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Diff for /imach/src/imach.c between versions 1.214 and 1.262

-version 1.214, 2015/12/16 06:57:54
+version 1.262, 2017/04/18 16:48:12
  Line 1
  /* $Id$
    $State$
    $Log$
+   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 ***
+   Revision 1.233  2016/08/23 07:40:50  brouard
+   Summary: not working
+   Revision 1.232  2016/08/22 14:20:21  brouard
+   Summary: not working
+   Revision 1.231  2016/08/22 07:17:15  brouard
+   Summary: not working
+   Revision 1.230  2016/08/22 06:55:53  brouard
+   Summary: Not working
+   Revision 1.229  2016/07/23 09:45:53  brouard
+   Summary: Completing for func too
+   Revision 1.228  2016/07/22 17:45:30  brouard
+   Summary: Fixing some arrays, still debugging
+   Revision 1.226  2016/07/12 18:42:34  brouard
+   Summary: temp
+   Revision 1.225  2016/07/12 08:40:03  brouard
+   Summary: saving but not running
+   Revision 1.224  2016/07/01 13:16:01  brouard
+   Summary: Fixes
+   Revision 1.223  2016/02/19 09:23:35  brouard
+   Summary: temporary
+   Revision 1.222  2016/02/17 08:14:50  brouard
+   Summary: Probably last 0.98 stable version 0.98r6
+   Revision 1.221  2016/02/15 23:35:36  brouard
+   Summary: minor bug
+   Revision 1.219  2016/02/15 00:48:12  brouard
+   *** empty log message ***
+   Revision 1.218  2016/02/12 11:29:23  brouard
+   Summary: 0.99 Back projections
+   Revision 1.217  2015/12/23 17:18:31  brouard
+   Summary: