+ /*        /\* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); *\/ */
+ /*        printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); */
+ /*        printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables  *\/ */
+ /*        /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline *\/ */
+ /*        cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]];  */
+ /*        /\* for (k=1; k<=nsq;k++) { /\\* For single varying covariates only *\\/ *\/ */
+ /*        /\*   /\\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\\/ *\/ */
+ /*        /\*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
+ /*        printf("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
+ /*        printf("hpxij new Quanti precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*      }else if( Dummy[k1]==2 ){ /\* For dummy with age product *\/ */
+ /*        /\* Tvar[k1] Variable in the age product age*V1 is 1 *\/ */
+ /*        /\* [Tinvresult[nres][V1] is its value in the resultline nres *\/ */
+ /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]*cov[2]; */
+ /*        printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d TinvDoQresult[nres=%d][%d]=%.f age=%.2f,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],nres,TinvDoQresult[nres][Tvar[k1]],cov[2],nagesqr,k1,cov[2+nagesqr+k1]); */
+ /*        printf("hpxij new Dummy with age product precov[nres=%d][k1=%d]=%.4f * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
+ /*        /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];    *\/ */
+ /*        /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1*age +V4 +age*V3 *\\/ *\/ */
+ /*        /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*\/ */
+ /*        /\* *\/ */
+ /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
+ /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
+ /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
+ /* /\*cptcovage=2                   1               2      *\/ */
+ /* /\*Tage[k]=                      5               8      *\/   */
+ /*      }else if( Dummy[k1]==3 ){ /\* For quant with age product *\/ */
+ /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];        */
+ /*        printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
+ /*        printf("hpxij new Quanti with age product precov[nres=%d][k1=%d] * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
+ /*        /\* if(Dummy[Tage[k]]== 2){ /\\* dummy with age *\\/ *\/ */
+ /*        /\* /\\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\\* dummy with age *\\\/ *\\/ *\/ */
+ /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\\/ *\/ */
+ /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\\/ *\/ */
+ /*        /\*   cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\/ */
+ /*        /\*   printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); *\/ */
+ /*        /\* } else if(Dummy[Tage[k]]== 3){ /\\* quantitative with age *\\/ *\/ */
+ /*        /\*   cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; *\/ */
+ /*        /\* } *\/ */
+ /*        /\* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+ /*      }else if(Typevar[k1]==2 ){ /\* For product (not with age) *\/ */
+ /* /\*       for (k=1; k<=cptcovprod;k++){ /\\*  For product without age *\\/ *\/ */
+ /* /\* /\\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\\/ *\/ */
+ /* /\* /\\*    k        1  2   3   4     5    6    7     8    9 *\\/ *\/ */
+ /* /\* /\\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\\/ *\/ */
+ /* /\* /\\*cptcovprod=1            1               2            *\\/ *\/ */
+ /* /\* /\\*Tprod[]=                4               7            *\\/ *\/ */
+ /* /\* /\\*Tvard[][1]             4               1             *\\/ *\/ */
+ /* /\* /\\*Tvard[][2]               3               2           *\\/ *\/ */
+ /*        /\* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]=%d nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2],nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])],nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]); *\/ */
+ /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+ /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];     */
+ /*        printf("hPxij Prod ij=%d k1=%d  cov[2+%d+%d]=%.5f Tvard[%d][1]=V%d * Tvard[%d][2]=V%d ; TinvDoQresult[nres][Tvardk[k1][1]]=%.4f * TinvDoQresult[nres][Tvardk[k1][1]]=%.4f\n",ij,k1,nagesqr,k1,cov[2+nagesqr+k1],k1,Tvardk[k1][1], k1,Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]); */
+ /*        printf("hpxij new Product no age product precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
+ /*        /\* if(Dummy[Tvardk[k1][1]]==0){ *\/ */
+ /*        /\*   if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies *\\/ *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
+ /*            /\* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]];   *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; *\/ */
+ /*          /\* }else{ /\\* Product of dummy by quantitative *\\/ *\/ */
+ /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; *\/ */
+ /*            /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; *\/ */
+ /*        /\*   } *\/ */
+ /*        /\* }else{ /\\* Product of quantitative by...*\\/ *\/ */
+ /*        /\*   if(Dummy[Tvard[k][2]]==0){  /\\* quant by dummy *\\/ *\/ */
+ /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; *\\/ *\/ */
+ /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
+ /*        /\*   }else{ /\\* Product of two quant *\\/ *\/ */
+ /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\\/ *\/ */
+ /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
+ /*        /\*   } *\/ */
+ /*        /\* }/\\*end of products quantitative *\\/ *\/ */
+ /*      }/\*end of products *\/ */
+       /* } /\* End of loop on model equation *\/ */
+       /* for (k=1; k<=cptcovn;k++)  */
+       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
+       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
+       /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
+       /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
+       /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
-                         /* right multiplication of oldm by the current matrix */
+       /* right multiplication of oldm by the current matrix */
        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
                     pmij(pmmij,cov,ncovmodel,x,nlstate));
        /* if((int)age == 70){ */
- Line 2928  double ***hpxij(double ***po, int nhstep
+ Line 3667  double ***hpxij(double ***po, int nhstep
      }
      for(i=1; i<=nlstate+ndeath; i++)
        for(j=1;j<=nlstate+ndeath;j++) {
-                                 po[i][j][h]=newm[i][j];
+         po[i][j][h]=newm[i][j];
-                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
        }
      /*printf("h=%d ",h);*/
    } /* end h */
-         /*     printf("\n H=%d \n",h); */
+   /*     printf("\n H=%d \n",h); */
    return po;
  }
  /************* Higher Back Matrix Product ***************/
  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
- double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
+ double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
  {
-   /* Computes the transition matrix starting at age 'age' over
+   /* For dummy covariates given in each resultline (for historical, computes the corresponding combination ij),
+      computes the transition matrix starting at age 'age' over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 2949  double ***hbxij(double ***po, int nhstep
+ Line 3689  double ***hbxij(double ***po, int nhstep
       (typically every 2 years instead of every month which is too big
       for the memory).
       Model is determined by parameters x and covariates have to be
-      included manually here.
+      included manually here. Then we use a call to bmij(x and cov)
+      The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
    */
-   int i, j, d, h, k;
+   int i, j, d, h, k, k1;
-   double **out, cov[NCOVMAX+1];
+   double **out, cov[NCOVMAX+1], **bmij();
-   double **newm;
+   double **newm, ***newmm;
    double agexact;
    double agebegin, ageend;
    double **oldm, **savm;
-   oldm=oldms;savm=savms;
+   newmm=po; /* To be saved */
+   oldm=oldms;savm=savms; /* Global pointers */
    /* Hstepm could be zero and should return the unit matrix */
    for (i=1;i<=nlstate+ndeath;i++)
      for (j=1;j<=nlstate+ndeath;j++){
- Line 2973  double ***hbxij(double ***po, int nhstep
+ Line 3714  double ***hbxij(double ***po, int nhstep
        newm=savm;
        /* Covariates have to be included here again */
        cov[1]=1.;
-       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
+       agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
+         /* Debug */
+       /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
        cov[2]=agexact;
-       if(nagesqr==1)
+       if(nagesqr==1){
          cov[3]= agexact*agexact;
-       for (k=1; k<=cptcovn;k++)
+       }
-         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       /** New code */
-       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
-       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
+         if(Typevar[k1]==1){ /* A product with age */
-         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
-         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+         }else{
-       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+           cov[2+nagesqr+k1]=precov[nres][k1];
-       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+         }
-         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+       }/* End of loop on model equation */
-       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       /** End of new code */
+   /** This was old code */
+       /* for (k=1; k<=nsd;k++){ /\* For single dummy covariates only *\//\* cptcovn error *\/ */
-       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+       /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
-       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+       /* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
+       /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/\* Bug valgrind *\/ */
+       /*   /\* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
+       /* } */
+       /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
+       /*        /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
+       /*        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
+       /*        /\* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
+       /* } */
+       /* for (k=1; k<=cptcovage;k++){ /\* Should start at cptcovn+1 *\//\* For product with age *\/ */
+       /*        /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age error!!!*\\/ *\/ */
+       /*        if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
+       /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+       /*        } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
+       /*          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  */
+       /*        } */
+       /*        /\* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
+       /* } */
+       /* for (k=1; k<=cptcovprod;k++){ /\* Useless because included in cptcovn *\/ */
+       /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       /*        if(Dummy[Tvard[k][1]]==0){ */
+       /*          if(Dummy[Tvard[k][2]]==0){ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; */
+       /*          }else{ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
+       /*          } */
+       /*        }else{ */
+       /*          if(Dummy[Tvard[k][2]]==0){ */
+       /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
+       /*          }else{ */
+       /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+       /*          } */
+       /*        } */
+       /* }                       */
+       /* /\*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*\/ */
+       /* /\*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*\/ */
+ /** End of old code */
        /* Careful transposed matrix */
-       /* age is in cov[2] */
+       /* age is in cov[2], prevacurrent at beginning of transition. */
        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
-,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */
        /* if((int)age == 70){ */
        /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
        /*        for(i=1; i<=nlstate+ndeath; i++) { */
- Line 3018  double ***hbxij(double ***po, int nhstep
+ Line 3798  double ***hbxij(double ***po, int nhstep
      for(i=1; i<=nlstate+ndeath; i++)
        for(j=1;j<=nlstate+ndeath;j++) {
          po[i][j][h]=newm[i][j];
-         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+         /* if(h==nhstepm) */
+         /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
        }
-     /*printf("h=%d ",h);*/
+     /* printf("h=%d %.1f ",h, agexact); */
    } /* end h */
-   /*     printf("\n H=%d \n",h); */
+   /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
    return po;
  }
- Line 3080  double func( double *x)
+ Line 3861  double func( double *x)
           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
           to be observed in j being in i according to the model.
        */
-       ioffset=2+nagesqr+cptcovage;
+       ioffset=2+nagesqr ;
     /* Fixed */
-       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
+       for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */
-         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
+         /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
+         /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+         /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
+         /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
+         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
+         /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
        }
        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
-          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
+          is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6
           has been calculated etc */
        /* For an individual i, wav[i] gives the number of effective waves */
        /* We compute the contribution to Likelihood of each effective transition
- Line 3098  double func( double *x)
+ Line 3884  double func( double *x)
           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
        */
        for(mi=1; mi<= wav[i]-1; mi++){
-         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
+         for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
-           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
+           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
          }
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
- Line 3113  double func( double *x)
+ Line 3900  double func( double *x)
            if(nagesqr==1)
              cov[3]= agexact*agexact;  /* Should be changed here */
            for (kk=1; kk<=cptcovage;kk++) {
-             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
+             if(!FixedV[Tvar[Tage[kk]]])
+               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
+             else
+               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 3221  double func( double *x)
+ Line 4011  double func( double *x)
      } /* end of individual */
    }  else if(mle==2){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-       for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
+       ioffset=2+nagesqr ;
+       for (k=1; k<=ncovf;k++)
+         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
+         for(k=1; k <= ncovv ; k++){
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
+         }
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 3395  double funcone( double *x)
+ Line 4190  double funcone( double *x)
    for(k=1; k<=nlstate; k++) ll[k]=0.;
    ioffset=0;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     ioffset=2+nagesqr+cptcovage;
+     /* ioffset=2+nagesqr+cptcovage; */
+     ioffset=2+nagesqr;
      /* Fixed */
      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
      /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
-     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
+     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
        cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
  /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
  /*    cov[2+6]=covar[Tvar[6]][i];  */
- Line 3422  double funcone( double *x)
+ Line 4218  double funcone( double *x)
      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
      /* Wave varying (but not age varying) */
        for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
-                                 cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
+         /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
-                         }
+         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
+       }
        /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
-                                 /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-                                 /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
-                                 /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
+       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
-                                 /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
+       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
-                                 /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
+       /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
        /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
-                         /*      iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-                         /*      /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
+       /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
-                         /*      cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
+       /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
        /* } */
        for (ii=1;ii<=nlstate+ndeath;ii++)
-                                 for (j=1;j<=nlstate+ndeath;j++){
+         for (j=1;j<=nlstate+ndeath;j++){
-                                         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-                                         savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-                                 }
+         }
        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-                                 /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
-                                         and mw[mi+1][i]. dh depends on stepm.*/
+         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-                                 newm=savm;
+           and mw[mi+1][i]. dh depends on stepm.*/
-                                 agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         newm=savm;
-                                 cov[2]=agexact;
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
-                                 if(nagesqr==1)
+         cov[2]=agexact;
-                                         cov[3]= agexact*agexact;
+         if(nagesqr==1)
-                                 for (kk=1; kk<=cptcovage;kk++) {
+           cov[3]= agexact*agexact;
-                                         cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+         for (kk=1; kk<=cptcovage;kk++) {
-                                 }
+           if(!FixedV[Tvar[Tage[kk]]])
-                                 /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-                                 /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+           else
-                                 out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         }
-                                 /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
-                                 /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-                                 savm=oldm;
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-                                 oldm=newm;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+         savm=oldm;
+         oldm=newm;
        } /* end mult */
        s1=s[mw[mi][i]][i];
        s2=s[mw[mi+1][i]][i];
        /* if(s2==-1){ */
-       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
+       /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
        /*        /\* exit(1); *\/ */
        /* } */
        bbh=(double)bh[mi][i]/(double)stepm;
- Line 3475  double funcone( double *x)
+ Line 4276  double funcone( double *x)
         * is higher than the multiple of stepm and negative otherwise.
         */
        if( s2 > nlstate && (mle <5) ){  /* Jackson */
-                                 lli=log(out[s1][s2] - savm[s1][s2]);
+         lli=log(out[s1][s2] - savm[s1][s2]);
        } else if  ( s2==-1 ) { /* alive */
-                                 for (j=1,survp=0. ; j<=nlstate; j++)
+         for (j=1,survp=0. ; j<=nlstate; j++)
-                                         survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-                                 lli= log(survp);
+         lli= log(survp);
        }else if (mle==1){
-                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        } else if(mle==2){
-                                 lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
        } else if(mle==3){  /* exponential inter-extrapolation */
-                                 lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
        } else if (mle==4){  /* mle=4 no inter-extrapolation */
-                                 lli=log(out[s1][s2]); /* Original formula */
+         lli=log(out[s1][s2]); /* Original formula */
        } else{  /* mle=0 back to 1 */
-                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-                                 /*lli=log(out[s1][s2]); */ /* Original formula */
+         /*lli=log(out[s1][s2]); */ /* Original formula */
        } /* End of if */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
        if(globpr){
-                                 fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
+         fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
   %11.6f %11.6f %11.6f ", \
-                                                                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
+                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
-                                 for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-                                         llt +=ll[k]*gipmx/gsw;
+           llt +=ll[k]*gipmx/gsw;
-                                         fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-                                 }
+         }
-                                 fprintf(ficresilk," %10.6f\n", -llt);
+         fprintf(ficresilk," %10.6f\n", -llt);
        }
          } /* end of wave */
  } /* end of individual */
- Line 3521  return -l;
+ Line 4322  return -l;
  /*************** function likelione ***********/
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
  {
    /* This routine should help understanding what is done with
       the selection of individuals/waves and
- Line 3545  void likelione(FILE *ficres,double p[],
+ Line 4346  void likelione(FILE *ficres,double p[],
      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
    }
-   *fretone=(*funcone)(p);
+   *fretone=(*func)(p);
    if(*globpri !=0){
      fclose(ficresilk);
      if (mle ==0)
- Line 3553  void likelione(FILE *ficres,double p[],
+ Line 4354  void likelione(FILE *ficres,double p[],
      else if(mle >=1)
        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
      for (k=1; k<= nlstate ; k++) {
        fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
- Line 3573  void likelione(FILE *ficres,double p[],
+ Line 4374  void likelione(FILE *ficres,double p[],
  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  {
-   int i,j, iter=0;
+   int i,j,k, jk, jkk=0, iter=0;
    double **xi;
    double fret;
    double fretone; /* Only one call to likelihood */
- Line 3607  void mlikeli(FILE *ficres,double p[], in
+ Line 4408  void mlikeli(FILE *ficres,double p[], in
        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
    fprintf(ficrespow,"\n");
  #ifdef POWELL
+ #ifdef LINMINORIGINAL
+ #else /* LINMINORIGINAL */
+   flatdir=ivector(1,npar);
+   for (j=1;j<=npar;j++) flatdir[j]=0;
+ #endif /*LINMINORIGINAL */
+ #ifdef FLATSUP
+   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
+   /* reorganizing p by suppressing flat directions */
+   for(i=1, jk=1; i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
+         if(flatdir[jk]==1){
+           printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
+         }
+         for(j=1; j <=ncovmodel; j++){
+           printf("%12.7f ",p[jk]);
+           jk++;
+         }
+         printf("\n");
+       }
+     }
+   }
+ /* skipping */
+   /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
+   for(i=1, jk=1, jkk=1;i <=nlstate; i++){
+     for(k=1; k <=(nlstate+ndeath); k++){
+       if (k != i) {
+         printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
+         if(flatdir[jk]==1){
+           printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
+           for(j=1; j <=ncovmodel;  jk++,j++){
+             printf(" p[%d]=%12.7f",jk, p[jk]);
+             /*q[jjk]=p[jk];*/
+           }
+         }else{
+           printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
+           for(j=1; j <=ncovmodel;  jk++,jkk++,j++){
+             printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
+             /*q[jjk]=p[jk];*/
+           }
+         }
+         printf("\n");
+       }
+       fflush(stdout);
+     }
+   }
+   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
+ #else  /* FLATSUP */
    powell(p,xi,npar,ftol,&iter,&fret,func);
- #endif
+ #endif  /* FLATSUP */
+ #ifdef LINMINORIGINAL
+ #else
+       free_ivector(flatdir,1,npar);
+ #endif  /* LINMINORIGINAL*/
+ #endif /* POWELL */
  #ifdef NLOPT
  #ifdef NEWUOA
- Line 3636  void mlikeli(FILE *ficres,double p[], in
+ Line 4494  void mlikeli(FILE *ficres,double p[], in
    }
    nlopt_destroy(opt);
  #endif
+ #ifdef FLATSUP
+   /* npared = npar -flatd/ncovmodel; */
+   /* xired= matrix(1,npared,1,npared); */
+   /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
+   /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
+   /* free_matrix(xire,1,npared,1,npared); */
+ #else  /* FLATSUP */
+ #endif /* FLATSUP */
    free_matrix(xi,1,npar,1,npar);
    fclose(ficrespow);
    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
- Line 3855  double hessij( double x[], double **hess
+ Line 4721  double hessij( double x[], double **hess
        kmax=kmax+10;
      }
      if(kmax >=10 || firstime ==1){
-       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
-       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      }
- Line 3945  void ludcmp(double **a, int n, int *indx
+ Line 4811  void ludcmp(double **a, int n, int *indx
      big=0.0;
      for (j=1;j<=n;j++)
        if ((temp=fabs(a[i][j])) > big) big=temp;
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+     if (big == 0.0){
+       printf(" Singular Hessian matrix at row %d:\n",i);
+       for (j=1;j<=n;j++) {
+         printf(" a[%d][%d]=%f,",i,j,a[i][j]);
+         fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
+       }
+       fflush(ficlog);
+       fclose(ficlog);
+       nrerror("Singular matrix in routine ludcmp");
+     }
      vv[i]=1.0/big;
    }
    for (j=1;j<=n;j++) {
- Line 4011  void pstamp(FILE *fichier)
+ Line 4886  void pstamp(FILE *fichier)
    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
  }
+ void date2dmy(double date,double *day, double *month, double *year){
+   double yp=0., yp1=0., yp2=0.;
+   yp1=modf(date,&yp);/* extracts integral of date in yp  and
+                         fractional in yp1 */
+   *year=yp;
+   yp2=modf((yp1*12),&yp);
+   *month=yp;
+   yp1=modf((yp2*30.5),&yp);
+   *day=yp;
+   if(*day==0) *day=1;
+   if(*month==0) *month=1;
+ }
  /************ Frequencies ********************/
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
+ void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
- {  /* Some frequencies */
+ {  /* Some frequencies as well as proposing some starting values */
+   /* Frequencies of any combination of dummy covariate used in the model equation */
-   int i, m, jk, j1, bool, z1,j, k, iv;
+   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
    int iind=0, iage=0;
    int mi; /* Effective wave */
    int first;
    double ***freq; /* Frequencies */
-   double *meanq;
+   double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
+   int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
+   double *meanq, *stdq, *idq;
    double **meanqt;
    double *pp, **prop, *posprop, *pospropt;
    double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
- Line 4030  void  freqsummary(char fileres[], int ia
+ Line 4923  void  freqsummary(char fileres[], int ia
    double agebegin, ageend;
    pp=vector(1,nlstate);
-   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
    pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
    meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
    meanqt=matrix(1,lastpass,1,nqtveff);
    strcpy(fileresp,"P_");
    strcat(fileresp,fileresu);
- Line 4044  void  freqsummary(char fileres[], int ia
+ Line 4939  void  freqsummary(char fileres[], int ia
      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      exit(0);
    }
    strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
    if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
      printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
- Line 4054  void  freqsummary(char fileres[], int ia
+ Line 4949  void  freqsummary(char fileres[], int ia
    }
    else{
      fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
              fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);
    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
      printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
      fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
      fflush(ficlog);
      exit(70);
-   }
+   } else{
-   else{
      fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ ,<hr size=\"2\" color=\"#EC5E5E\"> \n                                   \
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
              fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+   x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    j1=0;
    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
    j=cptcoveff;  /* Only dummy covariates of the model */
+   /* j=cptcovn;  /\* Only dummy covariates of the model *\/ */
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   first=1;
    /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
       reference=low_education V1=0,V2=0
       med_educ                V1=1 V2=0,
       high_educ               V1=0 V2=1
-      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
+      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn
    */
+   dateintsum=0;
+   k2cpt=0;
-   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
+   if(cptcoveff == 0 )
-     posproptt=0.;
+     nl=1;  /* Constant and age model only */
-     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   else
-       scanf("%d", i);*/
+     nl=2;
-     for (i=-5; i<=nlstate+ndeath; i++)
-       for (jk=-5; jk<=nlstate+ndeath; jk++)
+   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
-                                 for(m=iagemin; m <= iagemax+3; m++)
+   /* Loop on nj=1 or 2 if dummy covariates j!=0
-                                         freq[i][jk][m]=0;
+    *   Loop on j1(1 to 2**cptcovn) covariate combination
+    *     freq[s1][s2][iage] =0.
-     for (i=1; i<=nlstate; i++)  {
+    *     Loop on iind
-       for(m=iagemin; m <= iagemax+3; m++)
+    *       ++freq[s1][s2][iage] weighted
-                                 prop[i][m]=0;
+    *     end iind
-       posprop[i]=0;
+    *     if covariate and j!0
-       pospropt[i]=0;
+    *       headers Variable on one line
-     }
+    *     endif cov j!=0
-     /* for (z1=1; z1<= nqfveff; z1++) {   */
+    *     header of frequency table by age
-     /*   meanq[z1]+=0.; */
+    *     Loop on age
-     /*   for(m=1;m<=lastpass;m++){ */
+    *       pp[s1]+=freq[s1][s2][iage] weighted
-     /*  meanqt[m][z1]=0.; */
+    *       pos+=freq[s1][s2][iage] weighted
-     /*   } */
+    *       Loop on s1 initial state
-     /* } */
+    *         fprintf(ficresp
+    *       end s1
-     dateintsum=0;
+    *     end age
-     k2cpt=0;
+    *     if j!=0 computes starting values
-     /* For that combination of covariate j1, we count and print the frequencies in one pass */
+    *     end compute starting values
-     for (iind=1; iind<=imx; iind++) { /* For each individual iind */
+    *   end j1
-       bool=1;
+    * end nl
-       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
+    */
-         if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
-           /* for (z1=1; z1<= nqfveff; z1++) {   */
+     if(nj==1)
-           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
+       j=0;  /* First pass for the constant */
-           /* } */
+     else{
-           for (z1=1; z1<=cptcoveff; z1++) {
+       j=cptcovs; /* Other passes for the covariate values */
-             /* if(Tvaraff[z1] ==-20){ */
+     }
-             /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
+     first=1;
-             /* }else  if(Tvaraff[z1] ==-10){ */
+     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
-             /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
+       posproptt=0.;
-             /* }else  */
+       /*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
-             if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
+         scanf("%d", i);*/
-               /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
+       for (i=-5; i<=nlstate+ndeath; i++)
-               bool=0;
+         for (s2=-5; s2<=nlstate+ndeath; s2++)
-               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
+           for(m=iagemin; m <= iagemax+3; m++)
-                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
+             freq[i][s2][m]=0;
-                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+       for (i=1; i<=nlstate; i++)  {
-             } /* Onlyf fixed */
+         for(m=iagemin; m <= iagemax+3; m++)
-           } /* end z1 */
+           prop[i][m]=0;
-         } /* cptcovn > 0 */
+         posprop[i]=0;
-       } /* end any */
+         pospropt[i]=0;
-       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
+       }
-         /* for(m=firstpass; m<=lastpass; m++){ */
+       for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
-         for(mi=1; mi<wav[iind];mi++){ /* For that wave */
+         idq[z1]=0.;
-           m=mw[mi][iind];
+         meanq[z1]=0.;
-           if(anyvaryingduminmodel==1){ /* Some are varying covariates */
+         stdq[z1]=0.;
-             for (z1=1; z1<=cptcoveff; z1++) {
+       }
-               if( Fixed[Tmodelind[z1]]==1){
+       /* for (z1=1; z1<= nqtveff; z1++) { */
-                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+       /*   for(m=1;m<=lastpass;m++){ */
-                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
+       /*          meanqt[m][z1]=0.; */
-                   bool=0;
+       /*        } */
-               }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
+       /* }       */
-                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
+       /* dateintsum=0; */
-                   bool=0;
+       /* k2cpt=0; */
+       /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
+       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
+         bool=1;
+         if(j !=0){
+           if(anyvaryingduminmodel==0){ /* If All fixed covariates */
+             if (cptcovn >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+               for (z1=1; z1<=cptcovn; z1++) { /* loops on covariates in the model */
+                 /* if(Tvaraff[z1] ==-20){ */
+                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
+                 /* }else  if(Tvaraff[z1] ==-10){ */
+                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
+                 /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */
+                   /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
+                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
+                   /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", */
+                   /*   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),*/
+                   /*   j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+                 } /* Onlyf fixed */
+               } /* end z1 */
+             } /* cptcovn > 0 */
+           } /* end any */
+         }/* end j==0 */
+         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
+           /* for(m=firstpass; m<=lastpass; m++){ */
+           for(mi=1; mi<wav[iind];mi++){ /* For each wave */
+             m=mw[mi][iind];
+             if(j!=0){
+               if(anyvaryingduminmodel==1){ /* Some are varying covariates */
+                 for (z1=1; z1<=cptcovn; z1++) {
+                   if( Fixed[Tmodelind[z1]]==1){
+                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's
+                                                                                       value is -1, we don't select. It differs from the
+                                                                                       constant and age model which counts them. */
+                       bool=0; /* not selected */
+                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
+                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
+                       bool=0;
+                     }
+                   }
+                 }
+               }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
+             } /* end j==0 */
+             /* bool =0 we keep that guy which corresponds to the combination of dummy values */
+             if(bool==1){ /*Selected */
+               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+                  and mw[mi+1][iind]. dh depends on stepm. */
+               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+               ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+               if(m >=firstpass && m <=lastpass){
+                 k2=anint[m][iind]+(mint[m][iind]/12.);
+                 /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+                 if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+                 if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+                 if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                   prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+                 if (m<lastpass) {
+                   /* if(s[m][iind]==4 && s[m+1][iind]==4) */
+                   /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
+                   if(s[m][iind]==-1)
+                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
+                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
+                     if(!isnan(covar[ncovcol+z1][iind])){
+                       idq[z1]=idq[z1]+weight[iind];
+                       meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
+                       /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
+                       stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
+                     }
+                   }
+                   /* if((int)agev[m][iind] == 55) */
+                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
+                   /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
+                   freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
                  }
+               } /* end if between passes */
+               if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
+                 dateintsum=dateintsum+k2; /* on all covariates ?*/
+                 k2cpt++;
+                 /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
                }
+             }else{
+               bool=1;
+             }/* end bool 2 */
+           } /* end m */
+           /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
+           /*   idq[z1]=idq[z1]+weight[iind]; */
+           /*   meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /\* Computes mean of quantitative with selected filter *\/ */
+           /*   stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/  /\* Computes mean of quantitative with selected filter *\/ */
+           /* } */
+         } /* end bool */
+       } /* end iind = 1 to imx */
+       /* prop[s][age] is fed for any initial and valid live state as well as
+          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+       if(cptcovn==0 && nj==1) /* no covariate and first pass */
+         pstamp(ficresp);
+       if  (cptcovn>0 && j!=0){
+         pstamp(ficresp);
+         printf( "\n#********** Variable ");
+         fprintf(ficresp, "\n#********** Variable ");
+         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+         fprintf(ficlog, "\n#********** Variable ");
+         for (z1=1; z1<=cptcovs; z1++){
+           if(!FixedV[Tvaraff[z1]]){
+             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+           }else{
+             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+           }
+         }
+         printf( "**********\n#");
+         fprintf(ficresp, "**********\n#");
+         fprintf(ficresphtm, "**********</h3>\n");
+         fprintf(ficresphtmfr, "**********</h3>\n");
+         fprintf(ficlog, "**********\n");
+       }
+       /*
+         Printing means of quantitative variables if any
+       */
+       for (z1=1; z1<= nqfveff; z1++) {
+         fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
+         fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
+         if(weightopt==1){
+           printf(" Weighted mean and standard deviation of");
+           fprintf(ficlog," Weighted mean and standard deviation of");
+           fprintf(ficresphtmfr," Weighted mean and standard deviation of");
+         }
+         /* mu = \frac{w x}{\sum w}
+            var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
+         */
+         printf(" fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+         fprintf(ficlog," fixed quantitative variable V%d on  %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+         fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
+       }
+       /* for (z1=1; z1<= nqtveff; z1++) { */
+       /*        for(m=1;m<=lastpass;m++){ */
+       /*          fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
+       /*   } */
+       /* } */
+       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
+       if((cptcovn==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
+         fprintf(ficresp, " Age");
+       if(nj==2) for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+       for(i=1; i<=nlstate;i++) {
+         if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
+         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
+       }
+       if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
+       fprintf(ficresphtm, "\n");
+       /* Header of frequency table by age */
+       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
+       fprintf(ficresphtmfr,"<th>Age</th> ");
+       for(s2=-1; s2 <=nlstate+ndeath; s2++){
+         for(m=-1; m <=nlstate+ndeath; m++){
+           if(s2!=0 && m!=0)
+             fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
+         }
+       }
+       fprintf(ficresphtmfr, "\n");
+       /* For each age */
+       for(iage=iagemin; iage <= iagemax+3; iage++){
+         fprintf(ficresphtm,"<tr>");
+         if(iage==iagemax+1){
+           fprintf(ficlog,"1");
+           fprintf(ficresphtmfr,"<tr><th>0</th> ");
+         }else if(iage==iagemax+2){
+           fprintf(ficlog,"0");
+           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+         }else if(iage==iagemax+3){
+           fprintf(ficlog,"Total");
+           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
+         }else{
+           if(first==1){
+             first=0;
+             printf("See log file for details...\n");
+           }
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
+           fprintf(ficlog,"Age %d", iage);
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
+             pp[s1] += freq[s1][m][iage];
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           for(m=-1, pos=0; m <=0 ; m++)
+             pos += freq[s1][m][iage];
+           if(pp[s1]>=1.e-10){
+             if(first==1){
+               printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
+             }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
+           }
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           /* posprop[s1]=0; */
+           for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+             pp[s1] += freq[s1][m][iage];
+         }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
+         for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
+           pos += pp[s1]; /* pos is the total number of transitions until this age */
+           posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
+                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+           pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
+                                           from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+         }
+         /* Writing ficresp */
+         if(cptcovn==0 && nj==1){ /* no covariate and first pass */
+           if( iage <= iagemax){
+             fprintf(ficresp," %d",iage);
+           }
+         }else if( nj==2){
+           if( iage <= iagemax){
+             fprintf(ficresp," %d",iage);
+             for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
+           }
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           if(pos>=1.e-5){
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
+           }
+           if( iage <= iagemax){
+             if(pos>=1.e-5){
+               if(cptcovn==0 && nj==1){ /* no covariate and first pass */
+                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               }else if( nj==2){
+                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               }
+               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               /*probs[iage][s1][j1]= pp[s1]/pos;*/
+               /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
+             } else{
+               if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
+               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
              }
-           }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
+           }
-           /* bool =0 we keep that guy which corresponds to the combination of dummy values */
+           pospropt[s1] +=posprop[s1];
-           if(bool==1){
+         } /* end loop s1 */
-             /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+         /* pospropt=0.; */
-                and mw[mi+1][iind]. dh depends on stepm. */
+         for(s1=-1; s1 <=nlstate+ndeath; s1++){
-             agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+           for(m=-1; m <=nlstate+ndeath; m++){
-             ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+             if(freq[s1][m][iage] !=0 ) { /* minimizing output */
-             if(m >=firstpass && m <=lastpass){
+               if(first==1){
-               k2=anint[m][iind]+(mint[m][iind]/12.);
+                 printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
-               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
-               if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
-               if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
-                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
-               if (m<lastpass) {
-                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-                 /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
-                 if(s[m][iind]==-1)
-                   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
-                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
-                 /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
-                 freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
                }
-             } /* end if between passes */
+               /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
-             if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
+               fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
-               dateintsum=dateintsum+k2;
-               k2cpt++;
-               /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
              }
-           } /* end bool 2 */
+             if(s1!=0 && m!=0)
-         } /* end m */
+               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
-       } /* end bool */
+           }
-     } /* end iind = 1 to imx */
+         } /* end loop s1 */
-     /* prop[s][age] is feeded for any initial and valid live state as well as
+         posproptt=0.;
-        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
+         for(s1=1; s1 <=nlstate; s1++){
+           posproptt += pospropt[s1];
+         }
-     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+         fprintf(ficresphtmfr,"</tr>\n ");
-     pstamp(ficresp);
+         fprintf(ficresphtm,"</tr>\n");
-     /* if  (ncoveff>0) { */
+         if((cptcovn==0 && nj==1)|| nj==2 ) {
-     if  (cptcoveff>0) {
+           if(iage <= iagemax)
-       fprintf(ficresp, "\n#********** Variable ");
+             fprintf(ficresp,"\n");
-       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+         }
-       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+         if(first==1)
-       for (z1=1; z1<=cptcoveff; z1++){
+           printf("Others in log...\n");
-         fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         fprintf(ficlog,"\n");
-         fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       } /* end loop age iage */
-         fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       }
+       fprintf(ficresphtm,"<tr><th>Tot</th>");
-       fprintf(ficresp, "**********\n#");
+       for(s1=1; s1 <=nlstate ; s1++){
-       fprintf(ficresphtm, "**********</h3>\n");
+         if(posproptt < 1.e-5){
-       fprintf(ficresphtmfr, "**********</h3>\n");
+           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
-       fprintf(ficlog, "\n#********** Variable ");
+         }else{
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
-       fprintf(ficlog, "**********\n");
+         }
-     }
-     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
-     for(i=1; i<=nlstate;i++) {
-       fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-     }
-     fprintf(ficresp, "\n");
-     fprintf(ficresphtm, "\n");
-     /* Header of frequency table by age */
-     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-     fprintf(ficresphtmfr,"<th>Age</th> ");
-     for(jk=-1; jk <=nlstate+ndeath; jk++){
-       for(m=-1; m <=nlstate+ndeath; m++){
-         if(jk!=0 && m!=0)
-           fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
        }
-     }
+       fprintf(ficresphtm,"</tr>\n");
-     fprintf(ficresphtmfr, "\n");
+       fprintf(ficresphtm,"</table>\n");
+       fprintf(ficresphtmfr,"</table>\n");
-     /* For each age */
+       if(posproptt < 1.e-5){
-     for(iage=iagemin; iage <= iagemax+3; iage++){
+         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       fprintf(ficresphtm,"<tr>");
+         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       if(iage==iagemax+1){
+         fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
-                                 fprintf(ficlog,"1");
+         printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
-                                 fprintf(ficresphtmfr,"<tr><th>0</th> ");
+         invalidvarcomb[j1]=1;
-       }else if(iage==iagemax+2){
-                                 fprintf(ficlog,"0");
-                                 fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-       }else if(iage==iagemax+3){
-                                 fprintf(ficlog,"Total");
-                                 fprintf(ficresphtmfr,"<tr><th>Total</th> ");
        }else{
-                                 if(first==1){
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
-                                         first=0;
+         invalidvarcomb[j1]=0;
-                                         printf("See log file for details...\n");
-                                 }
-                                 fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
-                                 fprintf(ficlog,"Age %d", iage);
-       }
-       for(jk=1; jk <=nlstate ; jk++){
-                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-                                         pp[jk] += freq[jk][m][iage];
-       }
-       for(jk=1; jk <=nlstate ; jk++){
-                                 for(m=-1, pos=0; m <=0 ; m++)
-                                         pos += freq[jk][m][iage];
-                                 if(pp[jk]>=1.e-10){
-                                         if(first==1){
-                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-                                         }
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-                                 }else{
-                                         if(first==1)
-                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-                                 }
-       }
-       for(jk=1; jk <=nlstate ; jk++){
-                                 /* posprop[jk]=0; */
-                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-                                         pp[jk] += freq[jk][m][iage];
-       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
-       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
-                                 pos += pp[jk]; /* pos is the total number of transitions until this age */
-                                 posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
-                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
-                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-       }
-       for(jk=1; jk <=nlstate ; jk++){
-                                 if(pos>=1.e-5){
-                                         if(first==1)
-                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-                                 }else{
-                                         if(first==1)
-                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-                                 }
-                                 if( iage <= iagemax){
-                                         if(pos>=1.e-5){
-                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
-                                                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
-                                         }
-                                         else{
-                                                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
-                                                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
-                                         }
-                                 }
-                                 pospropt[jk] +=posprop[jk];
-       } /* end loop jk */
-       /* pospropt=0.; */
-       for(jk=-1; jk <=nlstate+ndeath; jk++){
-                                 for(m=-1; m <=nlstate+ndeath; m++){
-                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */
-                                                 if(first==1){
-                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
-                                                 }
-                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
-                                         }
-                                         if(jk!=0 && m!=0)
-                                                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
-                                 }
-       } /* end loop jk */
-       posproptt=0.;
-       for(jk=1; jk <=nlstate; jk++){
-                                 posproptt += pospropt[jk];
-       }
-       fprintf(ficresphtmfr,"</tr>\n ");
-       if(iage <= iagemax){
-                                 fprintf(ficresp,"\n");
-                                 fprintf(ficresphtm,"</tr>\n");
        }
-       if(first==1)
+       fprintf(ficresphtmfr,"</table>\n");
-                                 printf("Others in log...\n");
        fprintf(ficlog,"\n");
-     } /* end loop age iage */
+       if(j!=0){
-     fprintf(ficresphtm,"<tr><th>Tot</th>");
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
-     for(jk=1; jk <=nlstate ; jk++){
+         for(i=1,s1=1; i <=nlstate; i++){
-       if(posproptt < 1.e-5){
+           for(k=1; k <=(nlstate+ndeath); k++){
-                                 fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+             if (k != i) {
-       }else{
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
-                                 fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+                 if(jj==1){  /* Constant case (in fact cste + age) */
+                   if(j1==1){ /* All dummy covariates to zero */
+                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
+                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
+                     printf("%d%d ",i,k);
+                     fprintf(ficlog,"%d%d ",i,k);
+                     printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
+                     fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                     pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
+                   }
+                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
+                   for(iage=iagemin; iage <= iagemax+3; iage++){
+                     x[iage]= (double)iage;
+                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
+                     /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
+                   }
+                   /* Some are not finite, but linreg will ignore these ages */
+                   no=0;
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
+                   pstart[s1]=b;
+                   pstart[s1-1]=a;
+                 }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */
+                   printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
+                   printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
+                   pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
+                   printf("%d%d ",i,k);
+                   fprintf(ficlog,"%d%d ",i,k);
+                   printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
+                 }else{ /* Other cases, like quantitative fixed or varying covariates */
+                   ;
+                 }
+                 /* printf("%12.7f )", param[i][jj][k]); */
+                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+                 s1++;
+               } /* end jj */
+             } /* end k!= i */
+           } /* end k */
+         } /* end i, s1 */
+       } /* end j !=0 */
+     } /* end selected combination of covariate j1 */
+     if(j==0){ /* We can estimate starting values from the occurences in each case */
+       printf("#Freqsummary: Starting values for the constants:\n");
+       fprintf(ficlog,"\n");
+       for(i=1,s1=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(jj=1; jj <=ncovmodel; jj++){
+               pstart[s1]=p[s1]; /* Setting pstart to p values by default */
+               if(jj==1){ /* Age has to be done */
+                 pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
+                 printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                 fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+               }
+               /* printf("%12.7f )", param[i][jj][k]); */
+               /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+               s1++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       } /* end of state i */
+       printf("#Freqsummary\n");
+       fprintf(ficlog,"\n");
+       for(s1=-1; s1 <=nlstate+ndeath; s1++){
+         for(s2=-1; s2 <=nlstate+ndeath; s2++){
+           /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
+           printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
+           /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /* } */
+         }
+       } /* end loop s1 */
+       printf("\n");
+       fprintf(ficlog,"\n");
+     } /* end j=0 */
+   } /* end j */
+   if(mle == -2){  /* We want to use these values as starting values */
+     for(i=1, jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j!=i){
+           /*ca[0]= k+'a'-1;ca[1]='\0';*/
+           printf("%1d%1d",i,j);
+           fprintf(ficparo,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             /*    printf(" %lf",param[i][j][k]); */
+             /*    fprintf(ficparo," %lf",param[i][j][k]); */
+             p[jk]=pstart[jk];
+             printf(" %f ",pstart[jk]);
+             fprintf(ficparo," %f ",pstart[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficparo,"\n");
+         }
        }
      }
-     fprintf(ficresphtm,"</tr>\n");
+   } /* end mle=-2 */
-     fprintf(ficresphtm,"</table>\n");
-     fprintf(ficresphtmfr,"</table>\n");
-     if(posproptt < 1.e-5){
-       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
-       invalidvarcomb[j1]=1;
-     }else{
-       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
-       invalidvarcomb[j1]=0;
-     }
-     fprintf(ficresphtmfr,"</table>\n");
-   } /* end selected combination of covariate j1 */
    dateintmean=dateintsum/k2cpt;
+   date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
    fclose(ficresp);
    fclose(ficresphtm);
    fclose(ficresphtmfr);
+   free_vector(idq,1,nqfveff);
    free_vector(meanq,1,nqfveff);
+   free_vector(stdq,1,nqfveff);
    free_matrix(meanqt,1,lastpass,1,nqtveff);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
    free_vector(pospropt,1,nlstate);
    free_vector(posprop,1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
    free_vector(pp,1,nlstate);
    /* End of freqsummary */
  }
+ /* Simple linear regression */
+ int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
+   /* y=a+bx regression */
+   double   sumx = 0.0;                        /* sum of x                      */
+   double   sumx2 = 0.0;                       /* sum of x**2                   */
+   double   sumxy = 0.0;                       /* sum of x * y                  */
+   double   sumy = 0.0;                        /* sum of y                      */
+   double   sumy2 = 0.0;                       /* sum of y**2                   */
+   double   sume2 = 0.0;                       /* sum of square or residuals */
+   double yhat;
+   double denom=0;
+   int i;
+   int ne=*no;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     sumx  += x[i];
+     sumx2 += x[i]*x[i];
+     sumxy += x[i] * y[i];
+     sumy  += y[i];
+     sumy2 += y[i]*y[i];
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   denom = (ne * sumx2 - sumx*sumx);
+   if (denom == 0) {
+     // vertical, slope m is infinity
+     *b = INFINITY;
+     *a = 0;
+     if (r) *r = 0;
+     return 1;
+   }
+   *b = (ne * sumxy  -  sumx * sumy) / denom;
+   *a = (sumy * sumx2  -  sumx * sumxy) / denom;
+   if (r!=NULL) {
+     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
+       sqrt((sumx2 - sumx*sumx/ne) *
+            (sumy2 - sumy*sumy/ne));
+   }
+   *no=ne;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     yhat = y[i] - *a -*b* x[i];
+     sume2  += yhat * yhat ;
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
+   *sa= *sb * sqrt(sumx2/ne);
+   return 0;
+ }
  /************ Prevalence ********************/
  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
  {
- Line 4392  void prevalence(double ***probs, double
+ Line 5588  void prevalence(double ***probs, double
    iagemin= (int) agemin;
    iagemax= (int) agemax;
    /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
    /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   first=1;
+   first=0;
    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
      for (i=1; i<=nlstate; i++)
-       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
          prop[i][iage]=0.0;
      printf("Prevalence combination of varying and fixed dummies %d\n",j1);
      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
- Line 4418  void prevalence(double ***probs, double
+ Line 5614  void prevalence(double ***probs, double
          for (z1=1; z1<=cptcoveff; z1++){
            if( Fixed[Tmodelind[z1]]==1){
              iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
                bool=0;
            }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
                bool=0;
              }
          }
- Line 4433  void prevalence(double ***probs, double
+ Line 5629  void prevalence(double ***probs, double
              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
                  printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
                  exit(1);
                }
- Line 4457  void prevalence(double ***probs, double
+ Line 5653  void prevalence(double ***probs, double
            if(posprop>=1.e-5){
              probs[i][jk][j1]= prop[jk][i]/posprop;
            } else{
-             if(first==1){
+             if(!first){
-               first=0;
+               first=1;
-               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
+               printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
+             }else{
+               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
              }
            }
          }
- Line 4470  void prevalence(double ***probs, double
+ Line 5668  void prevalence(double ***probs, double
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
-   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
  }  /* End of prevalence */
  /************* Waves Concatenation ***************/
  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
  {
-   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+   /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
       Death is a valid wave (if date is known).
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-      and mw[mi+1][i]. dh depends on stepm.
+      and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
    */
    int i=0, mi=0, m=0, mli=0;
- Line 4502  void  concatwav(int wav[], int **dh, int
+ Line 5700  void  concatwav(int wav[], int **dh, int
    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
      mi=0;  /* First valid wave */
      mli=0; /* Last valid wave */
-     m=firstpass;
+     m=firstpass;  /* Loop on waves */
-     while(s[m][i] <= nlstate){  /* a live state */
+     while(s[m][i] <= nlstate){  /* a live state or unknown state  */
        if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
          mli=m-1;/* mw[++mi][i]=m-1; */
        }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
-         mw[++mi][i]=m;
+         mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition   */
          mli=m;
        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
        if(m < lastpass){ /* m < lastpass, standard case */
          m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
        }
-       else{ /* m >= lastpass, eventual special issue with warning */
+       else{ /* m = lastpass, eventual special issue with warning */
  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
          break;
  #else
-         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
            if(firsthree == 0){
-             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
              firsthree=1;
+           }else if(firsthree >=1 && firsthree < 10){
+             fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
+             firsthree++;
+           }else if(firsthree == 10){
+             printf("Information, too many Information flags: no more reported to log either\n");
+             fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
+             firsthree++;
+           }else{
+             firsthree++;
            }
-           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+           mw[++mi][i]=m; /* Valid transition with unknown status */
-           mw[++mi][i]=m;
            mli=m;
          }
          if(s[m][i]==-2){ /* Vital status is really unknown */
            nbwarn++;
-           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified?not a transition */
              printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
              fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
            }
- Line 4549  void  concatwav(int wav[], int **dh, int
+ Line 5755  void  concatwav(int wav[], int **dh, int
        /* if(mi==0)  never been interviewed correctly before death */
        /* Only death is a correct wave */
        mw[mi][i]=m;
-     }
+     } /* else not in a death state */
  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
+     else if ((int) andc[i] != 9999) {  /* Date of death is known */
-       /* m++; */
-       /* mi++; */
-       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
-       /* mw[mi][i]=m; */
        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
+         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
            nbwarn++;
            if(firstfiv==0){
-             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
              firstfiv=1;
            }else{
-             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
            }
-         }else{ /* Death occured afer last wave potential bias */
+             s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
+         }else{ /* Month of Death occured afer last wave month, potential bias */
            nberr++;
            if(firstwo==0){
-             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
              firstwo=1;
            }
-           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
          }
-       }else{ /* end date of interview is known */
+       }else{ /* if date of interview is unknown */
          /* death is known but not confirmed by death status at any wave */
          if(firstfour==0){
-           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
            firstfour=1;
          }
-         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d  with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
        }
      } /* end if date of death is known */
  #endif
-     wav[i]=mi; /* mi should be the last effective wave (or mli) */
+     wav[i]=mi; /* mi should be the last effective wave (or mli),  */
-     /* wav[i]=mw[mi][i]; */
+     /* wav[i]=mw[mi][i];   */
      if(mi==0){
        nbwarn++;
        if(first==0){
- Line 4598  void  concatwav(int wav[], int **dh, int
+ Line 5801  void  concatwav(int wav[], int **dh, int
    } /* End individuals */
    /* wav and mw are no more changed */
+   printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
+   fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
          dh[mi][i]=1;
        else{
-         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
            if (agedc[i] < 2*AGESUP) {
              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
              if(j==0) j=1;  /* Survives at least one month after exam */
- Line 4691  void  concatwav(int wav[], int **dh, int
+ Line 5897  void  concatwav(int wav[], int **dh, int
  /*********** Tricode ****************************/
   void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
- {
+  {
-   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
+    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
+    /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-    * Boring subroutine which should only output nbcode[Tvar[j]][k]
+     * Boring subroutine which should only output nbcode[Tvar[j]][k]
-    * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
+     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
-    * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
+     * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
-   */
+     */
-   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   int modmaxcovj=0; /* Modality max of covariates j */
+    int modmaxcovj=0; /* Modality max of covariates j */
-   int cptcode=0; /* Modality max of covariates j */
+    int cptcode=0; /* Modality max of covariates j */
-   int modmincovj=0; /* Modality min of covariates j */
+    int modmincovj=0; /* Modality min of covariates j */
-   /* cptcoveff=0;  */
+    /* cptcoveff=0;  */
-         /* *cptcov=0; */
+    /* *cptcov=0; */
-   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
+    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
+    for (k=1; k <= maxncov; k++)
-   /* Loop on covariates without age and products and no quantitative variable */
+      for(j=1; j<=2; j++)
-   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
+        nbcode[k][j]=0; /* Valgrind */
-   for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-     for (j=-1; (j < maxncov); j++) Ndum[j]=0;
+    /* Loop on covariates without age and products and no quantitative variable */
-     if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
+    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-       switch(Fixed[k]) {
+      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-       case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
+      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-                                 for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
+        switch(Fixed[k]) {
-                                         ij=(int)(covar[Tvar[k]][i]);
+        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-                                         /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+          modmaxcovj=0;
-                                          * If product of Vn*Vm, still boolean *:
+          modmincovj=0;
-                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+          for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
-                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+            ij=(int)(covar[Tvar[k]][i]);
-                                         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-                                                  modality of the nth covariate of individual i. */
+             * If product of Vn*Vm, still boolean *:
-                                         if (ij > modmaxcovj)
+             * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-                                                 modmaxcovj=ij;
+             * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-                                         else if (ij < modmincovj)
+            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-                                                 modmincovj=ij;
+               modality of the nth covariate of individual i. */
-                                         if ((ij < -1) && (ij > NCOVMAX)){
+            if (ij > modmaxcovj)
-                                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+              modmaxcovj=ij;
-                                                 exit(1);
+            else if (ij < modmincovj)
-                                         }else
+              modmincovj=ij;
-                                                 Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+            if (ij <0 || ij >1 ){
-                                         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+              printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
-                                         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+              fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
-                                         /* getting the maximum value of the modality of the covariate
+              fflush(ficlog);
-                                                  (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+              exit(1);
-                                                  female ies 1, then modmaxcovj=1.
+            }
-                                         */
+            if ((ij < -1) || (ij > NCOVMAX)){
-                                 } /* end for loop on individuals i */
+              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-                                 printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+              exit(1);
-                                 fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+            }else
-                                 cptcode=modmaxcovj;
+              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-                                 /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-                                 /*for (i=0; i<=cptcode; i++) {*/
+            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-                                 for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
+            /* getting the maximum value of the modality of the covariate
-                                         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
+               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                                         fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
+               female ies 1, then modmaxcovj=1.
-                                         if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
+            */
-                                                 if( j != -1){
+          } /* end for loop on individuals i */
-                                                         ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
+          printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-                                                                                                                                  covariate for which somebody answered excluding
+          fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-                                                                                                                                  undefined. Usually 2: 0 and 1. */
+          cptcode=modmaxcovj;
-                                                 }
+          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-                                                 ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
+          /*for (i=0; i<=cptcode; i++) {*/
-                                                                                                                                                 covariate for which somebody answered including
+          for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
-                                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */
+            printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-                                         }       /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
+            fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-                                                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+            if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-                                 } /* Ndum[-1] number of undefined modalities */
+              if( j != -1){
+                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
+                                   covariate for which somebody answered excluding
+                                   undefined. Usually 2: 0 and 1. */
+              }
+              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
+                                      covariate for which somebody answered including
+                                      undefined. Usually 3: -1, 0 and 1. */
+            }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
+                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+          } /* Ndum[-1] number of undefined modalities */
-                                 /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-                                 /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
+          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
-                                 /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
+          /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
-                                 /* modmincovj=3; modmaxcovj = 7; */
+          /* modmincovj=3; modmaxcovj = 7; */
-                                 /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
+          /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
-                                 /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
+          /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
-                           /*             defining two dummy variables: variables V1_1 and V1_2.*/
+          /*              defining two dummy variables: variables V1_1 and V1_2.*/
-               /* nbcode[Tvar[j]][ij]=k; */
+          /* nbcode[Tvar[j]][ij]=k; */
-               /* nbcode[Tvar[j]][1]=0; */
+          /* nbcode[Tvar[j]][1]=0; */
-               /* nbcode[Tvar[j]][2]=1; */
+          /* nbcode[Tvar[j]][2]=1; */
-               /* nbcode[Tvar[j]][3]=2; */
+          /* nbcode[Tvar[j]][3]=2; */
-               /* To be continued (not working yet). */
+          /* To be continued (not working yet). */
-               ij=0; /* ij is similar to i but can jump over null modalities */
+          ij=0; /* ij is similar to i but can jump over null modalities */
-                                 for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+          /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-                   break;
+          /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
-                 }
+          /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
-                                         ij++;
+           * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
-                                         nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
+          /*, could be restored in the future */
-                                         cptcode = ij; /* New max modality for covar j */
+          for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-                                 } /* end of loop on modality i=-1 to 1 or more */
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-                                 break;
+              break;
-       case 1: /* Testing on varying covariate, could be simple and
+            }
-                * should look at waves or product of fixed *
+            ij++;
-                * varying. No time to test -1, assuming 0 and 1 only */
+            nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
-                                 ij=0;
+            cptcode = ij; /* New max modality for covar j */
-                                 for(i=0; i<=1;i++){
+          } /* end of loop on modality i=-1 to 1 or more */
-                                         nbcode[Tvar[k]][++ij]=i;
+          break;
-                                 }
+        case 1: /* Testing on varying covariate, could be simple and
-                                 break;
+                 * should look at waves or product of fixed *
-       default:
+                 * varying. No time to test -1, assuming 0 and 1 only */
-                                 break;
+          ij=0;
-       } /* end switch */
+          for(i=0; i<=1;i++){
-     } /* end dummy test */
+            nbcode[Tvar[k]][++ij]=i;
+          }
-     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+          break;
-     /*  /\*recode from 0 *\/ */
+        default:
-     /*                               k is a modality. If we have model=V1+V1*sex  */
+          break;
-     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+        } /* end switch */
-     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+      } /* end dummy test */
-     /*  } */
+      if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+        for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
-     /*  if (ij > ncodemax[j]) { */
+          if(isnan(covar[Tvar[k]][i])){
-     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+            printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
-     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+            fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
-     /*    break; */
+            fflush(ficlog);
-     /*  } */
+            exit(1);
-     /*   }  /\* end of loop on modality k *\/ */
+          }
-   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+        }
+      }
+    } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
-   for (k=-1; k< maxncov; k++) Ndum[k]=0;
+    for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   /* Look at fixed dummy (single or product) covariates to check empty modalities */
+    /* Look at fixed dummy (single or product) covariates to check empty modalities */
-   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
+    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-     ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
+      ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
-     Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
+      Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
-     /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
+      /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
-   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
-   ij=0;
+    ij=0;
-   /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
+    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
-   for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
+      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
+      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-       /* If product not in single variable we don't print results */
+        /* If product not in single variable we don't print results */
-       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-       ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
+        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
-       Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
+        Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
-       Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
+        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
-       TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
+        TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
-       if(Fixed[k]!=0)
+        if(Fixed[k]!=0)
-         anyvaryingduminmodel=1;
+          anyvaryingduminmodel=1;
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
-                         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
+        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
-                         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
-                         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
-     }
+      }
-   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
-   /* ij--; */
+    /* ij--; */
-   /* cptcoveff=ij; /\*Number of total covariates*\/ */
+    /* cptcoveff=ij; /\*Number of total covariates*\/ */
-   *cptcov=ij; /*Number of total real effective covariates: effective
+    *cptcov=ij; /* cptcov= Number of total real effective covariates: effective (used as cptcoveff in other functions)
-                                                          * because they can be excluded from the model and real
+                 * because they can be excluded from the model and real
-                                                          * if in the model but excluded because missing values, but how to get k from ij?*/
+                 * if in the model but excluded because missing values, but how to get k from ij?*/
-   for(j=ij+1; j<= cptcovt; j++){
+    for(j=ij+1; j<= cptcovt; j++){
-     Tvaraff[j]=0;
+      Tvaraff[j]=0;
-     Tmodelind[j]=0;
+      Tmodelind[j]=0;
-   }
+    }
-   for(j=ntveff+1; j<= cptcovt; j++){
+    for(j=ntveff+1; j<= cptcovt; j++){
-     TmodelInvind[j]=0;
+      TmodelInvind[j]=0;
-   }
+    }
-   /* To be sorted */
+    /* To be sorted */
-   ;
+    ;
- }
+  }
  /*********** Health Expectancies ****************/
- void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
  {
    /* Health expectancies, no variances */
+   /* cij is the combination in the list of combination of dummy covariates */
+   /* strstart is a string of time at start of computing */
    int i, j, nhstepm, hstepm, h, nstepm;
    int nhstepma, nstepma; /* Decreasing with age */
    double age, agelim, hf;
    double ***p3mat;
    double eip;
-   pstamp(ficreseij);
+   /* pstamp(ficreseij); */
    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
    fprintf(ficreseij,"# Age");
    for(i=1; i<=nlstate;i++){
- Line 4903  void evsij(double ***eij, double x[], in
+ Line 6123  void evsij(double ***eij, double x[], in
    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
       nhstepm is the number of hstepm from age to agelim
       nstepm is the number of stepm from age to agelin.
-      Look at hpijx to understand the reason of that which relies in memory size
+      Look at hpijx to understand the reason which relies in memory size consideration
       and note for a fixed period like estepm months */
    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       survival function given by stepm (the optimization length). Unfortunately it
- Line 4934  void evsij(double ***eij, double x[], in
+ Line 6154  void evsij(double ***eij, double x[], in
      /* If stepm=6 months */
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
+     /* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */
-     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- Line 4970  void evsij(double ***eij, double x[], in
+ Line 6190  void evsij(double ***eij, double x[], in
  }
- void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
  {
    /* Covariances of health expectancies eij and of total life expectancies according
- Line 5083  void cvevsij(double ***eij, double x[],
+ Line 6303  void cvevsij(double ***eij, double x[],
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
- Line 5123  void cvevsij(double ***eij, double x[],
+ Line 6343  void cvevsij(double ***eij, double x[],
              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
+     /* if((int)age ==50){ */
+     /*   printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
+     /* } */
      /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- Line 5134  void cvevsij(double ***eij, double x[],
+ Line 6356  void cvevsij(double ***eij, double x[],
            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
+     /* Standard deviation of expectancies ij */
      fprintf(ficresstdeij,"%3.0f",age );
      for(i=1; i<=nlstate;i++){
        eip=0.;
- Line 5149  void cvevsij(double ***eij, double x[],
+ Line 6372  void cvevsij(double ***eij, double x[],
      }
      fprintf(ficresstdeij,"\n");
+     /* Variance of expectancies ij */
      fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
- Line 5180  void cvevsij(double ***eij, double x[],
+ Line 6404  void cvevsij(double ***eij, double x[],
  }
  /************ Variance ******************/
-  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
   {
-    /* Variance of health expectancies */
+    /** Variance of health expectancies
-    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+     *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
-    /* double **newm;*/
+     * double **newm;
-    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
+     * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
+     */
     /* int movingaverage(); */
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
+    int first=0;
     int k;
     double *xp;
-    double **gp, **gm;  /* for var eij */
+    double **gp, **gm;  /**< for var eij */
-    double ***gradg, ***trgradg; /*for var eij */
+    double ***gradg, ***trgradg; /**< for var eij */
-    double **gradgp, **trgradgp; /* for var p point j */
+    double **gradgp, **trgradgp; /**< for var p point j */
-    double *gpp, *gmp; /* for var p point j */
+    double *gpp, *gmp; /**< for var p point j */
-    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+    double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     /* double ***mobaverage; */
- Line 5237  void cvevsij(double ***eij, double x[],
+ Line 6463  void cvevsij(double ***eij, double x[],
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
+    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+    }
+    for(j=1;j<=cptcoveff;j++)
+      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]);
+    fprintf(ficresprobmorprev,"\n");
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
- Line 5250  void cvevsij(double ***eij, double x[],
+ Line 6484  void cvevsij(double ***eij, double x[],
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-    /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
- Line 5305  void cvevsij(double ***eij, double x[],
+ Line 6539  void cvevsij(double ***eij, double x[],
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
+        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
-        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+         * returns into prlim .
+         */
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
+        /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
- Line 5317  void cvevsij(double ***eij, double x[],
+ Line 6554  void cvevsij(double ***eij, double x[],
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
+        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
-        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
+         */
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
+        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
+         * at horizon h in state j including mortality.
+         */
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
-        /* Next for computing probability of death (h=1 means
+        /* Next for computing shifted+ probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months)
-           as a weighted average of prlim.
+           as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }
-        /* end probability of death */
+        /* Again with minus shift */
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
-        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
         if (popbased==1) {
           if(mobilav ==0){
- Line 5350  void cvevsij(double ***eij, double x[],
+ Line 6592  void cvevsij(double ***eij, double x[],
           }
         }
-        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
- Line 5366  void cvevsij(double ***eij, double x[],
+ Line 6608  void cvevsij(double ***eij, double x[],
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }
-        /* end probability of death */
+        /* end shifting computations */
+        /**< Computing gradient matrix at horizon h
+         */
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
+        /**< Gradient of overall mortality p.3 (or p.j)
-        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+         */
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
       } /* End theta */
+      /* We got the gradient matrix for each theta and state j */
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(h=0; h<=nhstepm; h++) /* veij */
- Line 5389  void cvevsij(double ***eij, double x[],
+ Line 6635  void cvevsij(double ***eij, double x[],
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
+      /**< as well as its transposed matrix
+       */
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
+      /* Computing trgradg by matcov by gradg at age and summing over h
+       * and k (nhstepm) formula 15 of article
+       * Lievre-Brouard-Heathcote
+       */
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
- Line 5406  void cvevsij(double ***eij, double x[],
+ Line 6658  void cvevsij(double ***eij, double x[],
         }
       }
-      /* pptj */
+      /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
+       * p.j overall mortality formula 49 but computed directly because
+       * we compute the grad (wix pijx) instead of grad (pijx),even if
+       * wix is independent of theta.
+       */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
- Line 5415  void cvevsij(double ***eij, double x[],
+ Line 6671  void cvevsij(double ***eij, double x[],
       /* end ppptj */
       /*  x centered again */
-      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
       if (popbased==1) {
         if(mobilav ==0){
- Line 5431  void cvevsij(double ***eij, double x[],
+ Line 6687  void cvevsij(double ***eij, double x[],
          computed over hstepm (estepm) matrices product = hstepm*stepm months)
          as a weighted average of prlim.
       */
-      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++)
           gmp[j] += prlim[i][i]*p3mat[i][j][1];
- Line 5494  void cvevsij(double ***eij, double x[],
+ Line 6750  void cvevsij(double ***eij, double x[],
   }  /* end varevsij */
  /************ Variance of prevlim ******************/
-  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
+  void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
  {
    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **dnewm,**doldm;
+   double **dnewmpar,**doldm;
    int i, j, nhstepm, hstepm;
    double *xp;
    double *gp, *gm;
- Line 5509  void cvevsij(double ***eij, double x[],
+ Line 6765  void cvevsij(double ***eij, double x[],
    int theta;
    pstamp(ficresvpl);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+   fprintf(ficresvpl,"# Age ");
+   if(nresult >=1)
+     fprintf(ficresvpl," Result# ");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
    fprintf(ficresvpl,"\n");
    xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+   dnewmpar=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
    hstepm=1*YEARM; /* Every year of age */
- Line 5536  void cvevsij(double ***eij, double x[],
+ Line 6794  void cvevsij(double ***eij, double x[],
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
-       else
+       /* else */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gp[i] = prlim[i][i];
          mgp[theta][i] = prlim[i][i];
        }
        for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
-       else
+       /* else */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gm[i] = prlim[i][i];
          mgm[theta][i] = prlim[i][i];
- Line 5586  void cvevsij(double ***eij, double x[],
+ Line 6844  void cvevsij(double ***eij, double x[],
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] =0.;
      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
      }else{
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
      }
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      fprintf(ficresvpl,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
+     if(nresult >=1)
+       fprintf(ficresvpl,"%d ",nres );
+     for(i=1; i<=nlstate;i++){
        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+       /* for(j=1;j<=nlstate;j++) */
+       /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
+     }
      fprintf(ficresvpl,"\n");
      free_vector(gp,1,nlstate);
      free_vector(gm,1,nlstate);
- Line 5609  void cvevsij(double ***eij, double x[],
+ Line 6872  void cvevsij(double ***eij, double x[],
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
+ }
+ /************ Variance of backprevalence limit ******************/
+  void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
+ {
+   /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+   double **dnewmpar,**doldm;
+   int i, j, nhstepm, hstepm;
+   double *xp;
+   double *gp, *gm;
+   double **gradg, **trgradg;
+   double **mgm, **mgp;
+   double age,agelim;
+   int theta;
+   pstamp(ficresvbl);
+   fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
+   fprintf(ficresvbl,"# Age ");
+   if(nresult >=1)
+     fprintf(ficresvbl," Result# ");
+   for(i=1; i<=nlstate;i++)
+       fprintf(ficresvbl," %1d-%1d",i,i);
+   fprintf(ficresvbl,"\n");
+   xp=vector(1,npar);
+   dnewmpar=matrix(1,nlstate,1,npar);
+   doldm=matrix(1,nlstate,1,nlstate);
+   hstepm=1*YEARM; /* Every year of age */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   agelim = AGEINF;
+   for (age=fage; age>=bage; age --){ /* If stepm=6 months */
+     nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     if (stepm >= YEARM) hstepm=1;
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     gradg=matrix(1,npar,1,nlstate);
+     mgp=matrix(1,npar,1,nlstate);
+     mgm=matrix(1,npar,1,nlstate);
+     gp=vector(1,nlstate);
+     gm=vector(1,nlstate);
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
+       if(mobilavproj > 0 )
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+       else
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+       for(i=1;i<=nlstate;i++){
+         gp[i] = bprlim[i][i];
+         mgp[theta][i] = bprlim[i][i];
+       }
+      for(i=1; i<=npar; i++) /* Computes gradient */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+        if(mobilavproj > 0 )
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+        else
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+       for(i=1;i<=nlstate;i++){
+         gm[i] = bprlim[i][i];
+         mgm[theta][i] = bprlim[i][i];
+       }
+       for(i=1;i<=nlstate;i++)
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
+     } /* End theta */
+     trgradg =matrix(1,nlstate,1,npar);
+     for(j=1; j<=nlstate;j++)
+       for(theta=1; theta <=npar; theta++)
+         trgradg[j][theta]=gradg[theta][j];
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\nmgm mgp %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf(" %d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\n gradg %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf("%d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     for(i=1;i<=nlstate;i++)
+       varbpl[i][(int)age] =0.;
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+     }else{
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+     }
+     for(i=1;i<=nlstate;i++)
+       varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+     fprintf(ficresvbl,"%.0f ",age );
+     if(nresult >=1)
+       fprintf(ficresvbl,"%d ",nres );
+     for(i=1; i<=nlstate;i++)
+       fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
+     fprintf(ficresvbl,"\n");
+     free_vector(gp,1,nlstate);
+     free_vector(gm,1,nlstate);
+     free_matrix(mgm,1,npar,1,nlstate);
+     free_matrix(mgp,1,npar,1,nlstate);
+     free_matrix(gradg,1,npar,1,nlstate);
+     free_matrix(trgradg,1,nlstate,1,npar);
+   } /* End age */
+   free_vector(xp,1,npar);
+   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
  }
- Line 5620  void varprob(char optionfilefiname[], do
+ Line 7008  void varprob(char optionfilefiname[], do
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
+    int nres=0; /* New */
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
- Line 5689  void varprob(char optionfilefiname[], do
+ Line 7078  void varprob(char optionfilefiname[], do
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
-    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
+    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
  and drawn. It helps understanding how is the covariance between two incidences.\
- Line 5707  To be simple, these graphs help to under
+ Line 7096  To be simple, these graphs help to under
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
-    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
+    for(nres=1;nres <=nresult; nres++){ /* For each resultline */
+    for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */
+      printf("Varprob  TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d \n",  TKresult[nres], j1, nres, cptcovn, cptcoveff, tj);
+      if(tj != 1 && TKresult[nres]!= j1)
+        continue;
+    /* for(j1=1; j1<=tj;j1++){  /\* For each valid combination of covariates or only once*\/ */
+      /* for(nres=1;nres <=1; nres++){ /\* For each resultline *\/ */
+      /* /\* for(nres=1;nres <=nresult; nres++){ /\\* For each resultline *\\/ *\/ */
       if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
         fprintf(ficresprob, "**********\n#\n");
         fprintf(ficresprobcov, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
         fprintf(ficresprobcov, "**********\n#\n");
         fprintf(ficgp, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
         fprintf(ficgp, "**********\n#\n");
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        /* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         fprintf(ficresprobcor, "\n#********** Variable ");
-        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
         fprintf(ficresprobcor, "**********\n#");
         if(invalidvarcomb[j1]){
           fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
- Line 5742  To be simple, these graphs help to under
+ Line 7141  To be simple, these graphs help to under
         cov[2]=age;
         if(nagesqr==1)
           cov[3]= age*age;
-        for (k=1; k<=cptcovn;k++) {
+        /* for (k=1; k<=cptcovn;k++) { */
-          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
+        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */
+        for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
+          /* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */
+          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])];
           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                                      * 1  1 1 1 1
                                                                      * 2  2 1 1 1
- Line 5751  To be simple, these graphs help to under
+ Line 7153  To be simple, these graphs help to under
                                                                      */
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         }
-        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+        /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
-        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+        /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
-        for (k=1; k<=cptcovprod;k++)
+        /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+        for (k=1; k<=cptcovage;k++){  /* For product with age */
+          if(Dummy[Tage[k]]==2){ /* dummy with age */
+            cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[k]]])]*cov[2];
+            /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
+          } else if(Dummy[Tage[k]]==3){ /* quantitative with age */
+            printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]);
+            /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; *\/ */
+            /* exit(1); */
+            /* cov[++k1]=Tqresult[nres][k];  */
+          }
+          /* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
+        }
+        for (k=1; k<=cptcovprod;k++){/* For product without age */
+          if(Dummy[Tvard[k][1]]==0){
+            if(Dummy[Tvard[k][2]]==0){
+              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])];
+              /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
+            }else{ /* Should we use the mean of the quantitative variables? */
+              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[nres][k]];
+              /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
+            }
+          }else{
+            if(Dummy[Tvard[k][2]]==0){
+              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[Tvard[k][1]]];
+              /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
+            }else{
+              cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][TnsdVar[Tvard[k][1]]]*  Tqinvresult[nres][TnsdVar[Tvard[k][2]]];
+              /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
+            }
+          }
+          /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
+        }
+ /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/
         for(theta=1; theta <=npar; theta++){
           for(i=1; i<=npar; i++)
             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
- Line 5886  To be simple, these graphs help to under
+ Line 7318  To be simple, these graphs help to under
                   }
                   /* Eigen vectors */
-                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                  if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
+                    printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+                    fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+                    v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
+                  }else
+                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   /*v21=sqrt(1.-v11*v11); *//* error */
                   v21=(lc1-v1)/cv12*v11;
                   v12=-v21;
- Line 5906  To be simple, these graphs help to under
+ Line 7343  To be simple, these graphs help to under
                     fprintf(ficgp,"\nset parametric;unset label");
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                     fprintf(ficgp,"\nset ter svg size 640, 480");
-                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+                    fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
- Line 5917  To be simple, these graphs help to under
+ Line 7354  To be simple, these graphs help to under
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
-                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
+                            mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
-                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                            mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
                   }else{
                     first=0;
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
-                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
-                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
                   }/* if first */
                 } /* age mod 5 */
               } /* end loop age */
- Line 5937  To be simple, these graphs help to under
+ Line 7374  To be simple, these graphs help to under
         } /*l1 */
       }/* k1 */
     }  /* loop on combination of covariates j1 */
+    } /* loop on nres */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- Line 5954  To be simple, these graphs help to under
+ Line 7392  To be simple, these graphs help to under
  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int prevfcast, int backcast, int estepm , \
+                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
-                   double jprev1, double mprev1,double anprev1, double dateprev1, \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
-                   double jprev2, double mprev2,double anprev2, double dateprev2){
+                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
-   int jj1, k1, i1, cpt;
+   int jj1, k1, i1, cpt, k4, nres;
+   /* In fact some results are already printed in fichtm which is open */
     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  </ul>");
+ /*    fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
+ /* </ul>", model); */
     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
-    fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
+    fprintf(fichtm,"<li> - Observed prevalence (cross-sectional prevalence) in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
     fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
     fprintf(fichtm,"\
- Line 5975  void printinghtml(char fileresu[], char
+ Line 7415  void printinghtml(char fileresu[], char
   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
             stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
     fprintf(fichtm,"\
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+  - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
     fprintf(fichtm,"\
-  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+  - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
     fprintf(fichtm,"\
   - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
- Line 5990  void printinghtml(char fileresu[], char
+ Line 7430  void printinghtml(char fileresu[], char
     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
     }
-    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     m=pow(2,cptcoveff);
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    fprintf(fichtm," \n<ul><li><b>Graphs (first order)</b></li><p>");
     jj1=0;
-    for(k1=1; k1<=m;k1++){
+    fprintf(fichtm," \n<ul>");
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        fprintf(fichtm,"\">");
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm,"************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
+          continue;
+        }
+        fprintf(fichtm,"</a></li>");
+      } /* cptcovn >0 */
+    }
+    fprintf(fichtm," \n</ul>");
+    jj1=0;
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
+        fprintf(fichtm,"\n<p><a name=\"rescov");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        fprintf(fichtm,"\"</a>");
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         for (cpt=1; cpt<=cptcoveff;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
-          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
+          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+          /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
         }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
+       }
         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
         if(invalidvarcomb[k1]){
           fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
           printf("\nCombination (%d) ignored because no cases \n",k1);
- Line 6015  void printinghtml(char fileresu[], char
+ Line 7511  void printinghtml(char fileresu[], char
         }
       }
       /* aij, bij */
-      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
+      fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
- <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Pij */
-      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
+      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
- <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Quasi-incidences */
       fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
- divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
- <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Survival functions (period) in state j */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+        fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
- <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
       }
       /* State specific survival functions (period) */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
+        fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
-  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
+  And probability to be observed in various states (up to %d) being in state %d at different ages.       \
-  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
+  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
       }
-      /* Period (stable) prevalence in each health state */
+      /* Period (forward stable) prevalence in each health state */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
- <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_"));
+       fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
       }
-      if(backcast==1){
+      if(prevbcast==1){
-        /* Period (stable) back prevalence in each health state */
+        /* Backward prevalence in each health state */
         for(cpt=1; cpt<=nlstate;cpt++){
-          fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
         }
       }
       if(prevfcast==1){
-        /* Projection of prevalence up to period (stable) prevalence in each health state */
+        /* Projection of prevalence up to period (forward stable) prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
+          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
+          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
+                  subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+        }
+      }
+      if(prevbcast==1){
+       /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
         for(cpt=1; cpt<=nlstate;cpt++){
-          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
- <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
+  from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
+  account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
+ with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
+          fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
         }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
- <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
+        fprintf(fichtm," (data from text file  <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
       }
       /* } /\* end i1 *\/ */
     }/* End k1 */
- Line 6095  See page 'Matrix of variance-covariance
+ Line 7609  See page 'Matrix of variance-covariance
     <a href=\"%s\">%s</a> <br>\n</li>",
             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
     fprintf(fichtm,"\
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
     fprintf(fichtm,"\
   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
     fprintf(fichtm,"\
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+  - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
- Line 6111  See page 'Matrix of variance-covariance
+ Line 7625  See page 'Matrix of variance-covariance
  /*  else  */
  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     fflush(fichtm);
-    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     m=pow(2,cptcoveff);
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");
+   jj1=0;
+    fprintf(fichtm," \n<ul>");
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        fprintf(fichtm,"\">");
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm,"************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
+          continue;
+        }
+        fprintf(fichtm,"</a></li>");
+      } /* cptcovn >0 */
+    }
+    fprintf(fichtm," \n</ul>");
     jj1=0;
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k1=1; k1<=m;k1++){
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
+        fprintf(fichtm,"\n<p><a name=\"rescovsecond");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        fprintf(fichtm,"\"</a>");
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
+        for (cpt=1; cpt<=cptcoveff;cpt++){  /**< cptcoveff number of variables */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
-        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
         if(invalidvarcomb[k1]){
           fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
- Line 6132  See page 'Matrix of variance-covariance
+ Line 7702  See page 'Matrix of variance-covariance
         }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
- <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
+        fprintf(fichtm," (data from text file  <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
       }
       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
- health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+ health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
  true period expectancies (those weighted with period prevalences are also\
   drawn in addition to the population based expectancies computed using\
-  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
+  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
- <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
+      fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
+      fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
       /* } /\* end i1 *\/ */
     }/* End k1 */
+   }/* End nres */
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
    char dirfileres[132],optfileres[132];
-   char gplotcondition[132];
+   char gplotcondition[132], gplotlabel[132];
-   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
    int lv=0, vlv=0, kl=0;
    int ng=0;
    int vpopbased;
    int ioffset; /* variable offset for columns */
+   int iyearc=1; /* variable column for year of projection  */
+   int iagec=1; /* variable column for age of projection  */
+   int nres=0; /* Index of resultline */
+   int istart=1; /* For starting graphs in projections */
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
- Line 6169  void printinggnuplot(char fileresu[], ch
+ Line 7746  void printinggnuplot(char fileresu[], ch
    /*#endif */
    m=pow(2,cptcoveff);
+   /* diagram of the model */
+   fprintf(ficgp,"\n#Diagram of the model \n");
+   fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
+   fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
+   fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\n#show arrow\nunset label\n");
+   fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
+   fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
+   fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
+   fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
    /* Contribution to likelihood */
    /* Plot the probability implied in the likelihood */
    fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
- Line 6201  void printinggnuplot(char fileresu[], ch
+ Line 7792  void printinggnuplot(char fileresu[], ch
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
    /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
+   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
-     for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
+     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
-       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
+         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+         if(m != 1 && TKresult[nres]!= k1)
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
+           continue;
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* We are interested in selected combination by the resultline */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
-         vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
+         strcpy(gplotlabel,"(");
-         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the value of the covariate corresponding to k1 combination *\/ */
-       }
+           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
-       fprintf(ficgp,"\n#\n");
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       if(invalidvarcomb[k1]){
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         continue;
+           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-       }
+           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
+           /* printf(" V%d=%d ",Tvaraff[k],vlv); */
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
-       fprintf(ficgp,"set xlabel \"Age\" \n\
+         }
- set ylabel \"Probability\" \n   \
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
- set ter svg size 640, 480\n     \
+           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       for (i=1; i<= nlstate ; i ++) {
+         }
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         strcpy(gplotlabel+strlen(gplotlabel),")");
-         else        fprintf(ficgp," %%*lf (%%*lf)");
+         /* printf("\n#\n"); */
-       }
+         fprintf(ficgp,"\n#\n");
-       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+         if(invalidvarcomb[k1]){
-       for (i=1; i<= nlstate ; i ++) {
+           /*k1=k1-1;*/ /* To be checked */
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         else fprintf(ficgp," %%*lf (%%*lf)");
+           continue;
-       }
+         }
-       fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
-       for (i=1; i<= nlstate ; i ++) {
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
-         else fprintf(ficgp," %%*lf (%%*lf)");
+         /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
-       }
+         fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
-       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
-       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+         /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
-         /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+       /* k1-1 error should be nres-1*/
-         fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
+         for (i=1; i<= nlstate ; i ++) {
-         if(cptcoveff ==0){
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
+           else        fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+         for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+         for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
+         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
+         if(cptcoveff ==0){
+           fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
          }else{
            kl=0;
            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
-             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+             /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+             lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
- Line 6261  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7869  plot [%.f:%.f] \"%s\" every :::%d::%d u
              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
              if(k==cptcoveff){
-               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
-+(cpt-1),  cpt );  /* 4 or 6 ?*/
++cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
              }else{
                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                kl++;
              }
            } /* end covariate */
          } /* end if no covariate */
-       } /* end if backcast */
-       fprintf(ficgp,"\nset out \n");
+         if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
+           if(cptcoveff ==0){
+             fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
+           }else{
+             kl=0;
+             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+               lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               /* vlv= nbcode[Tvaraff[k]][lv]; */
+               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+               kl++;
+               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+               if(k==cptcoveff){
+                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
+               }else{
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]);
+                 kl++;
+               }
+             } /* end covariate */
+           } /* end if no covariate */
+           if(prevbcast == 1){
+             fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             /* k1-1 error should be nres-1*/
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else        fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"\" w l lt 4");
+           } /* end if backprojcast */
+         } /* end if prevbcast */
+         /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+         fprintf(ficgp,"\nset out ;unset title;\n");
+       } /* nres */
      } /* k1 */
    } /* cpt */
-   /*2 eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-     for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-       lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       vlv= nbcode[Tvaraff[k]][lv];
-       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-     }
-     fprintf(ficgp,"\n#\n");
-     if(invalidvarcomb[k1]){
-       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       continue;
-     }
-     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       if(vpopbased==0)
-         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-       else
-         fprintf(ficgp,"\nreplot ");
-       for (i=1; i<= nlstate+1 ; i ++) {
-         k=2*i;
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         fprintf(ficgp,"\" t\"\" w l lt 0,");
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-       } /* state */
-     } /* vpopbased */
-     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-   } /* k1 */
-   /*3eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
+   /*2 eme*/
+   for (k1=1; k1<= m ; k1 ++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
+       strcpy(gplotlabel,"(");
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */
+         lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
+         /* vlv= nbcode[Tvaraff[k]][lv]; */
+         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
        }
+       /* for(k=1; k <= ncovds; k++){ */
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
        }
-       /*       k=2+nlstate*(2*cpt-2); */
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
-       k=2+(nlstate+1)*(cpt-1);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
+         fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
-       fprintf(ficgp,"set ter svg size 640, 480\n\
+         if(vpopbased==0){
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
+           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         }else
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\nreplot ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         for (i=1; i<= nlstate+1 ; i ++) {
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           k=2*i;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
+           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           fprintf(ficgp,"\" t\"\" w l lt 0,");
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+           else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+         } /* state */
+       } /* vpopbased */
+       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
+     } /* end nres */
+   } /* k1 end 2 eme*/
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */
+         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */
+           lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           /* vlv= nbcode[Tvaraff[k]][lv]; */
+           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         /*       k=2+nlstate*(2*cpt-2); */
+         k=2+(nlstate+1)*(cpt-1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+         fprintf(ficgp,"set ter svg size 640, 480\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
+         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-       */
+         */
-       for (i=1; i< nlstate ; i ++) {
+         for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
+           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+           /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-       }
+         }
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
-     }
+       }
-   }
+       fprintf(ficgp,"\nunset label;\n");
+     } /* end nres */
+   } /* end kl 3eme */
    /* 4eme */
    /* Survival functions (period) from state i in state j by initial state i */
-   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       if(m != 1 && TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
+         strcpy(gplotlabel,"(");
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
- set ter svg size 640, 480\n                                                                                                                                                                                     \
+           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
- unset log y\n                                                                                                                                                                                                                                           \
+           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       k=3;
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       for (i=1; i<= nlstate ; i ++){
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         if(i==1){
+           /* vlv= nbcode[Tvaraff[k]][lv]; */
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
-         }else{
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-           fprintf(ficgp,", '' ");
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
          }
-         l=(nlstate+ndeath)*(i-1)+1;
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
-         for (j=2; j<= nlstate+ndeath ; j ++)
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
-           fprintf(ficgp,"+$%d",k+l+j-1);
+         }
-         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         strcpy(gplotlabel+strlen(gplotlabel),")");
-       } /* nlstate */
+         fprintf(ficgp,"\n#\n");
-       fprintf(ficgp,"\nset out\n");
+         if(invalidvarcomb[k1]){
-     } /* end cpt state*/
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-   } /* end covariate */
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
+         for (i=1; i<= nlstate ; i ++){
+           if(i==1){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           }else{
+             fprintf(ficgp,", '' ");
+           }
+           l=(nlstate+ndeath)*(i-1)+1;
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+           for (j=2; j<= nlstate+ndeath ; j ++)
+             fprintf(ficgp,"+$%d",k+l+j-1);
+           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end nres */
+   } /* end covariate k1 */
  /* 5eme */
    /* Survival functions (period) from state i in state j by final state j */
-   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
+   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
+           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           /* vlv= nbcode[Tvaraff[k]][lv]; */
+           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
- set ter svg size 640, 480\n                                             \
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
- unset log y\n                                                           \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
-       k=3;
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           if(j==1)
-         if(j==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           else
-         else
+             fprintf(ficgp,", '' ");
-           fprintf(ficgp,", '' ");
+           l=(nlstate+ndeath)*(cpt-1) +j;
-         l=(nlstate+ndeath)*(cpt-1) +j;
+           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+           /* for (i=2; i<= nlstate+ndeath ; i ++) */
-         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+         } /* nlstate */
-       } /* nlstate */
+         fprintf(ficgp,", '' ");
-       fprintf(ficgp,", '' ");
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           l=(nlstate+ndeath)*(cpt-1) +j;
-         l=(nlstate+ndeath)*(cpt-1) +j;
+           if(j < nlstate)
-         if(j < nlstate)
+             fprintf(ficgp,"$%d +",k+l);
-           fprintf(ficgp,"$%d +",k+l);
+           else
-         else
+             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         }
-       }
+         fprintf(ficgp,"\nset out; unset label;\n");
-       fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
-     } /* end cpt state*/
+     } /* end covariate */
-   } /* end covariate */
+   } /* end nres */
  /* 6eme */
    /* CV preval stable (period) for each covariate */
-   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     if(m != 1 && TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       continue;
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
+       strcpy(gplotlabel,"(");
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+         /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */
+         lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
+         /* vlv= nbcode[Tvaraff[k]][lv]; */
+         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
        }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
        }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+       fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
        k=3; /* Offset */
-       for (i=1; i<= nlstate ; i ++){
+       for (i=1; i<= nlstate ; i ++){ /* State of origin */
          if(i==1)
            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
          else
            fprintf(ficgp,", '' ");
-         l=(nlstate+ndeath)*(i-1)+1;
+         l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
          for (j=2; j<= nlstate ; j ++)
            fprintf(ficgp,"+$%d",k+l+j-1);
          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
        } /* nlstate */
-       fprintf(ficgp,"\nset out\n");
+       fprintf(ficgp,"\nset out; unset label;\n");
      } /* end cpt state*/
    } /* end covariate */
  /* 7eme */
-   if(backcast == 1){
+   if(prevbcast == 1){
-     /* CV back preval stable (period) for each covariate */
+     /* CV backward prevalence  for each covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
-       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */
+           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-           vlv= nbcode[Tvaraff[k]][lv];
+           /* vlv= nbcode[Tvaraff[k]][lv]; */
+           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
          }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
            continue;
          }
-         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
          k=3; /* Offset */
-         for (i=1; i<= nlstate ; i ++){
+         for (i=1; i<= nlstate ; i ++){ /* State of arrival */
            if(i==1)
              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
            else
              fprintf(ficgp,", '' ");
            /* l=(nlstate+ndeath)*(i-1)+1; */
-           l=(nlstate+ndeath)*(cpt-1)+1;
+           l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
-           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
-           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
-           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
            /* for (j=2; j<= nlstate ; j ++) */
            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
-           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
          } /* nlstate */
-         fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
-   } /* End if backcast */
+   } /* End if prevbcast */
    /* 8eme */
    if(prevfcast==1){
-     /* Projection from cross-sectional to stable (period) for each covariate */
+     /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
-           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-           vlv= nbcode[Tvaraff[k]][lv];
+           /* vlv= nbcode[Tvaraff[k]][lv]; */
+           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
          }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
- Line 6568  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8314  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          }
          fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
-         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
-         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+         istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+         /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+         for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
            /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
            /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
            /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-           if(i==1){
+           if(i==istart){
              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
            }else{
              fprintf(ficgp,",\\\n '' ");
- Line 6590  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8339  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
              /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
              fprintf(ficgp," u %d:(", ioffset);
-             if(i==nlstate+1)
+             if(i==nlstate+1){
-               fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
+               fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-             else
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",ioffset);
+               fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
+                      offyear,                           \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
+             }else
                fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
            }else{ /* more than 2 covariates */
-             if(cptcoveff ==1){
+             ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
-               ioffset=4; /* Age is in 4 */
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-             }else{
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-               ioffset=6; /* Age is in 6 */
+             iyearc=ioffset-1;
-               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+             iagec=ioffset;
-               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-             }
              fprintf(ficgp," u %d:(",ioffset);
              kl=0;
              strcpy(gplotcondition,"(");
              for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
-               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+               lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
+               /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
+               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
                kl++;
                sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                kl++;
- Line 6625  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8379  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
              if(i==nlstate+1){
-               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
-                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",iagec);
+               fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
+                       iyearc, iagec, offyear,                           \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
+ /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
              }else{
                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
              }
            } /* end if covariate */
          } /* nlstate */
-         fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if prevfcast */
+   if(prevbcast==1){
+     /* Back projection from cross-sectional to stable (mixed) for each covariate */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+           lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           /* vlv= nbcode[Tvaraff[k]][lv]; */
+           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
+         istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+         /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+         for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           if(i==istart){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
+           }else{
+             fprintf(ficgp,",\\\n '' ");
+           }
+           if(cptcoveff ==0){ /* No covariate */
+             ioffset=2; /* Age is in 2 */
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             fprintf(ficgp," u %d:(", ioffset);
+             if(i==nlstate+1){
+               fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",ioffset);
+               fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
+                      offbyear,                          \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
+             }else
+               fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
+           }else{ /* more than 2 covariates */
+             ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             iyearc=ioffset-1;
+             iagec=ioffset;
+             fprintf(ficgp," u %d:(",ioffset);
+             kl=0;
+             strcpy(gplotcondition,"(");
+             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
+               lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
+               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+               kl++;
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+               kl++;
+               if(k <cptcoveff && cptcoveff>1)
+                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+             }
+             strcpy(gplotcondition+strlen(gplotcondition),")");
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             if(i==nlstate+1){
+               fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",iagec);
+               /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
+               fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
+                       iyearc,iagec,offbyear,                            \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
+ /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
+             }else{
+               /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
+               fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
+             }
+           } /* end if covariate */
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if prevbcast */
-   /* proba elementaires */
-   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
+   /* 9eme writing MLE parameters */
+   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
    for(i=1,jk=1; i <=nlstate; i++){
      fprintf(ficgp,"# initial state %d\n",i);
      for(k=1; k <=(nlstate+ndeath); k++){
- Line 6657  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8536  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"##############\n#\n");
    /*goto avoid;*/
-   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
+   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
+   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
- Line 6672  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8552  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
    fprintf(ficgp,"#\n");
    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-     fprintf(ficgp,"# ng=%d\n",ng);
+     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
-     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
+     fprintf(ficgp,"#model=%s \n",model);
-     for(jk=1; jk <=m; jk++) {
+     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
-       fprintf(ficgp,"#    jk=%d\n",jk);
+     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
+     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
+       strcpy(gplotlabel,"(");
+       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
+       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+         /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
+         lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */
+         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         /* vlv= nbcode[Tvaraff[k]][lv]; */
+         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+       }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
+       fprintf(ficgp,"\n#\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
+       fprintf(ficgp,"\nset key outside ");
+       /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
+       fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
        fprintf(ficgp,"\nset ter svg size 640, 480 ");
        if (ng==1){
          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
- Line 6716  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8623  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                break;
              }
              ij=1;/* To be checked else nbcode[0][0] wrong */
-             for(j=3; j <=ncovmodel-nagesqr; j++) {
+             ijp=1; /* product no age */
+             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
+             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
-               if(ij <=cptcovage) { /* Bug valgrind */
+               switch(Typevar[j]){
-                 if((j-2)==Tage[ij]) { /* Bug valgrind */
+               case 1:
-                   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                 if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                   if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */
-                   ij++;
+                     if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+                       if(DummyV[j]==0){/* Bug valgrind */
+                         fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+                       }else{ /* quantitative */
+                         fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                         /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                       }
+                       ij++;
+                     }
+                   }
                  }
-               }
+                 break;
-               else
+               case 2:
-                 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
+                 if(cptcovprod >0){
-             }
+                   if(j==Tprod[ijp]) { /* */
-           }else{
+                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
-             i=i-ncovmodel;
+                     if(ijp <=cptcovprod) { /* Product */
-             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
+                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
-               fprintf(ficgp," (1.");
+                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                           /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
+                           fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                         }else{ /* Vn is dummy and Vm is quanti */
+                           /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                         }
+                       }else{ /* Vn*Vm Vn is quanti */
+                         if(DummyV[Tvard[ijp][2]]==0){
+                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+                         }else{ /* Both quanti */
+                           fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                         }
+                       }
+                       ijp++;
+                     }
+                   } /* end Tprod */
+                 }
+                 break;
+               case 0:
+                 /* simple covariate */
+                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
+                 if(Dummy[j]==0){
+                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
+                 }else{ /* quantitative */
+                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
+                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                 }
+                /* end simple */
+                 break;
+               default:
+                 break;
+               } /* end switch */
+             } /* end j */
+           }else{ /* k=k2 */
+             if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */
+               fprintf(ficgp," (1.");i=i-ncovmodel;
+             }else
+               i=i-ncovmodel;
            }
            if(ng != 1){
              fprintf(ficgp,")/(1");
-             for(k1=1; k1 <=nlstate; k1++){
+             for(cpt=1; cpt <=nlstate; cpt++){
                if(nagesqr==0)
-                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
                else /* nagesqr =1 */
-                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
+                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                ij=1;
-               for(j=3; j <=ncovmodel-nagesqr; j++){
+               ijp=1;
-                 if(ij <=cptcovage) { /* Bug valgrind */
+               /* for(j=3; j <=ncovmodel-nagesqr; j++){ */
-                   if((j-2)==Tage[ij]) { /* Bug valgrind */
+               for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
-                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                 switch(Typevar[j]){
-                     /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                 case 1:
-                     ij++;
+                   if(cptcovage >0){
+                     if(j==Tage[ij]) { /* Bug valgrind */
+                       if(ij <=cptcovage) { /* Bug valgrind */
+                         if(DummyV[j]==0){/* Bug valgrind */
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); */
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); */
+                           fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]);
+                           /* fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */
+                           /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                         }else{ /* quantitative */
+                           /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
+                           fprintf(ficgp,"+p%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                           /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
+                           /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                         }
+                         ij++;
+                       }
+                     }
                    }
-                 }
+                   break;
-                 else
+                 case 2:
-                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
+                   if(cptcovprod >0){
+                     if(j==Tprod[ijp]) { /* */
+                       /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                       if(ijp <=cptcovprod) { /* Product */
+                         if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
+                           if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                             /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
+                             fprintf(ficgp,"+p%d*%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
+                           }else{ /* Vn is dummy and Vm is quanti */
+                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                             fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           }
+                         }else{ /* Vn*Vm Vn is quanti */
+                           if(DummyV[Tvard[ijp][2]]==0){
+                             fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
+                           }else{ /* Both quanti */
+                             fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                             /* fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
+                           }
+                         }
+                         ijp++;
+                       }
+                     } /* end Tprod */
+                   } /* end if */
+                   break;
+                 case 0:
+                   /* simple covariate */
+                   /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
+                   if(Dummy[j]==0){
+                     /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
+                     fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /*  */
+                     /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
+                   }else{ /* quantitative */
+                     fprintf(ficgp,"+p%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */
+                     /* fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* *\/ */
+                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                   }
+                   /* end simple */
+                   /* fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode *\/ */
+                   break;
+                 default:
+                   break;
+                 } /* end switch */
                }
                fprintf(ficgp,")");
              }
              fprintf(ficgp,")");
              if(ng ==2)
-               fprintf(ficgp," t \"p%d%d\" ", k2,k);
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
              else /* ng= 3 */
-               fprintf(ficgp," t \"i%d%d\" ", k2,k);
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
            }else{ /* end ng <> 1 */
              if( k !=k2) /* logit p11 is hard to draw */
-               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
            }
            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
              fprintf(ficgp,",");
- Line 6773  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8791  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            i=i+ncovmodel;
          } /* end k */
        } /* end k2 */
-       fprintf(ficgp,"\n set out\n");
+       /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
-     } /* end jk */
+       fprintf(ficgp,"\n set out; unset title;set key default;\n");
+     } /* end k1 */
    } /* end ng */
    /* avoid: */
    fflush(ficgp);
- Line 6789  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8808  plot [%.f:%.f]  ", ageminpar, agemaxpar)
     int modcovmax =1;
     int mobilavrange, mob;
     int iage=0;
+    int firstA1=0, firstA2=0;
-    double sum=0.;
+    double sum=0., sumr=0.;
     double age;
-    double *sumnewp, *sumnewm;
+    double *sumnewp, *sumnewm, *sumnewmr;
-    double *agemingood, *agemaxgood; /* Currently identical for all covariates */
+    double *agemingood, *agemaxgood;
+    double *agemingoodr, *agemaxgoodr;
-    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
+    /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
-    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
+    /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
     sumnewp = vector(1,ncovcombmax);
     sumnewm = vector(1,ncovcombmax);
+    sumnewmr = vector(1,ncovcombmax);
     agemingood = vector(1,ncovcombmax);
+    agemingoodr = vector(1,ncovcombmax);
     agemaxgood = vector(1,ncovcombmax);
+    agemaxgoodr = vector(1,ncovcombmax);
     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-      sumnewm[cptcod]=0.;
+      sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
       sumnewp[cptcod]=0.;
-      agemingood[cptcod]=0;
+      agemingood[cptcod]=0, agemingoodr[cptcod]=0;
-      agemaxgood[cptcod]=0;
+      agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
     }
     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
-    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+    if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-      if(mobilav==1) mobilavrange=5; /* default */
+      if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
- Line 6825  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8849  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       */
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-          for (i=1; i<=nlstate;i++){
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+            sumnewm[cptcod]=0.;
+            for (i=1; i<=nlstate;i++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
               for (cpt=1;cpt<=(mob-1)/2;cpt++){
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
               }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-            }
+              sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-          }
+            } /* end i */
+            if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
+          } /* end cptcod */
         }/* end age */
       }/* end mob */
-    }else
+    }else{
+      printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
       return -1;
-    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+    }
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
       if(invalidvarcomb[cptcod]){
         printf("\nCombination (%d) ignored because no cases \n",cptcod);
         continue;
       }
-      agemingood[cptcod]=fage-(mob-1)/2;
+      for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
-      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
         sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemingoodr[cptcod]=age;
         }
         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
-          agemingood[cptcod]=age;
+            agemingood[cptcod]=age;
-        }else{ /* bad */
+        }
-          for (i=1; i<=nlstate;i++){
+      } /* age */
-            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
-          } /* i */
-        } /* end bad */
-      }/* age */
-      sum=0.;
-      for (i=1; i<=nlstate;i++){
-        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
-      }
-      if(fabs(sum - 1.) > 1.e-3) { /* bad */
-        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
-        /* for (i=1; i<=nlstate;i++){ */
-        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
-        /* } /\* i *\/ */
-      } /* end bad */
-      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
-      /* From youngest, finding the oldest wrong */
-      agemaxgood[cptcod]=bage+(mob-1)/2;
-      for (age=bage+(mob-1)/2; age<=fage; age++){
         sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemaxgoodr[cptcod]=age;
         }
         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
           agemaxgood[cptcod]=age;
-        }else{ /* bad */
+        }
-          for (i=1; i<=nlstate;i++){
+      } /* age */
-            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
-          } /* i */
+      /* but they will change */
+      firstA1=0;firstA2=0;
+      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
+        sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
+          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+            agemaxgoodr[cptcod]=age;  /* age min */
+            for (i=1; i<=nlstate;i++)
+              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }else{
+          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemaxgood[cptcod]=age;
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }/* end else */
+        sum=0.;sumr=0.;
+        for (i=1; i<=nlstate;i++){
+          sum+=mobaverage[(int)age][i][cptcod];
+          sumr+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sum - 1.) > 1.e-3) { /* bad */
+          if(!firstA1){
+            firstA1=1;
+            printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
+          }
+          fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
+        } /* end bad */
+        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
+          if(!firstA2){
+            firstA2=1;
+            printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
+          }
+          fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
         } /* end bad */
       }/* age */
-      sum=0.;
-      for (i=1; i<=nlstate;i++){
+      for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
-        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+        sumnewm[cptcod]=0.;
-      }
+        sumnewmr[cptcod]=0.;
-      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        for (i=1; i<=nlstate;i++){
-        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-        /* for (i=1; i<=nlstate;i++){ */
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
-        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        }
-        /* } /\* i *\/ */
+        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
-      } /* end bad */
+          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemingoodr[cptcod]=age;
+            for (i=1; i<=nlstate;i++)
+              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }else{
+          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemingood[cptcod]=age;
+          }else{ /* bad */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }/* end else */
+        sum=0.;sumr=0.;
+        for (i=1; i<=nlstate;i++){
+          sum+=mobaverage[(int)age][i][cptcod];
+          sumr+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sum - 1.) > 1.e-3) { /* bad */
+          printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
+        } /* end bad */
+        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
+          printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
+        } /* end bad */
+      }/* age */
       for (age=bage; age<=fage; age++){
-        printf("%d %d ", cptcod, (int)age);
+        /* printf("%d %d ", cptcod, (int)age); */
         sumnewp[cptcod]=0.;
         sumnewm[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
- Line 6910  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 9009  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       }
       /* printf("\n"); */
       /* } */
       /* brutal averaging */
-      for (i=1; i<=nlstate;i++){
+      /* for (i=1; i<=nlstate;i++){ */
-        for (age=1; age<=bage; age++){
+      /*   for (age=1; age<=bage; age++){ */
-          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
-          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
-        }
+      /*   }      */
-        for (age=fage; age<=AGESUP; age++){
+      /*   for (age=fage; age<=AGESUP; age++){ */
-          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
-          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
-        }
+      /*   } */
-      } /* end i status */
+      /* } /\* end i status *\/ */
-      for (i=nlstate+1; i<=nlstate+ndeath;i++){
+      /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
-        for (age=1; age<=AGESUP; age++){
+      /*   for (age=1; age<=AGESUP; age++){ */
-          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
+      /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
-          mobaverage[(int)age][i][cptcod]=0.;
+      /*          mobaverage[(int)age][i][cptcod]=0.; */
-        }
+      /*   } */
-      }
+      /* } */
     }/* end cptcod */
-    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(agemaxgoodr,1, ncovcombmax);
-    free_vector(sumnewp,1, ncovcombmax);
     free_vector(agemaxgood,1, ncovcombmax);
     free_vector(agemingood,1, ncovcombmax);
+    free_vector(agemingoodr,1, ncovcombmax);
+    free_vector(sumnewmr,1, ncovcombmax);
+    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
     return 0;
   }/* End movingaverage */
  /************** Forecasting ******************/
- void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+ /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
-   /* proj1, year, month, day of starting projection
+ void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
+   /* dateintemean, mean date of interviews
+      dateprojd, year, month, day of starting projection
+      dateprojf date of end of projection;year of end of projection (same day and month as proj1).
       agemin, agemax range of age
       dateprev1 dateprev2 range of dates during which prevalence is computed
-      anproj2 year of en of projection (same day and month as proj1).
    */
-   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
+   /* double anprojd, mprojd, jprojd; */
+   /* double anprojf, mprojf, jprojf; */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
    double agec; /* generic age */
-   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double agelim, ppij, yp,yp1,yp2;
    double *popeffectif,*popcount;
    double ***p3mat;
    /* double ***mobaverage; */
- Line 6965  void prevforecast(char fileres[], double
+ Line 9073  void prevforecast(char fileres[], double
      printf("Problem with forecast resultfile: %s\n", fileresf);
      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
    }
-   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
+   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
+   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
- Line 6976  void prevforecast(char fileres[], double
+ Line 9084  void prevforecast(char fileres[], double
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
-   else  hstepm=estepm;
+   else{
+     hstepm=estepm;
+   }
+   if(estepm > stepm){ /* Yes every two year */
+     stepsize=2;
+   }
+   hstepm=hstepm/stepm;
+   /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
+   /*                              fractional in yp1 *\/ */
+   /* aintmean=yp; */
+   /* yp2=modf((yp1*12),&yp); */
+   /* mintmean=yp; */
+   /* yp1=modf((yp2*30.5),&yp); */
+   /* jintmean=yp; */
+   /* if(jintmean==0) jintmean=1; */
+   /* if(mintmean==0) mintmean=1; */
-   hstepm=hstepm/stepm;
-   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
-                                fractional in yp1 */
-   anprojmean=yp;
-   yp2=modf((yp1*12),&yp);
-   mprojmean=yp;
-   yp1=modf((yp2*30.5),&yp);
-   jprojmean=yp;
-   if(jprojmean==0) jprojmean=1;
-   if(mprojmean==0) jprojmean=1;
+   /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
+   /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
+   /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
    i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
    fprintf(ficresf,"#****** Routine prevforecast **\n");
  /*            if (h==(int)(YEARM*yearp)){ */
-   for(k=1;k<=i1;k++){
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) */
+     if(i1 != 1 && TKresult[nres]!= k)
+       continue;
+     if(invalidvarcomb[k]){
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
+       continue;
+     }
+     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+     for(j=1;j<=cptcoveff;j++) {
+       /* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */
+       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+     }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+     }
+     fprintf(ficresf," yearproj age");
+     for(j=1; j<=nlstate+ndeath;j++){
+       for(i=1; i<=nlstate;i++)
+         fprintf(ficresf," p%d%d",i,j);
+       fprintf(ficresf," wp.%d",j);
+     }
+     for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
+       fprintf(ficresf,"\n");
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
+       /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
+       for (agec=fage; agec>=(bage); agec--){
+         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+         nhstepm = nhstepm/hstepm;
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         /* We compute pii at age agec over nhstepm);*/
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
+         /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+         for (h=0; h<=nhstepm; h++){
+           if (h*hstepm/YEARM*stepm ==yearp) {
+             break;
+           }
+         }
+         fprintf(ficresf,"\n");
+         for(j=1;j<=cptcoveff;j++)
+           /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */
+           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* TnsdVar[Tvaraff]  correct */
+         fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
+         for(j=1; j<=nlstate+ndeath;j++) {
+           ppij=0.;
+           for(i=1; i<=nlstate;i++) {
+             if (mobilav>=1)
+              ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
+             else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+             }
+             fprintf(ficresf," %.3f", p3mat[i][j][h]);
+           } /* end i */
+           fprintf(ficresf," %.3f", ppij);
+         }/* end j */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+       /* diffyear=(int) anproj1+yearp-ageminpar-1; */
+       /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
+     } /* end yearp */
+   } /* end  k */
+   fclose(ficresf);
+   printf("End of Computing forecasting \n");
+   fprintf(ficlog,"End of Computing forecasting\n");
+ }
+ /************** Back Forecasting ******************/
+  /* void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
+  void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
+   /* back1, year, month, day of starting backprojection
+      agemin, agemax range of age
+      dateprev1 dateprev2 range of dates during which prevalence is computed
+      anback2 year of end of backprojection (same day and month as back1).
+      prevacurrent and prev are prevalences.
+   */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
+   double agec; /* generic age */
+   double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
+   double *popeffectif,*popcount;
+   double ***p3mat;
+   /* double ***mobaverage; */
+   char fileresfb[FILENAMELENGTH];
+   agelim=AGEINF;
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
+   */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
+   /*Do we need to compute prevalence again?*/
+   /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+   strcpy(fileresfb,"FB_");
+   strcat(fileresfb,fileresu);
+   if((ficresfb=fopen(fileresfb,"w"))==NULL) {
+     printf("Problem with back forecast resultfile: %s\n", fileresfb);
+     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
+   }
+   printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else{
+     hstepm=estepm;
+   }
+   if(estepm >= stepm){ /* Yes every two year */
+     stepsize=2;
+   }
+   hstepm=hstepm/stepm;
+   /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
+   /*                              fractional in yp1 *\/ */
+   /* aintmean=yp; */
+   /* yp2=modf((yp1*12),&yp); */
+   /* mintmean=yp; */
+   /* yp1=modf((yp2*30.5),&yp); */
+   /* jintmean=yp; */
+   /* if(jintmean==0) jintmean=1; */
+   /* if(mintmean==0) jintmean=1; */
+   i1=pow(2,cptcoveff);
+   if (cptcovn < 1){i1=1;}
+   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
+   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
+   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(k=1; k<=i1;k++){
+     if(i1 != 1 && TKresult[nres]!= k)
+       continue;
      if(invalidvarcomb[k]){
        printf("\nCombination (%d) projection ignored because no cases \n",k);
        continue;
      }
-     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
      for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
      }
-     fprintf(ficresf," yearproj age");
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-     for(j=1; j<=nlstate+ndeath;j++){
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       for(i=1; i<=nlstate;i++)
-         fprintf(ficresf," p%d%d",i,j);
-       fprintf(ficresf," wp.%d",j);
      }
-     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+     fprintf(ficresfb," yearbproj age");
-       fprintf(ficresf,"\n");
+     for(j=1; j<=nlstate+ndeath;j++){
-       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+       for(i=1; i<=nlstate;i++)
-       for (agec=fage; agec>=(ageminpar-1); agec--){
+         fprintf(ficresfb," b%d%d",i,j);
-         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       fprintf(ficresfb," b.%d",j);
-         nhstepm = nhstepm/hstepm;
+     }
+     for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
+       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
+       fprintf(ficresfb,"\n");
+       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
+       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
+       /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
+       for (agec=bage; agec<=fage; agec++){  /* testing */
+         /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
+         nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
+         nhstepm = nhstepm/hstepm;
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+         /* computes hbxij at age agec over 1 to nhstepm */
+         /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
+         hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
+         /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
+         /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+         /* printf(" agec=%.2f\n",agec);fflush(stdout); */
          for (h=0; h<=nhstepm; h++){
-           if (h*hstepm/YEARM*stepm ==yearp) {
+           if (h*hstepm/YEARM*stepm ==-yearp) {
-             fprintf(ficresf,"\n");
+             break;
-             for(j=1;j<=cptcoveff;j++)
+           }
-               fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
-             fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+         fprintf(ficresfb,"\n");
-           }
+         for(j=1;j<=cptcoveff;j++)
-           for(j=1; j<=nlstate+ndeath;j++) {
+           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-             ppij=0.;
+         fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
-             for(i=1; i<=nlstate;i++) {
+         for(i=1; i<=nlstate+ndeath;i++) {
-               if (mobilav==1)
+           ppij=0.;ppi=0.;
-                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
+           for(j=1; j<=nlstate;j++) {
-               else {
+             /* if (mobilav==1) */
-                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+             ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
-               }
+             ppi=ppi+prevacurrent[(int)agec][j][k];
-               if (h*hstepm/YEARM*stepm== yearp) {
+             /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
-                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
+             /* ppi=ppi+mobaverage[(int)agec][j][k]; */
-               }
+               /* else { */
-             } /* end i */
+               /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
-             if (h*hstepm/YEARM*stepm==yearp) {
+               /* } */
-               fprintf(ficresf," %.3f", ppij);
+             fprintf(ficresfb," %.3f", p3mat[i][j][h]);
-             }
+           } /* end j */
-           }/* end j */
+           if(ppi <0.99){
-         } /* end h */
+             printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+             fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+           }
+           fprintf(ficresfb," %.3f", ppij);
+         }/* end j */
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        } /* end agec */
      } /* end yearp */
-   } /* end  k */
+   } /* end k */
-   fclose(ficresf);
-   printf("End of Computing forecasting \n");
-   fprintf(ficlog,"End of Computing forecasting\n");
- }
- /* /\************** Back Forecasting ******************\/ */
- /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
- /*   /\* back1, year, month, day of starting backection  */
- /*      agemin, agemax range of age */
- /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
- /*      anback2 year of en of backection (same day and month as back1). */
- /*   *\/ */
- /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
- /*   double agec; /\* generic age *\/ */
- /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
- /*   double *popeffectif,*popcount; */
- /*   double ***p3mat; */
- /*   /\* double ***mobaverage; *\/ */
- /*   char fileresfb[FILENAMELENGTH]; */
- /*   agelim=AGESUP; */
- /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
- /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
- /*      We still use firstpass and lastpass as another selection. */
- /*   *\/ */
- /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
- /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
- /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
- /*   strcpy(fileresfb,"FB_");  */
- /*   strcat(fileresfb,fileresu); */
- /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
- /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
- /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
- /*   } */
- /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
- /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
- /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
- /*   /\* if (mobilav!=0) { *\/ */
- /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
- /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
- /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
- /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
- /*   /\*   } *\/ */
- /*   /\* } *\/ */
- /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
- /*   if (stepm<=12) stepsize=1; */
- /*   if(estepm < stepm){ */
- /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
- /*   } */
- /*   else  hstepm=estepm;    */
- /*   hstepm=hstepm/stepm;  */
- /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
- /*                                fractional in yp1 *\/ */
- /*   anprojmean=yp; */
- /*   yp2=modf((yp1*12),&yp); */
- /*   mprojmean=yp; */
- /*   yp1=modf((yp2*30.5),&yp); */
- /*   jprojmean=yp; */
- /*   if(jprojmean==0) jprojmean=1; */
- /*   if(mprojmean==0) jprojmean=1; */
- /*   i1=cptcoveff; */
- /*   if (cptcovn < 1){i1=1;} */
- /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
+   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
- /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
+   fclose(ficresfb);
+   printf("End of Computing Back forecasting \n");
- /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
+   fprintf(ficlog,"End of Computing Back forecasting\n");
- /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
- /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
- /*       k=k+1; */
- /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
- /*       for(j=1;j<=cptcoveff;j++) { */
- /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
- /*       } */
- /*       fprintf(ficresfb," yearbproj age"); */
- /*       for(j=1; j<=nlstate+ndeath;j++){  */
- /*                              for(i=1; i<=nlstate;i++)               */
- /*           fprintf(ficresfb," p%d%d",i,j); */
- /*                              fprintf(ficresfb," p.%d",j); */
- /*       } */
- /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
- /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
- /*                              fprintf(ficresfb,"\n"); */
- /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
- /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
- /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
- /*                                      nhstepm = nhstepm/hstepm;  */
- /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
- /*                                      oldm=oldms;savm=savms; */
- /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
- /*                                      for (h=0; h<=nhstepm; h++){ */
- /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
- /*               fprintf(ficresfb,"\n"); */
- /*               for(j=1;j<=cptcoveff;j++)  */
- /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
- /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
- /*                                              }  */
- /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
- /*                                                      ppij=0.; */
- /*                                                      for(i=1; i<=nlstate;i++) { */
- /*                                                              if (mobilav==1)  */
- /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
- /*                                                              else { */
- /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
- /*                                                              } */
- /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
- /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
- /*                                                              } */
- /*                                                      } /\* end i *\/ */
- /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
- /*                                                              fprintf(ficresfb," %.3f", ppij); */
- /*                                                      } */
- /*                                              }/\* end j *\/ */
- /*                                      } /\* end h *\/ */
- /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
- /*                              } /\* end agec *\/ */
- /*       } /\* end yearp *\/ */
- /*     } /\* end cptcod *\/ */
- /*   } /\* end  cptcov *\/ */
- /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
- /*   fclose(ficresfb); */
+ }
- /*   printf("End of Computing Back forecasting \n"); */
- /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
+ /* Variance of prevalence limit: varprlim */
+  void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
- /* } */
+     /*------- Variance of forward period (stable) prevalence------*/
+    char fileresvpl[FILENAMELENGTH];
+    FILE *ficresvpl;
+    double **oldm, **savm;
+    double **varpl; /* Variances of prevalence limits by age */
+    int i1, k, nres, j ;
+     strcpy(fileresvpl,"VPL_");
+     strcat(fileresvpl,fileresu);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+       for(k=1; k<=i1;k++){ /* We find the combination equivalent to result line values of dummies */
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
+       fprintf(ficresvpl,"\n#****** ");
+       printf("\n#****** ");
+       fprintf(ficlog,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+       }
+       fprintf(ficresvpl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
+  }
+ /* Variance of back prevalence: varbprlim */
+  void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
+       /*------- Variance of back (stable) prevalence------*/
+    char fileresvbl[FILENAMELENGTH];
+    FILE  *ficresvbl;
+    double **oldm, **savm;
+    double **varbpl; /* Variances of back prevalence limits by age */
+    int i1, k, nres, j ;
+    strcpy(fileresvbl,"VBL_");
+    strcat(fileresvbl,fileresu);
+    if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
+      printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
+      exit(0);
+    }
+    printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
+    fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
+    i1=pow(2,cptcoveff);
+    if (cptcovn < 1){i1=1;}
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+      for(k=1; k<=i1;k++){
+        if(i1 != 1 && TKresult[nres]!= k)
+          continue;
+        fprintf(ficresvbl,"\n#****** ");
+        printf("\n#****** ");
+        fprintf(ficlog,"\n#****** ");
+        for(j=1;j<=cptcoveff;j++) {
+          fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+        }
+        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+          fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+        }
+        fprintf(ficresvbl,"******\n");
+        printf("******\n");
+        fprintf(ficlog,"******\n");
+        varbpl=matrix(1,nlstate,(int) bage, (int) fage);
+        oldm=oldms;savm=savms;
+        varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
+        free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
+        /*}*/
+      }
+    fclose(ficresvbl);
+    printf("done variance-covariance of back prevalence\n");fflush(stdout);
+    fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
+  } /* End of varbprlim */
  /************** Forecasting *****not tested NB*************/
  /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
- Line 7485  void prwizard(int ncovmodel, int nlstate
+ Line 9752  void prwizard(int ncovmodel, int nlstate
  /******************* Gompertz Likelihood ******************************/
  double gompertz(double x[])
  {
-   double A,B,L=0.0,sump=0.,num=0.;
+   double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
    int i,n=0; /* n is the size of the sample */
    for (i=1;i<=imx ; i++) {
- Line 7493  double gompertz(double x[])
+ Line 9760  double gompertz(double x[])
      /*    sump=sump+1;*/
      num=num+1;
    }
+   L=0.0;
+   /* agegomp=AGEGOMP; */
    /* for (i=0; i<=imx; i++)
       if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
-   for (i=1;i<=imx ; i++)
+   for (i=1;i<=imx ; i++) {
-     {
+     /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
-       if (cens[i] == 1 && wav[i]>1)
+        mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
-         A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+      * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
+      *   and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
-       if (cens[i] == 0 && wav[i]>1)
+      * +
+      * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
+      */
+      if (wav[i] > 1 || agedc[i] < AGESUP) {
+        if (cens[i] == 1){
+          A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
+        } else if (cens[i] == 0){
          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
-              +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
+           +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
+       } else
+          printf("Gompertz cens[%d] neither 1 nor 0\n",i);
        /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
-       if (wav[i] > 1 ) { /* ??? */
+        L=L+A*weight[i];
-         L=L+A*weight[i];
          /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
-       }
+      }
-     }
+   }
-  /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+   /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    return -2*L*num/sump;
  }
- Line 7523  double gompertz(double x[])
+ Line 9796  double gompertz(double x[])
  /******************* Gompertz_f Likelihood ******************************/
  double gompertz_f(const gsl_vector *v, void *params)
  {
-   double A,B,LL=0.0,sump=0.,num=0.;
+   double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
    double *x= (double *) v->data;
    int i,n=0; /* n is the size of the sample */
- Line 7613  int readdata(char datafile[], int firsto
+ Line 9886  int readdata(char datafile[], int firsto
    /*-------- data file ----------*/
    FILE *fic;
    char dummy[]="                         ";
-   int i=0, j=0, n=0, iv=0;
+   int i=0, j=0, n=0, iv=0, v;
    int lstra;
    int linei, month, year,iout;
+   int noffset=0; /* This is the offset if BOM data file */
    char line[MAXLINE], linetmp[MAXLINE];
    char stra[MAXLINE], strb[MAXLINE];
    char *stratrunc;
+   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
+   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
+   for(v=1;v<NCOVMAX;v++){
+     DummyV[v]=0;
+     FixedV[v]=0;
+   }
+   for(v=1; v <=ncovcol;v++){
+     DummyV[v]=0;
+     FixedV[v]=0;
+   }
+   for(v=ncovcol+1; v <=ncovcol+nqv;v++){
+     DummyV[v]=1;
+     FixedV[v]=0;
+   }
+   for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
+     DummyV[v]=0;
+     FixedV[v]=1;
+   }
+   for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
+     DummyV[v]=1;
+     FixedV[v]=1;
+   }
+   for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
+     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
+     fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
+   }
    if((fic=fopen(datafile,"r"))==NULL)    {
      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
    }
-   i=1;
+     /* Is it a BOM UTF-8 Windows file? */
+   /* First data line */
    linei=0;
+   while(fgets(line, MAXLINE, fic)) {
+     noffset=0;
+     if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
+     {
+       noffset=noffset+3;
+       printf("# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
+       fprintf(ficlog,"# Data file '%s'  is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
+       fflush(ficlog); return 1;
+     }
+     /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
+     else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
+     {
+       noffset=noffset+2;
+       printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
+       fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
+       fflush(ficlog); return 1;
+     }
+     else if( line[0] == 0 && line[1] == 0)
+     {
+       if( line[2] == (char)0xFE && line[3] == (char)0xFF){
+         noffset=noffset+4;
+         printf("# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
+         fprintf(ficlog,"# Error Data file '%s'  is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
+         fflush(ficlog); return 1;
+       }
+     } else{
+       ;/*printf(" Not a BOM file\n");*/
+     }
+         /* If line starts with a # it is a comment */
+     if (line[noffset] == '#') {
+       linei=linei+1;
+       break;
+     }else{
+       break;
+     }
+   }
+   fclose(fic);
+   if((fic=fopen(datafile,"r"))==NULL)    {
+     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
+     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
+   }
+   /* Not a Bom file */
+   i=1;
    while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
      linei=linei+1;
      for(j=strlen(line); j>=0;j--){  /* Untabifies line */
- Line 7650  int readdata(char datafile[], int firsto
+ Line 9995  int readdata(char datafile[], int firsto
      /* Loops on waves */
      for (j=maxwav;j>=1;j--){
        for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
-                                 cutv(stra, strb, line, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                         cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
+           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
-                                         cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
+           cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
-                                         if(isalpha(strb[1])) { /* .m or .d Really Missing value */
+           if(isalpha(strb[1])) { /* .m or .d Really Missing value */
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                 }else{
+         }else{
-                                         errno=0;
+           errno=0;
-                                         /* what_kind_of_number(strb); */
+           /* what_kind_of_number(strb); */
-                                         dval=strtod(strb,&endptr);
+           dval=strtod(strb,&endptr);
-                                         /* if( strb[0]=='\0' || (*endptr != '\0')){ */
+           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
-                                         /* if(strb != endptr && *endptr == '\0') */
+           /* if(strb != endptr && *endptr == '\0') */
-                                         /*    dval=dlval; */
+           /*    dval=dlval; */
-                                         /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
-                                         if( strb[0]=='\0' || (*endptr != '\0')){
+           if( strb[0]=='\0' || (*endptr != '\0')){
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                         cotqvar[j][iv][i]=dval;
+           cotqvar[j][iv][i]=dval;
-                                         cotvar[j][ntv+iv][i]=dval;
+           cotvar[j][ntv+iv][i]=dval;
-                                 }
+         }
-                                 strcpy(line,stra);
+         strcpy(line,stra);
        }/* end loop ntqv */
        for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
-                                 cutv(stra, strb, line, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                 }else{
+         }else{
-                                         errno=0;
+           errno=0;
-                                         lval=strtol(strb,&endptr,10);
+           lval=strtol(strb,&endptr,10);
-                                         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+           /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-                                         if( strb[0]=='\0' || (*endptr != '\0')){
+           if( strb[0]=='\0' || (*endptr != '\0')){
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                 }
+         }
-                                 if(lval <-1 || lval >1){
+         if(lval <-1 || lval >1){
-                                         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-  For example, for multinomial values like 1, 2 and 3,\n                                                                 \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \n                                                                                                                                                                            \
+         V1=1 V2=0 for (2) \n                                            \
   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-  output of IMaCh is often meaningless.\n                                                                                                                                \
+  output of IMaCh is often meaningless.\n                                \
-  Exiting.\n",lval,linei, i,line,j);
+  Exiting.\n",lval,linei, i,line,iv,j);
-                                         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
-  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+  Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-  For example, for multinomial values like 1, 2 and 3,\n                                                                 \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \n                                                                                                                                                                            \
+         V1=1 V2=0 for (2) \n                                            \
   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-  output of IMaCh is often meaningless.\n                                                                                                                                \
+  output of IMaCh is often meaningless.\n                                \
-  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+  Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
-                                         return 1;
+           return 1;
-                                 }
+         }
-                                 cotvar[j][iv][i]=(double)(lval);
+         cotvar[j][iv][i]=(double)(lval);
-                                 strcpy(line,stra);
+         strcpy(line,stra);
        }/* end loop ntv */
        /* Statuses  at wave */
        cutv(stra, strb, line, ' ');
        if(strb[0]=='.') { /* Missing value */
-                                 lval=-1;
+         lval=-1;
        }else{
-                                 errno=0;
+         errno=0;
-                                 lval=strtol(strb,&endptr,10);
+         lval=strtol(strb,&endptr,10);
-                                 /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-                                 if( strb[0]=='\0' || (*endptr != '\0')){
+         if( strb[0]=='\0' || (*endptr != '\0')){
-                                         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-                                         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
-                                         return 1;
+           return 1;
-                                 }
+         }
        }
        s[j][i]=lval;
- Line 7749  int readdata(char datafile[], int firsto
+ Line 10094  int readdata(char datafile[], int firsto
          return 1;
        }
        anint[j][i]= (double) year;
        mint[j][i]= (double)month;
+       /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
+       /*        printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
+       /*        fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
+       /* } */
        strcpy(line,stra);
      } /* End loop on waves */
- Line 7788  int readdata(char datafile[], int firsto
+ Line 10137  int readdata(char datafile[], int firsto
      }
      annais[i]=(double)(year);
      moisnais[i]=(double)(month);
+     for (j=1;j<=maxwav;j++){
+       if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
+         printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
+         fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
+       }
+     }
      strcpy(line,stra);
      /* Sample weight */
- Line 7808  int readdata(char datafile[], int firsto
+ Line 10164  int readdata(char datafile[], int firsto
        cutv(stra, strb, line, ' ');
        if(strb[0]=='.') { /* Missing value */
          lval=-1;
+         coqvar[iv][i]=NAN;
+         covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
        }else{
          errno=0;
          /* what_kind_of_number(strb); */
- Line 7890  int readdata(char datafile[], int firsto
+ Line 10248  int readdata(char datafile[], int firsto
  void removefirstspace(char **stri){/*, char stro[]) {*/
    char *p1 = *stri, *p2 = *stri;
-   if (*p2 == ' ')
+   while (*p2 == ' ')
      p2++;
    /* while ((*p1++ = *p2++) !=0) */
    /*   ; */
- Line 7901  void removefirstspace(char **stri){/*, c
+ Line 10259  void removefirstspace(char **stri){/*, c
    *stri=p2;
  }
- int decoderesult ( char resultline[])
+ int decoderesult( char resultline[], int nres)
  /**< This routine decode one result line and returns the combination # of dummy covariates only **/
  {
-   int j=0, k=0, k1=0, k2=0, match=0;
+   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
    char resultsav[MAXLINE];
-   int resultmodel[MAXLINE];
+   /* int resultmodel[MAXLINE]; */
    int modelresult[MAXLINE];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
    removefirstspace(&resultline);
    printf("decoderesult:%s\n",resultline);
-   if (strstr(resultline,"v") !=0){
+   strcpy(resultsav,resultline);
-     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
+   printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);
-     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
-     return 1;
-   }
-   trimbb(resultsav, resultline);
    if (strlen(resultsav) >1){
      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
    }
+   if(j == 0){ /* Resultline but no = */
+     TKresult[nres]=0; /* Combination for the nresult and the model */
+     return (0);
+   }
    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
-     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+     printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of variables used in the model line, %s.\n",j, cptcovs, model);
-     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+     fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of variables used in the model line, %s.\n",j, cptcovs, model);
+     /* return 1;*/
    }
    for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
      if(nbocc(resultsav,'=') >1){
-        cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
+       cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
-                                       resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
+       /* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */
-        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
+       cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */
+       /* If a blank, then strc="V4=" and strd='\0' */
+       if(strc[0]=='\0'){
+       printf("Error in resultline, probably a blank after the \"%s\", \"result:%s\", stra=\"%s\" resultsav=\"%s\"\n",strb,resultline, stra, resultsav);
+         fprintf(ficlog,"Error in resultline, probably a blank after the \"V%s=\", resultline=%s\n",strb,resultline);
+         return 1;
+       }
      }else
        cutl(strc,strd,resultsav,'=');
-     Tvalsel[k]=atof(strc); /* 1 */
+     Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
      cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
-     Tvarsel[k]=atoi(strc);
+     Tvarsel[k]=atoi(strc);  /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
      /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
      /* cptcovsel++;     */
      if (nbocc(stra,'=') >0)
        strcpy(resultsav,stra); /* and analyzes it */
    }
-   /* Checking if no missing or useless values in comparison of current model needs */
+   /* Checking for missing or useless values in comparison of current model needs */
-   for(k1=1; k1<= cptcovt ;k1++){ /* model line */
+   /* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
-     if(Typevar[k1]==0){
+   for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     if(Typevar[k1]==0){ /* Single covariate in model */
+       /* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
        match=0;
-       for(k2=1; k2 <=j;k2++){
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
-         if(Tvar[k1]==Tvarsel[k2]) {
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
-           modelresult[k2]=k1;
+           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
-           match=1;
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
            break;
          }
        }
        if(match == 0){
-         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+         printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);
+         fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=%s\n",Tvar[k1], resultline, model);
+         return 1;
        }
-     }
+     }else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/
-   }
+       /* We feed resultmodel[k1]=k2; */
+       match=0;
-   for(k2=1; k2 <=j;k2++){ /* result line */
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline.  jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[k2]=k1;/* we found a Vn=1 corrresponding to Vn*age in the model modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           resultmodel[nres][k1]=k2; /* Added here */
+           printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
+         fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
+       return 1;
+       }
+     }else if(Typevar[k1]==2){ /* Product No age We want to get the position in the resultline of the product in the model line*/
+       /* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */
+       match=0;
+       printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]);
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           /* modelresult[k2]=k1; */
+           printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]);
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
+         fprintf(ficlog,"Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
+         return 1;
+       }
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
+           /* modelresult[k2]=k1;*/
+           printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]);
+           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line (Product without age second variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][2], resultline, model);
+         fprintf(ficlog,"Error in result line (Product without age second variable): V%d is missing in result : %s according to model=%s\n",Tvardk[k1][2], resultline, model);
+         return 1;
+       }
+     }/* End of testing */
+   }/* End loop cptcovt */
+   /* Checking for missing or useless values in comparison of current model needs */
+   /* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
+   for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
      match=0;
-     for(k1=1; k1<= cptcovt ;k1++){ /* model line */
+     for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-       if(Typevar[k1]==0){
+       if(Typevar[k1]==0){ /* Single only */
-         if(Tvar[k1]==Tvarsel[k2]) {
+         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
-           resultmodel[k1]=k2;
+           resultmodel[nres][k1]=k2;  /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
            ++match;
          }
        }
      }
      if(match == 0){
-       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+       printf("Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
+       fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
+       return 1;
      }else if(match > 1){
        printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+       fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+       return 1;
      }
    }
    /* We need to deduce which combination number is chosen and save quantitative values */
+   /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+   /* nres=1st result line: V4=1 V5=25.1 V3=0  V2=8 V1=1 */
+   /* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 1*1 + 0*2 + 1*4 = 5 + (1offset) = 6*/
+   /* nres=2nd result line: V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
+   /*    1 0 0 0 */
+   /*    2 1 0 0 */
+   /*    3 0 1 0 */
+   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 (nres=2)*/
+   /*    5 0 0 1 */
+   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 (nres=1)*/
+   /*    7 0 1 1 */
+   /*    8 1 1 1 */
+   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
+   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
+   /* V5*age V5 known which value for nres?  */
+   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
+   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop k1 on position in the model line (excluding product) */
+     /* k counting number of combination of single dummies in the equation model */
+     /* k4 counting single dummies in the equation model */
+     /* k4q counting single quantitatives in the equation model */
+     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single */
+        /* k4+1= position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
+       /* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
+       /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
+       /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline                        */
+       /*      k3 is the position in the nres result line of the k1th variable of the model equation                                  */
+       /* Tvarsel[k3]: Name of the variable at the k3th position in the result line.                                                  */
+       /* Tvalsel[k3]: Value of the variable at the k3th position in the result line.                                                 */
+       /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                   */
+       /* Tvresult[nres][result_position]= id of the dummy variable at the result_position in the nres resultline                     */
+       /* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line                                        */
+       /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line                                                      */
+       k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
+       /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
+       k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
+       k+=Tvalsel[k3]*pow(2,k4);  /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
+       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Stores the value into the name of the variable. */
+       /* Tinvresult[nres][4]=1 */
+       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */
+       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
+       precov[nres][k1]=Tvalsel[k3];
+       printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4);
+       k4++;;
+     }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
+       /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */
+       /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline                                 */
+       /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */
+       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
+       k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */
+       /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
+       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
+       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
+       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       precov[nres][k1]=Tvalsel[k3q];
+       printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+       k4q++;;
+     }else if( Dummy[k1]==2 ){ /* For dummy with age product */
+       /* Tvar[k1]; */ /* Age variable */
+       /* Wrong we want the value of variable name Tvar[k1] */
+       k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
+       k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
+       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
+       precov[nres][k1]=Tvalsel[k3];
+       printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]);
+     }else if( Dummy[k1]==3 ){ /* For quant with age product */
+       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
+       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
+       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       precov[nres][k1]=Tvalsel[k3q];
+       printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+     }else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */
+       precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
+       printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]);
+     }else{
+       printf("Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
+       fprintf(ficlog,"Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
+     }
+   }
+   TKresult[nres]=++k; /* Combination for the nresult and the model */
    return (0);
  }
- int selected( int kvar){ /* Selected combination of covariates */
-   if(Tvarsel[kvar])
-     return (0);
-   else
-     return(1);
- }
  int decodemodel( char model[], int lastobs)
   /**< This routine decodes the model and returns:
          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
- Line 7996  int decodemodel( char model[], int lasto
+ Line 10495  int decodemodel( char model[], int lasto
          * - cptcovs number of simple covariates
          * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
          *     which is a new column after the 9 (ncovcol) variables.
-         * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+         * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
          * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
          *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
          */
+ /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
  {
-   int i, j, k, ks;
+   int i, j, k, ks, v;
    int  j1, k1, k2, k3, k4;
    char modelsav[80];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
- Line 8078  int decodemodel( char model[], int lasto
+ Line 10578  int decodemodel( char model[], int lasto
         *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
         *          k=  1    2      3       4     5       6      7        8    9   10   11  12
         *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
-        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
+        * p Tvar[1]@12={2,   1,     3,      3,  11,     10,     8,       8,   7,   8,   5,  6}
         * p Tprod[1]@2={                         6, 5}
         *p Tvard[1][1]@4= {7, 8, 5, 6}
         * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8
         *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
-        *How to reorganize?
+        *How to reorganize? Tvars(orted)
         * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
         * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
         *       {2,   1,     4,      8,    5,      6,     3,       7}
- Line 8108  int decodemodel( char model[], int lasto
+ Line 10608  int decodemodel( char model[], int lasto
          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
        }
        cptcovage=0;
-       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
-         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
-                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+                                          modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
-         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         if (nbocc(modelsav,'+')==0)
+           strcpy(strb,modelsav); /* and analyzes it */
          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
          /*scanf("%d",i);*/
-         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */
-           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
            if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
              /* covar is not filled and then is empty */
              cptcovprod--;
              cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+             Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
              Typevar[k]=1;  /* 1 for age product */
-             cptcovage++; /* Sums the number of covariates which include age as a product */
+             cptcovage++; /* Counts the number of covariates which include age as a product */
-             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
+             Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
              /*printf("stre=%s ", stre);*/
            } else if (strcmp(strd,"age")==0) { /* or age*Vn */
              cptcovprod--;
- Line 8140  int decodemodel( char model[], int lasto
+ Line 10641  int decodemodel( char model[], int lasto
              Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                                  because this model-covariate is a construction we invent a new column
                                                  which is after existing variables ncovcol+nqv+ntv+nqtv + k1
-                                                 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                                 If already ncovcol=4 and model=V2 + V1 +V1*V4 +age*V3 +V3*V2
-                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+                                                 thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
+                                                 Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */
              Typevar[k]=2;  /* 2 for double fixed dummy covariates */
              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
+             Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvardk[k][1] =atoi(strc); /* m 1 for V1*/
              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             Tvardk[k][2] =atoi(stre); /* n 4 for V4*/
              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
              /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
              /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
- Line 8160  int decodemodel( char model[], int lasto
+ Line 10664  int decodemodel( char model[], int lasto
              }
            } /* End age is not in the model */
          } /* End if model includes a product */
-         else { /* no more sum */
+         else { /* not a product */
            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
            /*  scanf("%d",i);*/
            cutl(strd,strc,strb,'V');
- Line 8191  int decodemodel( char model[], int lasto
+ Line 10695  int decodemodel( char model[], int lasto
     model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
     k =           1    2   3     4       5       6      7      8        9
     Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
-    Typevar[k]=   0    0   0     2       1       0      2      1        1
+    Typevar[k]=   0    0   0     2       1       0      2      1        0
     Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
     Dummy[k]      1    0   0     0       3       1      1      2        3
            Tmodelind[combination of covar]=k;
- Line 8200  int decodemodel( char model[], int lasto
+ Line 10704  int decodemodel( char model[], int lasto
    /* If Tvar[k] >ncovcol it is a product */
    /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
          /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
-   printf("Model=%s\n\
+   printf("Model=1+age+%s\n\
  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
-   fprintf(ficlog,"Model=%s\n\
+   fprintf(ficlog,"Model=1+age+%s\n\
  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
    for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
        Fixed[k]= 0;
- Line 8219  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10723  Dummy[k] 0=dummy (0 1), 1 quantitative (
        modell[k].maintype= FTYPE;
        TvarsD[nsd]=Tvar[k];
        TvarsDind[nsd]=k;
+       TnsdVar[Tvar[k]]=nsd;
        TvarF[ncovf]=Tvar[k];
        TvarFind[ncovf]=k;
        TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
- Line 8230  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10735  Dummy[k] 0=dummy (0 1), 1 quantitative (
        ncovf++;
        modell[k].maintype= FTYPE;
        TvarF[ncovf]=Tvar[k];
+       /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */
        TvarFind[ncovf]=k;
        TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
        TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ /* Only simple fixed quantitative variable */
+     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
        Fixed[k]= 0;
        Dummy[k]= 1;
        nqfveff++;
- Line 8247  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10753  Dummy[k] 0=dummy (0 1), 1 quantitative (
        TvarFind[ncovf]=k;
        TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
        TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */
+     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
        Fixed[k]= 1;
        Dummy[k]= 0;
        ntveff++; /* Only simple time varying dummy variable */
- Line 8256  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10762  Dummy[k] 0=dummy (0 1), 1 quantitative (
        nsd++;
        TvarsD[nsd]=Tvar[k];
        TvarsDind[nsd]=k;
+       TnsdVar[Tvar[k]]=nsd; /* To be verified */
        ncovv++; /* Only simple time varying variables */
        TvarV[ncovv]=Tvar[k];
-       TvarVind[ncovv]=k;
+       TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
        TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
        TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
        printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
- Line 8271  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10778  Dummy[k] 0=dummy (0 1), 1 quantitative (
        modell[k].subtype= VQ;
        ncovv++; /* Only simple time varying variables */
        nsq++;
-       TvarsQ[nsq]=Tvar[k];
+       TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
-       TvarsQind[nsq]=k;
+       TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate */
        TvarV[ncovv]=Tvar[k];
-       TvarVind[ncovv]=k;
+       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
        TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
        TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
        TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
- Line 8286  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10793  Dummy[k] 0=dummy (0 1), 1 quantitative (
        TvarA[ncova]=Tvar[k];
        TvarAind[ncova]=k;
        if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
          Fixed[k]= 2;
          Dummy[k]= 2;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APFD;
          /* ncoveff++; */
        }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
          Fixed[k]= 2;
          Dummy[k]= 3;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
          /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
        }else if( Tvar[k] <=ncovcol+nqv+ntv ){
          Fixed[k]= 3;
          Dummy[k]= 2;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APVD;                /*      Product age * varying dummy */
          /* ntveff++; /\* Only simple time varying dummy variable *\/ */
        }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
          Fixed[k]= 3;
          Dummy[k]= 3;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
          /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
        }
      }else if (Typevar[k] == 2) {  /* product without age */
        k1=Tposprod[k];
        if(Tvard[k1][1] <=ncovcol){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 1;
            Dummy[k]= 0;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
            ncovf++; /* Fixed variables without age */
            TvarF[ncovf]=Tvar[k];
            TvarFind[ncovf]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv){
            Fixed[k]= 0;  /* or 2 ?*/
            Dummy[k]= 1;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
            ncovf++; /* Varying variables without age */
            TvarF[ncovf]=Tvar[k];
            TvarFind[ncovf]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 0;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else if(Tvard[k1][1] <=ncovcol+nqv){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 0;  /* or 2 ?*/
            Dummy[k]= 1;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
            ncovf++; /* Fixed variables without age */
            TvarF[ncovf]=Tvar[k];
            TvarFind[ncovf]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 0;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else{
          printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
          fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
-       } /* end k1 */
+       } /*end k1*/
      }else{
        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
- Line 8458  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10965  Dummy[k] 0=dummy (0 1), 1 quantitative (
    /* Searching for doublons in the model */
    for(k1=1; k1<= cptcovt;k1++){
      for(k2=1; k2 <k1;k2++){
-       if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
+       /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
+       if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
          if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
            if(Tvar[k1]==Tvar[k2]){
-             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
+             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
-             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
              return(1);
            }
          }else if (Typevar[k1] ==2){
- Line 8488  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10996  Dummy[k] 0=dummy (0 1), 1 quantitative (
  }
  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
- {
+ {/* Check ages at death */
    int i, m;
    int firstone=0;
- Line 8503  int calandcheckages(int imx, int maxwav,
+ Line 11011  int calandcheckages(int imx, int maxwav,
          *nberr = *nberr + 1;
          if(firstone == 0){
            firstone=1;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
          }
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
-         s[m][i]=-1;
+         s[m][i]=-1;  /* Droping the death status */
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
          (*nberr)++;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+         s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
        }
      }
    }
- Line 8634  BOOL IsWow64()
+ Line 11142  BOOL IsWow64()
  #endif
  void syscompilerinfo(int logged)
-  {
+ {
-    /* #include "syscompilerinfo.h"*/
+ #include <stdint.h>
+   /* #include "syscompilerinfo.h"*/
     /* command line Intel compiler 32bit windows, XP compatible:*/
     /* /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
- Line 8670  void syscompilerinfo(int logged)
+ Line 11180  void syscompilerinfo(int logged)
        /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
        /NOLOGO /TLBID:1
     */
  #if defined __INTEL_COMPILER
  #if defined(__GNUC__)
          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
- Line 8686  void syscompilerinfo(int logged)
+ Line 11198  void syscompilerinfo(int logged)
     }
  #endif
- #include <stdint.h>
     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
  #if defined(__clang__)
     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
- Line 8773  void syscompilerinfo(int logged)
+ Line 11283  void syscompilerinfo(int logged)
  #endif
  #endif
-    //   void main()
+    //   void main ()
     //   {
  #if defined(_MSC_VER)
     if (IsWow64()){
- Line 8794  void syscompilerinfo(int logged)
+ Line 11304  void syscompilerinfo(int logged)
  }
  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
-   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
-   int i, j, k, i1 ;
+   /* Computes the prevalence limit for each combination of the dummy covariates */
+   int i, j, k, i1, k4=0, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
    double tot;
- Line 8803  int prevalence_limit(double *p, double *
+ Line 11314  int prevalence_limit(double *p, double *
    strcpy(filerespl,"PL_");
    strcat(filerespl,fileresu);
    if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
    }
-   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
    pstamp(ficrespl);
-   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
    fprintf(ficrespl,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
    fprintf(ficrespl,"\n");
- Line 8823  int prevalence_limit(double *p, double *
+ Line 11334  int prevalence_limit(double *p, double *
    i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
    if (cptcovn < 1){i1=1;}
-   for(k=1; k<=i1;k++){
+   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
-   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       if(i1 != 1 && TKresult[nres]!= k)
-     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         continue;
-     /* k=k+1; */
-     /* to clean */
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     fprintf(ficrespl,"#******");
-     printf("#******");
-     fprintf(ficlog,"#******");
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
-     fprintf(ficrespl,"******\n");
-     printf("******\n");
-     fprintf(ficlog,"******\n");
-     if(invalidvarcomb[k]){
-       printf("\nCombination (%d) ignored because no case \n",k);
-       fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
-       fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
-                                                 continue;
-     }
-     fprintf(ficrespl,"#Age ");
+       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-     for(j=1;j<=cptcoveff;j++) {
+       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
-       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     }
+       /* k=k+1; */
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       /* to clean */
-     fprintf(ficrespl,"Total Years_to_converge\n");
+       /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/
+       fprintf(ficrespl,"#******");
+       printf("#******");
+       fprintf(ficlog,"#******");
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+         /* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy*\/ */
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* Here problem for varying dummy*/
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       fprintf(ficrespl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       if(invalidvarcomb[k]){
+         printf("\nCombination (%d) ignored because no case \n",k);
+         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
+         continue;
+       }
+       fprintf(ficrespl,"#Age ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       }
+       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       fprintf(ficrespl,"Total Years_to_converge\n");
-     for (age=agebase; age<=agelim; age++){
+       for (age=agebase; age<=agelim; age++){
-       /* for (age=agebase; age<=agebase; age++){ */
+         /* for (age=agebase; age<=agebase; age++){ */
-       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
-       fprintf(ficrespl,"%.0f ",age );
+         fprintf(ficrespl,"%.0f ",age );
-       for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-       tot=0.;
+         tot=0.;
-       for(i=1; i<=nlstate;i++){
+         for(i=1; i<=nlstate;i++){
-         tot +=  prlim[i][i];
+           tot +=  prlim[i][i];
-         fprintf(ficrespl," %.5f", prlim[i][i]);
+           fprintf(ficrespl," %.5f", prlim[i][i]);
-       }
+         }
-       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
-     } /* Age */
+       } /* Age */
-     /* was end of cptcod */
+       /* was end of cptcod */
-   } /* cptcov */
+     } /* cptcov */
+   } /* nres */
    return 0;
  }
  int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
-         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+         /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
          /* Computes the back prevalence limit  for any combination      of covariate values
     * at any age between ageminpar and agemaxpar
           */
-   int i, j, k, i1 ;
+   int i, j, k, i1, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
    double tot;
- Line 8889  int back_prevalence_limit(double *p, dou
+ Line 11411  int back_prevalence_limit(double *p, dou
    strcpy(fileresplb,"PLB_");
    strcat(fileresplb,fileresu);
    if((ficresplb=fopen(fileresplb,"w"))==NULL) {
-     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
-     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
    }
-   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
-   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
    pstamp(ficresplb);
-   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
    fprintf(ficresplb,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
    fprintf(ficresplb,"\n");
- Line 8910  int back_prevalence_limit(double *p, dou
+ Line 11432  int back_prevalence_limit(double *p, dou
    i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-   for(k=1; k<=i1;k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-     fprintf(ficresplb,"#******");
+      if(i1 != 1 && TKresult[nres]!= k)
-     printf("#******");
+         continue;
-     fprintf(ficlog,"#******");
+      /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       fprintf(ficresplb,"#******");
-       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       printf("#******");
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficlog,"#******");
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-     }
+         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-     fprintf(ficresplb,"******\n");
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-     printf("******\n");
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-     fprintf(ficlog,"******\n");
+       }
-     if(invalidvarcomb[k]){
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-       printf("\nCombination (%d) ignored because no cases \n",k);
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
-       fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
-       fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
-       continue;
+       }
-     }
+       fprintf(ficresplb,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       if(invalidvarcomb[k]){
+         printf("\nCombination (%d) ignored because no cases \n",k);
+         fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+         continue;
+       }
-     fprintf(ficresplb,"#Age ");
+       fprintf(ficresplb,"#Age ");
-     for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-     }
+       }
-     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
+       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
-     fprintf(ficresplb,"Total Years_to_converge\n");
+       fprintf(ficresplb,"Total Years_to_converge\n");
-     for (age=agebase; age<=agelim; age++){
+       for (age=agebase; age<=agelim; age++){
-       /* for (age=agebase; age<=agebase; age++){ */
+         /* for (age=agebase; age<=agebase; age++){ */
-       if(mobilavproj > 0){
+         if(mobilavproj > 0){
-         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
-         /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-         bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
+           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
-       }else if (mobilavproj == 0){
+         }else if (mobilavproj == 0){
-         printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
-         fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
-         exit(1);
+           exit(1);
-       }else{
+         }else{
-         /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-         bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
+           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
-       }
+           /* printf("TOTOT\n"); */
-       fprintf(ficresplb,"%.0f ",age );
+           /* exit(1); */
-       for(j=1;j<=cptcoveff;j++)
+         }
-         fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb,"%.0f ",age );
-       tot=0.;
+         for(j=1;j<=cptcoveff;j++)
-       for(i=1; i<=nlstate;i++){
+           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-         tot +=  bprlim[i][i];
+         tot=0.;
-         fprintf(ficresplb," %.5f", bprlim[i][i]);
+         for(i=1; i<=nlstate;i++){
-       }
+           tot +=  bprlim[i][i];
-       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+           fprintf(ficresplb," %.5f", bprlim[i][i]);
-     } /* Age */
+         }
-     /* was end of cptcod */
+         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
-   } /* cptcov */
+       } /* Age */
+       /* was end of cptcod */
+       /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
+     } /* end of any combination */
+   } /* end of nres */
    /* hBijx(p, bage, fage); */
    /* fclose(ficrespijb); */
- Line 8978  int hPijx(double *p, int bage, int fage)
+ Line 11511  int hPijx(double *p, int bage, int fage)
    int agelim;
    int hstepm;
    int nhstepm;
-   int h, i, i1, j, k;
+   int h, i, i1, j, k, k4, nres=0;
    double agedeb;
    double ***p3mat;
- Line 9005  int hPijx(double *p, int bage, int fage)
+ Line 11538  int hPijx(double *p, int bage, int fage)
                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                  /*      k=k+1;  */
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
        fprintf(ficrespij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
        fprintf(ficrespij,"******\n");
        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
- Line 9019  int hPijx(double *p, int bage, int fage)
+ Line 11559  int hPijx(double *p, int bage, int fage)
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
          fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
- Line 9049  int hPijx(double *p, int bage, int fage)
+ Line 11589  int hPijx(double *p, int bage, int fage)
          int ageminl;
    int hstepm;
    int nhstepm;
-   int h, i, i1, j, k;
+   int h, i, i1, j, k, nres;
    double agedeb;
    double ***p3mat;
- Line 9066  int hPijx(double *p, int bage, int fage)
+ Line 11606  int hPijx(double *p, int bage, int fage)
    /*if (stepm<=24) stepsize=2;*/
    /* agelim=AGESUP; */
-   ageminl=30;
+   ageminl=AGEINF; /* was 30 */
    hstepm=stepsize*YEARM; /* Every year of age */
    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
    /* hstepm=1;   aff par mois*/
    pstamp(ficrespijb);
-   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
+   fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
    i1= pow(2,cptcoveff);
    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*    k=k+1;  */
-   for (k=1; k <= (int) pow(2,cptcoveff); k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     fprintf(ficrespijb,"\n#****** ");
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-     for(j=1;j<=cptcoveff;j++)
+       if(i1 != 1 && TKresult[nres]!= k)
-       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         continue;
-     fprintf(ficrespijb,"******\n");
+       fprintf(ficrespijb,"\n#****** ");
-     if(invalidvarcomb[k]){
+       for(j=1;j<=cptcoveff;j++)
-       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-       continue;
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-     }
+         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+       }
-     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       fprintf(ficrespijb,"******\n");
-     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       if(invalidvarcomb[k]){  /* Is it necessary here? */
-       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
-       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         continue;
-       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+       }
-       /*          nhstepm=nhstepm*YEARM; aff par mois*/
+       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
-       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
-       /* oldm=oldms;savm=savms; */
+         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
-       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
-       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
-       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-       fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
-       for(i=1; i<=nlstate;i++)
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
-         for(j=1; j<=nlstate+ndeath;j++)
+         /* and memory limitations if stepm is small */
-           fprintf(ficrespijb," %1d-%1d",i,j);
-       fprintf(ficrespijb,"\n");
+         /* oldm=oldms;savm=savms; */
-       for (h=0; h<=nhstepm; h++){
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
-         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
+         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
+             fprintf(ficrespijb," %1d-%1d",i,j);
          fprintf(ficrespijb,"\n");
-       }
+         for (h=0; h<=nhstepm; h++){
-       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-       fprintf(ficrespijb,"\n");
+           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
-     }
+           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
-     /*}*/
+           for(i=1; i<=nlstate;i++)
-   }
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
+           fprintf(ficrespijb,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespijb,"\n");
+       } /* end age deb */
+     } /* end combination */
+   } /* end nres */
    return 0;
   } /*  hBijx */
- Line 9137  int main(int argc, char *argv[])
+ Line 11685  int main(int argc, char *argv[])
    double ssval;
  #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
+   int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
+   /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
    int ncvyear=0; /* Number of years needed for the period prevalence to converge */
    int jj, ll, li, lj, lk;
    int numlinepar=0; /* Current linenumber of parameter file */
- Line 9145  int main(int argc, char *argv[])
+ Line 11694  int main(int argc, char *argv[])
    int itimes;
    int NDIM=2;
    int vpopbased=0;
+   int nres=0;
+   int endishere=0;
+   int noffset=0;
+   int ncurrv=0; /* Temporary variable */
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
- Line 9159  int main(int argc, char *argv[])
+ Line 11712  int main(int argc, char *argv[])
    double dum=0.; /* Dummy variable */
    double ***p3mat;
    /* double ***mobaverage; */
+   double wald;
    char line[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
    char  modeltemp[MAXLINE];
-   char resultline[MAXLINE];
+   char resultline[MAXLINE], resultlineori[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
    char *tok, *val; /* pathtot */
-   int firstobs=1, lastobs=10;
+   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
    int c,  h , cpt, c2;
    int jl=0;
    int i1, j1, jk, stepsize=0;
- Line 9176  int main(int argc, char *argv[])
+ Line 11730  int main(int argc, char *argv[])
    int *tab;
    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-   int backcast=0;
+   /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
+   /* double anprojf, mprojf, jprojf; */
+   /* double jintmean,mintmean,aintmean;   */
+   int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
+   int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
+   double yrfproj= 10.0; /* Number of years of forward projections */
+   double yrbproj= 10.0; /* Number of years of backward projections */
+   int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
    int mobilav=0,popforecast=0;
    int hstepm=0, nhstepm=0;
    int agemortsup;
- Line 9188  int main(int argc, char *argv[])
+ Line 11749  int main(int argc, char *argv[])
    double ftolpl=FTOL;
    double **prlim;
    double **bprlim;
-   double ***param; /* Matrix of parameters */
+   double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel)
-   double  *p;
+                     state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
+   double ***paramstart; /* Matrix of starting parameter values */
+   double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
    double **matcov; /* Matrix of covariance */
    double **hess; /* Hessian matrix */
    double ***delti3; /* Scale */
    double *delti; /* Scale */
    double ***eij, ***vareij;
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double dateprev1, dateprev2;
-   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
+   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
    double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
- Line 9277  int main(int argc, char *argv[])
+ Line 11843  int main(int argc, char *argv[])
        if(pathr[0] == '\0') break; /* Dirty */
      }
    }
+   else if (argc<=2){
+     strcpy(pathtot,argv[1]);
+   }
    else{
      strcpy(pathtot,argv[1]);
+     strcpy(z,argv[2]);
+     printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
    }
    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
    /*cygwin_split_path(pathtot,path,optionfile);
- Line 9356  int main(int argc, char *argv[])
+ Line 11927  int main(int argc, char *argv[])
      exit(70);
    }
    strcpy(filereso,"o");
    strcat(filereso,fileresu);
    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
- Line 9366  int main(int argc, char *argv[])
+ Line 11935  int main(int argc, char *argv[])
      fflush(ficlog);
      goto end;
    }
+       /*-------- Rewriting parameter file ----------*/
+   strcpy(rfileres,"r");    /* "Rparameterfile */
+   strcat(rfileres,optionfilefiname);    /* Parameter file first name */
+   strcat(rfileres,".");    /* */
+   strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   if((ficres =fopen(rfileres,"w"))==NULL) {
+     printf("Problem writing new parameter file: %s\n", rfileres);goto end;
+     fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
+     fflush(ficlog);
+     goto end;
+   }
+   fprintf(ficres,"#IMaCh %s\n",version);
    /* Reads comments: lines beginning with '#' */
    numlinepar=0;
+   /* Is it a BOM UTF-8 Windows file? */
-     /* First parameter line */
+   /* First parameter line */
    while(fgets(line, MAXLINE, ficpar)) {
+     noffset=0;
+     if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
+     {
+       noffset=noffset+3;
+       printf("# File is an UTF8 Bom.\n"); // 0xBF
+     }
+ /*    else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
+     else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
+     {
+       noffset=noffset+2;
+       printf("# File is an UTF16BE BOM file\n");
+     }
+     else if( line[0] == 0 && line[1] == 0)
+     {
+       if( line[2] == (char)0xFE && line[3] == (char)0xFF){
+         noffset=noffset+4;
+         printf("# File is an UTF16BE BOM file\n");
+       }
+     } else{
+       ;/*printf(" Not a BOM file\n");*/
+     }
      /* If line starts with a # it is a comment */
-     if (line[0] == '#') {
+     if (line[noffset] == '#') {
        numlinepar++;
        fputs(line,stdout);
        fputs(line,ficparo);
+       fputs(line,ficres);
        fputs(line,ficlog);
        continue;
      }else
- Line 9386  int main(int argc, char *argv[])
+ Line 11991  int main(int argc, char *argv[])
                          title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
      if (num_filled != 5) {
        printf("Should be 5 parameters\n");
+       fprintf(ficlog,"Should be 5 parameters\n");
      }
      numlinepar++;
      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
    }
    /* Second parameter line */
    while(fgets(line, MAXLINE, ficpar)) {
-     /* If line starts with a # it is a comment */
+     /* while(fscanf(ficpar,"%[^\n]", line)) { */
+     /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
      if (line[0] == '#') {
        numlinepar++;
-       fputs(line,stdout);
+       printf("%s",line);
-       fputs(line,ficparo);
+       fprintf(ficres,"%s",line);
-       fputs(line,ficlog);
+       fprintf(ficparo,"%s",line);
+       fprintf(ficlog,"%s",line);
        continue;
      }else
        break;
- Line 9407  int main(int argc, char *argv[])
+ Line 12018  int main(int argc, char *argv[])
      if (num_filled != 11) {
        printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
        printf("but line=%s\n",line);
+       fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+       fprintf(ficlog,"but line=%s\n",line);
+     }
+     if( lastpass > maxwav){
+       printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+       fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+       fflush(ficlog);
+       goto end;
      }
-     printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+     fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+     fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
+     fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
    }
    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
- Line 9417  int main(int argc, char *argv[])
+ Line 12039  int main(int argc, char *argv[])
      /* If line starts with a # it is a comment */
      if (line[0] == '#') {
        numlinepar++;
-       fputs(line,stdout);
+       printf("%s",line);
-       fputs(line,ficparo);
+       fprintf(ficres,"%s",line);
-       fputs(line,ficlog);
+       fprintf(ficparo,"%s",line);
+       fprintf(ficlog,"%s",line);
        continue;
      }else
        break;
    }
    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
-     if (num_filled == 0)
+     if (num_filled != 1){
-             model[0]='\0';
+       printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
-     else if (num_filled != 1){
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
-       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
-       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
        model[0]='\0';
        goto end;
      }
- Line 9442  int main(int argc, char *argv[])
+ Line 12063  int main(int argc, char *argv[])
      }
      /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
      printf("model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
    }
    /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
    /* numlinepar=numlinepar+3; /\* In general *\/ */
    /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+   /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+   /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
    fflush(ficlog);
    /* if(model[0]=='#'|| model[0]== '\0'){ */
    if(model[0]=='#'){
-     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+     printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
-  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
+  'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
-  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
+  'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
      if(mle != -1){
-       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
        exit(1);
      }
    }
- Line 9475  int main(int argc, char *argv[])
+ Line 12099  int main(int argc, char *argv[])
    ungetc(c,ficpar);
-   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
-   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
+   if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
-   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
+   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
-   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
+   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
       v1+v2*age+v2*v3 makes cptcovn = 3
- Line 9500  int main(int argc, char *argv[])
+ Line 12124  int main(int argc, char *argv[])
    delti=delti3[1][1];
    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+ /* We could also provide initial parameters values giving by simple logistic regression
+  * only one way, that is without matrix product. We will have nlstate maximizations */
+       /* for(i=1;i<nlstate;i++){ */
+       /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
+       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
+       /* } */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
      printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
      fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
- Line 9529  int main(int argc, char *argv[])
+ Line 12159  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      for(i=1; i <=nlstate; i++){
        j=0;
        for(jj=1; jj <=nlstate+ndeath; jj++){
          if(jj==i) continue;
          j++;
+         while((c=getc(ficpar))=='#' && c!= EOF){
+           ungetc(c,ficpar);
+           fgets(line, MAXLINE, ficpar);
+           numlinepar++;
+           fputs(line,stdout);
+           fputs(line,ficparo);
+           fputs(line,ficlog);
+         }
+         ungetc(c,ficpar);
          fscanf(ficpar,"%1d%1d",&i1,&j1);
          if ((i1 != i) || (j1 != jj)){
            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
- Line 9565  run imach with mle=-1 to get a correct t
+ Line 12205  run imach with mle=-1 to get a correct t
      }
      fflush(ficlog);
-     /* Reads scales values */
+     /* Reads parameters values */
      p=param[1][1];
+     pstart=paramstart[1][1];
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
- Line 9669  Please run with mle=-1 to get a correct
+ Line 12310  Please run with mle=-1 to get a correct
      fflush(ficlog);
-     /*-------- Rewriting parameter file ----------*/
-     strcpy(rfileres,"r");    /* "Rparameterfile */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     strcat(rfileres,".");    /* */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
-       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
-     }
-     fprintf(ficres,"#%s\n",version);
    }    /* End of mle != -3 */
    /*  Main data
     */
-   n= lastobs;
+   nobs=lastobs-firstobs+1; /* was = lastobs;*/
-   num=lvector(1,n);
+   /* num=lvector(1,n); */
-   moisnais=vector(1,n);
+   /* moisnais=vector(1,n); */
-   annais=vector(1,n);
+   /* annais=vector(1,n); */
-   moisdc=vector(1,n);
+   /* moisdc=vector(1,n); */
-   andc=vector(1,n);
+   /* andc=vector(1,n); */
-   weight=vector(1,n);
+   /* weight=vector(1,n); */
-   agedc=vector(1,n);
+   /* agedc=vector(1,n); */
-   cod=ivector(1,n);
+   /* cod=ivector(1,n); */
-   for(i=1;i<=n;i++){
+   /* for(i=1;i<=n;i++){ */
+   num=lvector(firstobs,lastobs);
+   moisnais=vector(firstobs,lastobs);
+   annais=vector(firstobs,lastobs);
+   moisdc=vector(firstobs,lastobs);
+   andc=vector(firstobs,lastobs);
+   weight=vector(firstobs,lastobs);
+   agedc=vector(firstobs,lastobs);
+   cod=ivector(firstobs,lastobs);
+   for(i=firstobs;i<=lastobs;i++){
      num[i]=0;
      moisnais[i]=0;
      annais[i]=0;
- Line 9702  Please run with mle=-1 to get a correct
+ Line 12342  Please run with mle=-1 to get a correct
      cod[i]=0;
      weight[i]=1.0; /* Equal weights, 1 by default */
    }
-   mint=matrix(1,maxwav,1,n);
+   mint=matrix(1,maxwav,firstobs,lastobs);
-   anint=matrix(1,maxwav,1,n);
+   anint=matrix(1,maxwav,firstobs,lastobs);
-   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+   s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
+   printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel));
    tab=ivector(1,NCOVMAX);
    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
- Line 9723  Please run with mle=-1 to get a correct
+ Line 12364  Please run with mle=-1 to get a correct
    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
    TvarsDind=ivector(1,NCOVMAX); /*  */
+   TnsdVar=ivector(1,NCOVMAX); /*  */
    TvarsD=ivector(1,NCOVMAX); /*  */
    TvarsQind=ivector(1,NCOVMAX); /*  */
    TvarsQ=ivector(1,NCOVMAX); /*  */
- Line 9765  Please run with mle=-1 to get a correct
+ Line 12407  Please run with mle=-1 to get a correct
    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                              * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
                              * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
+   Tvardk=imatrix(1,NCOVMAX,1,2);
    Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
 covariates (3 plus signs)
                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
-                       */
+                            */
+   for(i=1;i<NCOVMAX;i++)
+     Tage[i]=0;
    Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                  * individual dummy, fixed or varying:
                                  * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
- Line 9806  Please run with mle=-1 to get a correct
+ Line 12451  Please run with mle=-1 to get a correct
    agegomp=(int)agemin;
-   free_vector(moisnais,1,n);
+   free_vector(moisnais,firstobs,lastobs);
-   free_vector(annais,1,n);
+   free_vector(annais,firstobs,lastobs);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
    /* free_vector(moisdc,1,n); */
- Line 9831  Please run with mle=-1 to get a correct
+ Line 12476  Please run with mle=-1 to get a correct
    */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-   /* */
+   /* Concatenates waves */
-   free_vector(moisdc,1,n);
+   free_vector(moisdc,firstobs,lastobs);
-   free_vector(andc,1,n);
+   free_vector(andc,firstobs,lastobs);
    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
- Line 9872  Please run with mle=-1 to get a correct
+ Line 12517  Please run with mle=-1 to get a correct
             * For k=4 covariates, h goes from 1 to m=2**k
             * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
             * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
-            *     h\k   1     2     3     4
+            *     h\k   1     2     3     4   *  h-1\k-1  4  3  2  1
-            *______________________________
+            *______________________________   *______________________
-            *     1 i=1 1 i=1 1 i=1 1 i=1 1
+            *     1 i=1 1 i=1 1 i=1 1 i=1 1   *     0     0  0  0  0
-            *     2     2     1     1     1
+            *     2     2     1     1     1   *     1     0  0  0  1
-            *     3 i=2 1     2     1     1
+            *     3 i=2 1     2     1     1   *     2     0  0  1  0
-            *     4     2     2     1     1
+            *     4     2     2     1     1   *     3     0  0  1  1
-            *     5 i=3 1 i=2 1     2     1
+            *     5 i=3 1 i=2 1     2     1   *     4     0  1  0  0
-            *     6     2     1     2     1
+            *     6     2     1     2     1   *     5     0  1  0  1
-            *     7 i=4 1     2     2     1
+            *     7 i=4 1     2     2     1   *     6     0  1  1  0
-            *     8     2     2     2     1
+            *     8     2     2     2     1   *     7     0  1  1  1
-            *     9 i=5 1 i=3 1 i=2 1     2
+            *     9 i=5 1 i=3 1 i=2 1     2   *     8     1  0  0  0
-            *    10     2     1     1     2
+            *    10     2     1     1     2   *     9     1  0  0  1
-            *    11 i=6 1     2     1     2
+            *    11 i=6 1     2     1     2   *    10     1  0  1  0
-            *    12     2     2     1     2
+            *    12     2     2     1     2   *    11     1  0  1  1
-            *    13 i=7 1 i=4 1     2     2
+            *    13 i=7 1 i=4 1     2     2   *    12     1  1  0  0
-            *    14     2     1     2     2
+            *    14     2     1     2     2   *    13     1  1  0  1
-            *    15 i=8 1     2     2     2
+            *    15 i=8 1     2     2     2   *    14     1  1  1  0
-            *    16     2     2     2     2
+            *    16     2     2     2     2   *    15     1  1  1  1
             */
    /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
       /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
       * and the value of each covariate?
- Line 9981  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 12626  Title=%s <br>Datafile=%s Firstpass=%d La
            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
+   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2022-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
  <font size=\"2\">IMaCh-%s <br> %s</font> \
  <hr size=\"2\" color=\"#EC5E5E\"> \n\
- Line 10012  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 12657  Title=%s <br>Datafile=%s Firstpass=%d La
    /* Calculates basic frequencies. Computes observed prevalence at single age
                   and for any valid combination of covariates
       and prints on file fileres'p'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
+   freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
                firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+   fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
+           ftol, stepm);
+   fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
+   ncurrv=1;
+   for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
+            nlstate, ndeath, maxwav, mle, weightopt);
+   fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
+ <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
+   fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) observations=%d <br>\n\
  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-           imx,agemin,agemax,jmin,jmax,jmean);
+   imx,agemin,agemax,jmin,jmax,jmean);
    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
    /* For Powell, parameters are in a vector p[] starting at p[1]
       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
- Line 10034  Interval (in months) between two waves:
+ Line 12700  Interval (in months) between two waves:
    /* For mortality only */
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
-                 for(i=1;i<=NDIM;i++)
+     for(i=1;i<=NDIM;i++)
-                         for(j=1;j<=NDIM;j++)
+       for(j=1;j<=NDIM;j++)
-                                 ximort[i][j]=0.;
+         ximort[i][j]=0.;
      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     cens=ivector(1,n);
+     cens=ivector(firstobs,lastobs);
-     ageexmed=vector(1,n);
+     ageexmed=vector(firstobs,lastobs);
-     agecens=vector(1,n);
+     agecens=vector(firstobs,lastobs);
-     dcwave=ivector(1,n);
+     dcwave=ivector(firstobs,lastobs);
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
- Line 10075  Interval (in months) between two waves:
+ Line 12741  Interval (in months) between two waves:
          ximort[i][j]=(i == j ? 1.0 : 0.0);
      }
-     /*p[1]=0.0268; p[NDIM]=0.083;*/
+     p[1]=0.0268; p[NDIM]=0.083;
-     /*printf("%lf %lf", p[1], p[2]);*/
+     /* printf("%lf %lf", p[1], p[2]); */
  #ifdef GSL
- Line 10202  Interval (in months) between two waves:
+ Line 12868  Interval (in months) between two waves:
        printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
        fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
      }
-     lsurv=vector(1,AGESUP);
+     lsurv=vector(agegomp,AGESUP);
-     lpop=vector(1,AGESUP);
+     lpop=vector(agegomp,AGESUP);
-     tpop=vector(1,AGESUP);
+     tpop=vector(agegomp,AGESUP);
      lsurv[agegomp]=100000;
      for (k=agegomp;k<=AGESUP;k++) {
- Line 10251  Please run with mle=-1 to get a correct
+ Line 12917  Please run with mle=-1 to get a correct
                       stepm, weightopt,\
                       model,imx,p,matcov,agemortsup);
-     free_vector(lsurv,1,AGESUP);
+     free_vector(lsurv,agegomp,AGESUP);
-     free_vector(lpop,1,AGESUP);
+     free_vector(lpop,agegomp,AGESUP);
-     free_vector(tpop,1,AGESUP);
+     free_vector(tpop,agegomp,AGESUP);
      free_matrix(ximort,1,NDIM,1,NDIM);
-     free_ivector(cens,1,n);
+     free_ivector(dcwave,firstobs,lastobs);
-     free_vector(agecens,1,n);
+     free_vector(agecens,firstobs,lastobs);
-     free_ivector(dcwave,1,n);
+     free_vector(ageexmed,firstobs,lastobs);
+     free_ivector(cens,firstobs,lastobs);
  #ifdef GSL
  #endif
    } /* Endof if mle==-3 mortality only */
- Line 10272  Please run with mle=-1 to get a correct
+ Line 12939  Please run with mle=-1 to get a correct
      printf("\n");
      if(mle>=1){ /* Could be 1 or 2, Real Maximization */
        /* mlikeli uses func not funcone */
+       /* for(i=1;i<nlstate;i++){ */
+       /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
+       /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
+       /* } */
        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
      }
      if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
- Line 10287  Please run with mle=-1 to get a correct
+ Line 12958  Please run with mle=-1 to get a correct
      printf("\n");
      /*--------- results files --------------*/
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
+     /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
-     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */
      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+     printf("#model=  1      +     age ");
+     fprintf(ficres,"#model=  1      +     age ");
+     fprintf(ficlog,"#model=  1      +     age ");
+     fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
+ </ul>", model);
+     fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
+     fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
+     if(nagesqr==1){
+       printf("  + age*age  ");
+       fprintf(ficres,"  + age*age  ");
+       fprintf(ficlog,"  + age*age  ");
+       fprintf(fichtm, "<th>+ age*age</th>");
+     }
+     for(j=1;j <=ncovmodel-2;j++){
+       if(Typevar[j]==0) {
+         printf("  +      V%d  ",Tvar[j]);
+         fprintf(ficres,"  +      V%d  ",Tvar[j]);
+         fprintf(ficlog,"  +      V%d  ",Tvar[j]);
+         fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
+       }else if(Typevar[j]==1) {
+         printf("  +    V%d*age ",Tvar[j]);
+         fprintf(ficres,"  +    V%d*age ",Tvar[j]);
+         fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
+         fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
+       }else if(Typevar[j]==2) {
+         printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+       }
+     }
+     printf("\n");
+     fprintf(ficres,"\n");
+     fprintf(ficlog,"\n");
+     fprintf(fichtm, "</tr>");
+     fprintf(fichtm, "\n");
      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
          if (k != i) {
+           fprintf(fichtm, "<tr>");
            printf("%d%d ",i,k);
            fprintf(ficlog,"%d%d ",i,k);
            fprintf(ficres,"%1d%1d ",i,k);
+           fprintf(fichtm, "<td>%1d%1d</td>",i,k);
            for(j=1; j <=ncovmodel; j++){
              printf("%12.7f ",p[jk]);
              fprintf(ficlog,"%12.7f ",p[jk]);
              fprintf(ficres,"%12.7f ",p[jk]);
+             fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
              jk++;
            }
            printf("\n");
            fprintf(ficlog,"\n");
            fprintf(ficres,"\n");
+           fprintf(fichtm, "</tr>\n");
          }
        }
      }
+     /* fprintf(fichtm,"</tr>\n"); */
+     fprintf(fichtm,"</table>\n");
+     fprintf(fichtm, "\n");
      if(mle != 0){
        /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
        ftolhess=ftol; /* Usually correct */
        hesscov(matcov, hess, p, npar, delti, ftolhess, func);
        printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
        fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
+       fprintf(fichtm, "\n<p>The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n</br>Parameters, Wald tests and Wald-based confidence intervals\n</br> W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n</br> And Wald-based confidence intervals plus and minus 1.96 * W \n </br> It might be better to visualize the covariance matrix. See the page '<a href=\"%s\">Matrix of variance-covariance of one-step probabilities and its graphs</a>'.\n</br>",optionfilehtmcov);
+       fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
+       fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
+       if(nagesqr==1){
+         printf("  + age*age  ");
+         fprintf(ficres,"  + age*age  ");
+         fprintf(ficlog,"  + age*age  ");
+         fprintf(fichtm, "<th>+ age*age</th>");
+       }
+       for(j=1;j <=ncovmodel-2;j++){
+         if(Typevar[j]==0) {
+           printf("  +      V%d  ",Tvar[j]);
+           fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
+         }else if(Typevar[j]==1) {
+           printf("  +    V%d*age ",Tvar[j]);
+           fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
+         }else if(Typevar[j]==2) {
+           fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
+         }
+       }
+       fprintf(fichtm, "</tr>\n");
        for(i=1,jk=1; i <=nlstate; i++){
          for(k=1; k <=(nlstate+ndeath); k++){
            if (k != i) {
+             fprintf(fichtm, "<tr valign=top>");
              printf("%d%d ",i,k);
              fprintf(ficlog,"%d%d ",i,k);
+             fprintf(fichtm, "<td>%1d%1d</td>",i,k);
              for(j=1; j <=ncovmodel; j++){
-               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               wald=p[jk]/sqrt(matcov[jk][jk]);
-               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
+               if(fabs(wald) > 1.96){
+                 fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
+               }else{
+                 fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
+               }
+               fprintf(fichtm,"W=%8.3f</br>",wald);
+               fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
                jk++;
              }
              printf("\n");
              fprintf(ficlog,"\n");
+             fprintf(fichtm, "</tr>\n");
            }
          }
        }
      } /* end of hesscov and Wald tests */
+     fprintf(fichtm,"</table>\n");
      /*  */
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
- Line 10449  Please run with mle=-1 to get a correct
+ Line 13202  Please run with mle=-1 to get a correct
          fputs(line,stdout);
          fputs(line,ficparo);
          fputs(line,ficlog);
+         fputs(line,ficres);
          continue;
        }else
          break;
- Line 10487  Please run with mle=-1 to get a correct
+ Line 13241  Please run with mle=-1 to get a correct
      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
      /* Other stuffs, more or less useful */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     while(fgets(line, MAXLINE, ficpar)) {
-       ungetc(c,ficpar);
+       /* If line starts with a # it is a comment */
-       fgets(line, MAXLINE, ficpar);
+       if (line[0] == '#') {
-       fputs(line,stdout);
+         numlinepar++;
-       fputs(line,ficparo);
+         fputs(line,stdout);
-     }
+         fputs(line,ficparo);
-     ungetc(c,ficpar);
+         fputs(line,ficlog);
+         fputs(line,ficres);
-     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+         continue;
-     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+       }else
-     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+         break;
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       fputs(line,stdout);
-       fputs(line,ficparo);
-     }
-     ungetc(c,ficpar);
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
-     fprintf(ficlog,"pop_based=%d\n",popbased);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
-     fprintf(ficres,"pop_based=%d\n",popbased);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       fputs(line,stdout);
-       fputs(line,ficparo);
      }
-     ungetc(c,ficpar);
+     if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
-     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+       if (num_filled != 7) {
-     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         goto end;
-     /* day and month of proj2 are not used but only year anproj2.*/
+       }
+       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       ungetc(c,ficpar);
+       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       fputs(line,stdout);
-       fputs(line,ficparo);
      }
-     ungetc(c,ficpar);
-     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
-     fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     /* day and month of proj2 are not used but only year anproj2.*/
-     /* Results */
      while(fgets(line, MAXLINE, ficpar)) {
        /* If line starts with a # it is a comment */
        if (line[0] == '#') {
- Line 10555  Please run with mle=-1 to get a correct
+ Line 13274  Please run with mle=-1 to get a correct
          fputs(line,stdout);
          fputs(line,ficparo);
          fputs(line,ficlog);
+         fputs(line,ficres);
          continue;
        }else
          break;
      }
-     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
-       if (num_filled == 0)
-         resultline[0]='\0';
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-       else if (num_filled != 1){
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
-       }
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
-       printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
+       if (num_filled != 1) {
-       decoderesult(resultline);
+         printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-       while(fgets(line, MAXLINE, ficpar)) {
+         fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+         goto end;
+       }
+       printf("pop_based=%d\n",popbased);
+       fprintf(ficlog,"pop_based=%d\n",popbased);
+       fprintf(ficparo,"pop_based=%d\n",popbased);
+       fprintf(ficres,"pop_based=%d\n",popbased);
+     }
+     /* Results */
+     /* Value of covariate in each resultine will be compututed (if product) and sorted according to model rank */
+     /* It is precov[] because we need the varying age in order to compute the real cov[] of the model equation */
+     precov=matrix(1,MAXRESULTLINESPONE,1,NCOVMAX+1);
+     endishere=0;
+     nresult=0;
+     parameterline=0;
+     do{
+       if(!fgets(line, MAXLINE, ficpar)){
+         endishere=1;
+         parameterline=15;
+       }else if (line[0] == '#') {
          /* If line starts with a # it is a comment */
-         if (line[0] == '#') {
+         numlinepar++;
-           numlinepar++;
+         fputs(line,stdout);
-           fputs(line,stdout);
+         fputs(line,ficparo);
-           fputs(line,ficparo);
+         fputs(line,ficlog);
-           fputs(line,ficlog);
+         fputs(line,ficres);
-           continue;
+         continue;
-         }else
+       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
-           break;
+         parameterline=11;
+       else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
+         parameterline=12;
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
+         parameterline=13;
+       }
+       else{
+         parameterline=14;
        }
-       if (feof(ficpar))
+       switch (parameterline){ /* =0 only if only comments */
+       case 11:
+         if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
+                   fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           /* day and month of proj2 are not used but only year anproj2.*/
+           dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
+           dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
+           prvforecast = 1;
+         }
+         else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
+           printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+           prvforecast = 2;
+         }
+         else {
+           printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           goto end;
+         }
          break;
-       else{ /* Processess output results for this combination of covariate values */
+       case 12:
-       }
+         if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
-     }
+           fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           /* day and month of back2 are not used but only year anback2.*/
+           dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
+           dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
+           prvbackcast = 1;
+         }
+         else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
+           printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+           prvbackcast = 2;
+         }
+         else {
+           printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
+           goto end;
+         }
+         break;
+       case 13:
+         num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
+         nresult++; /* Sum of resultlines */
+         printf("Result %d: result:%s\n",nresult, resultlineori);
+         /* removefirstspace(&resultlineori); */
+         if(strstr(resultlineori,"v") !=0){
+           printf("Error. 'v' must be in upper case 'V' result: %s ",resultlineori);
+           fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultlineori);fflush(ficlog);
+           return 1;
+         }
+         trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
+         printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori);
+         if(nresult > MAXRESULTLINESPONE-1){
+           printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
+           fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
+           goto end;
+         }
+         if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+           fprintf(ficparo,"result: %s\n",resultline);
+           fprintf(ficres,"result: %s\n",resultline);
+           fprintf(ficlog,"result: %s\n",resultline);
+         } else
+           goto end;
+         break;
+       case 14:
+         printf("Error: Unknown command '%s'\n",line);
+         fprintf(ficlog,"Error: Unknown command '%s'\n",line);
+         if(line[0] == ' ' || line[0] == '\n'){
+           printf("It should not be an empty line '%s'\n",line);
+           fprintf(ficlog,"It should not be an empty line '%s'\n",line);
+         }
+         if(ncovmodel >=2 && nresult==0 ){
+           printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+           fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+         }
+         /* goto end; */
+         break;
+       case 15:
+         printf("End of resultlines.\n");
+         fprintf(ficlog,"End of resultlines.\n");
+         break;
+       default: /* parameterline =0 */
+         nresult=1;
+         decoderesult(".",nresult ); /* No covariate */
+       } /* End switch parameterline */
+     }while(endishere==0); /* End do */
      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
- Line 10598  Please run with mle=-1 to get a correct
+ Line 13433  Please run with mle=-1 to get a correct
  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
      }else{
-       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
+       /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
+       /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
+       /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
+       if(prvforecast==1){
+         dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
+         jprojd=jproj1;
+         mprojd=mproj1;
+         anprojd=anproj1;
+         dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
+         jprojf=jproj2;
+         mprojf=mproj2;
+         anprojf=anproj2;
+       } else if(prvforecast == 2){
+         dateprojd=dateintmean;
+         date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
+         dateprojf=dateintmean+yrfproj;
+         date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
+       }
+       if(prvbackcast==1){
+         datebackd=(jback1+12*mback1+365*anback1)/365;
+         jbackd=jback1;
+         mbackd=mback1;
+         anbackd=anback1;
+         datebackf=(jback2+12*mback2+365*anback2)/365;
+         jbackf=jback2;
+         mbackf=mback2;
+         anbackf=anback2;
+       } else if(prvbackcast == 2){
+         datebackd=dateintmean;
+         date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
+         datebackf=dateintmean-yrbproj;
+         date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
+       }
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
      }
      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
-                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+                  jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
- Line 10611  Please run with mle=-1 to get a correct
+ Line 13480  Please run with mle=-1 to get a correct
      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
      /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
      /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
-     free_lvector(num,1,n);
+     free_lvector(num,firstobs,lastobs);
-     free_vector(agedc,1,n);
+     free_vector(agedc,firstobs,lastobs);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
      /*free_matrix(covar,1,NCOVMAX,1,n);*/
      fclose(ficparo);
- Line 10625  Please run with mle=-1 to get a correct
+ Line 13494  Please run with mle=-1 to get a correct
      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
      prlim=matrix(1,nlstate,1,nlstate);
+     /* Computes the prevalence limit for each combination k of the dummy covariates by calling prevalim(k) */
      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
      fclose(ficrespl);
      /*------------- h Pij x at various ages ------------*/
      /*#include "hpijx.h"*/
+     /** h Pij x Probability to be in state j at age x+h being in i at x, for each combination k of dummies in the model line or to nres?*/
+     /* calls hpxij with combination k */
      hPijx(p, bage, fage);
      fclose(ficrespij);
      /* ncovcombmax=  pow(2,cptcoveff); */
-     /*-------------- Variance of one-step probabilities---*/
+     /*-------------- Variance of one-step probabilities for a combination ij or for nres ?---*/
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-     /* Prevalence for each covariates in probs[age][status][cov] */
+     /* Prevalence for each covariate combination in probs[age][status][cov] */
-     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+     probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-     for(i=1;i<=AGESUP;i++)
+     for(i=AGEINF;i<=AGESUP;i++)
        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
          for(k=1;k<=ncovcombmax;k++)
            probs[i][j][k]=0.;
-     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
+                ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
      if (mobilav!=0 ||mobilavproj !=0 ) {
-       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+       mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-       for(i=1;i<=AGESUP;i++)
+       for(i=AGEINF;i<=AGESUP;i++)
-         for(j=1;j<=nlstate;j++)
+         for(j=1;j<=nlstate+ndeath;j++)
            for(k=1;k<=ncovcombmax;k++)
              mobaverages[i][j][k]=0.;
        mobaverage=mobaverages;
        if (mobilav!=0) {
+         printf("Movingaveraging observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging observed prevalence\n");
          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
-       }
+       } else if (mobilavproj !=0) {
-       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
+         printf("Movingaveraging projected observed prevalence\n");
-       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+         fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
-       else if (mobilavproj !=0) {
          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
          }
+       }else{
+         printf("Internal error moving average\n");
+         fflush(stdout);
+         exit(1);
        }
      }/* end if moving average */
      /*---------- Forecasting ------------------*/
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
+     if(prevfcast==1){
-     if(prevfcast==1){
+       /*   /\*    if(stepm ==1){*\/ */
-       /*    if(stepm ==1){*/
+       /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
-       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       /*This done previously after freqsummary.*/
+       /*   dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
+       /*   dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
+       /* } else if (prvforecast==2){ */
+       /*   /\*    if(stepm ==1){*\/ */
+       /*   /\*  anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
+       /* } */
+       /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
+       prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
      }
-     if(backcast==1){
+     /* Prevbcasting */
+     if(prevbcast==1){
        ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
        ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
        ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
- Line 10682  Please run with mle=-1 to get a correct
+ Line 13571  Please run with mle=-1 to get a correct
        /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
        bprlim=matrix(1,nlstate,1,nlstate);
        back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
        fclose(ficresplb);
        hBijx(p, bage, fage, mobaverage);
        fclose(ficrespijb);
-       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
-       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
+       /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
-          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+       /* /\*                   mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
+       /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
+       /*                       mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+       prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
+                        mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
+       varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
+       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
-     }
+     }    /* end  Prevbcasting */
      /* ------ Other prevalence ratios------------ */
- Line 10715  Please run with mle=-1 to get a correct
+ Line 13614  Please run with mle=-1 to get a correct
      }
      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
+     pstamp(ficreseij);
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
        fprintf(ficreseij,"\n#****** ");
+       printf("\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
        }
        fprintf(ficreseij,"******\n");
+       printf("******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       /* printf("HELLO Entering evsij bage=%d fage=%d k=%d estepm=%d nres=%d\n",(int) bage, (int)fage, k, estepm, nres); */
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
      }
      fclose(ficreseij);
      printf("done evsij\n");fflush(stdout);
      fprintf(ficlog,"done evsij\n");fflush(ficlog);
      /*---------- State-specific expectancies and variances ------------*/
      strcpy(filerest,"T_");
      strcat(filerest,fileresu);
      if((ficrest=fopen(filerest,"w"))==NULL) {
- Line 10744  Please run with mle=-1 to get a correct
+ Line 13659  Please run with mle=-1 to get a correct
      }
      printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
      fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
      strcpy(fileresstde,"STDE_");
      strcat(fileresstde,fileresu);
      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
- Line 10773  Please run with mle=-1 to get a correct
+ Line 13686  Please run with mle=-1 to get a correct
      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
-     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     if (cptcovn < 1){i1=1;}
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
-       printf("\n#****** ");
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-       fprintf(ficrest,"\n#****** ");
+       if(i1 != 1 && TKresult[nres]!= k)
-       fprintf(ficlog,"\n#****** ");
+         continue;
+       printf("\n# model %s \n#****** Result for:", model);
+       fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
+       fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
        for(j=1;j<=cptcoveff;j++){
-         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
        }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+       }
        fprintf(ficrest,"******\n");
        fprintf(ficlog,"******\n");
        printf("******\n");
- Line 10792  Please run with mle=-1 to get a correct
+ Line 13713  Please run with mle=-1 to get a correct
        fprintf(ficresstdeij,"\n#****** ");
        fprintf(ficrescveij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
-         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
        }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
+       }
        fprintf(ficresstdeij,"******\n");
        fprintf(ficrescveij,"******\n");
        fprintf(ficresvij,"\n#****** ");
+       /* pstamp(ficresvij); */
        for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[j]]])]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         /* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */
+         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
+       }
        fprintf(ficresvij,"******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       printf(" cvevsij combination#=%d, ",k);
+       printf(" cvevsij ");
-       fprintf(ficlog, " cvevsij combination#=%d, ",k);
+       fprintf(ficlog, " cvevsij ");
-       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
        printf(" end cvevsij \n ");
        fprintf(ficlog, " end cvevsij \n ");
- Line 10818  Please run with mle=-1 to get a correct
+ Line 13748  Please run with mle=-1 to get a correct
        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        pstamp(ficrest);
+       epj=vector(1,nlstate+1);
        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
          cptcod= 0; /* To be deleted */
          printf("varevsij vpopbased=%d \n",vpopbased);
          fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
          if(vpopbased==1)
            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
          else
-           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
          fprintf(ficrest,"\n");
          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
-         epj=vector(1,nlstate+1);
+         printf("Computing age specific forward period (stable) prevalences in each health state \n");
-         printf("Computing age specific period (stable) prevalences in each health state \n");
+         fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
-         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
          for(age=bage; age <=fage ;age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
            if (vpopbased==1) {
              if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
- Line 10872  Please run with mle=-1 to get a correct
+ Line 13801  Please run with mle=-1 to get a correct
            fprintf(ficrest,"\n");
          }
        } /* End vpopbased */
+       free_vector(epj,1,nlstate+1);
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       free_vector(epj,1,nlstate+1);
+       printf("done selection\n");fflush(stdout);
-       printf("done \n");fflush(stdout);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
-       fprintf(ficlog,"done\n");fflush(ficlog);
-       /*}*/
+     } /* End k selection */
-     } /* End k */
      printf("done State-specific expectancies\n");fflush(stdout);
      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
-     /*------- Variance of period (stable) prevalence------*/
+     /* variance-covariance of forward period prevalence*/
+     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
-     strcpy(fileresvpl,"VPL_");
-     strcat(fileresvpl,fileresu);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-       exit(0);
-     }
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
-     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
-     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-       fprintf(ficresvpl,"\n#****** ");
-       printf("\n#****** ");
-       fprintf(ficlog,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       }
-       fprintf(ficresvpl,"******\n");
-       printf("******\n");
-       fprintf(ficlog,"******\n");
-       varpl=matrix(1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
-       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-       /*}*/
-     }
-     fclose(ficresvpl);
-     printf("done variance-covariance of period prevalence\n");fflush(stdout);
-     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
-     free_vector(weight,1,n);
+     free_vector(weight,firstobs,lastobs);
+     free_imatrix(Tvardk,1,NCOVMAX,1,2);
      free_imatrix(Tvard,1,NCOVMAX,1,2);
-     free_imatrix(s,1,maxwav+1,1,n);
+     free_imatrix(s,1,maxwav+1,firstobs,lastobs);
-     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(anint,1,maxwav,firstobs,lastobs);
-     free_matrix(mint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,firstobs,lastobs);
-     free_ivector(cod,1,n);
+     free_ivector(cod,firstobs,lastobs);
      free_ivector(tab,1,NCOVMAX);
      fclose(ficresstdeij);
      fclose(ficrescveij);
- Line 10938  Please run with mle=-1 to get a correct
+ Line 13833  Please run with mle=-1 to get a correct
      /*---------- End : free ----------------*/
      if (mobilav!=0 ||mobilavproj !=0)
-       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
+       free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
-     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+     free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
    }  /* mle==-3 arrives here for freeing */
- Line 10947  Please run with mle=-1 to get a correct
+ Line 13842  Please run with mle=-1 to get a correct
    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
+   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
-   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
+   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
-   free_matrix(coqvar,1,maxwav,1,n);
+   if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
-   free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
    free_matrix(matcov,1,npar,1,npar);
    free_matrix(hess,1,npar,1,npar);
    /*free_vector(delti,1,npar);*/
    free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
    free_matrix(agev,1,maxwav,1,imx);
+   free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
    free_ivector(ncodemax,1,NCOVMAX);
    free_ivector(ncodemaxwundef,1,NCOVMAX);
    free_ivector(Dummy,-1,NCOVMAX);
    free_ivector(Fixed,-1,NCOVMAX);
+   free_ivector(DummyV,1,NCOVMAX);
+   free_ivector(FixedV,1,NCOVMAX);
    free_ivector(Typevar,-1,NCOVMAX);
    free_ivector(Tvar,1,NCOVMAX);
    free_ivector(TvarsQ,1,NCOVMAX);
    free_ivector(TvarsQind,1,NCOVMAX);
    free_ivector(TvarsD,1,NCOVMAX);
+   free_ivector(TnsdVar,1,NCOVMAX);
    free_ivector(TvarsDind,1,NCOVMAX);
    free_ivector(TvarFD,1,NCOVMAX);
    free_ivector(TvarFDind,1,NCOVMAX);
- Line 10992  Please run with mle=-1 to get a correct
+ Line 13891  Please run with mle=-1 to get a correct
    free_ivector(Tmodelind,1,NCOVMAX);
    free_ivector(TmodelInvind,1,NCOVMAX);
    free_ivector(TmodelInvQind,1,NCOVMAX);
+   free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /* Could be elsewhere ?*/
    free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
    /* free_imatrix(codtab,1,100,1,10); */
    fflush(fichtm);
- Line 11030  Please run with mle=-1 to get a correct
+ Line 13931  Please run with mle=-1 to get a correct
    fclose(ficlog);
    /*------ End -----------*/
+ /* Executes gnuplot */
    printf("Before Current directory %s!\n",pathcd);
  #ifdef WIN32
- Line 11065  Please run with mle=-1 to get a correct
+ Line 13968  Please run with mle=-1 to get a correct
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   strcpy(pplotcmd,plotcmd);
    if((outcmd=system(plotcmd)) != 0){
-     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
-     if((outcmd=system(plotcmd)) != 0)
+     if((outcmd=system(plotcmd)) != 0){
        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+       strcpy(plotcmd,pplotcmd);
+     }
    }
    printf(" Successful, please wait...");
    while (z[0] != 'q') {
- Line 11098  end:
+ Line 14004  end:
      printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
+   printf("End\n");
+   exit(0);
  }

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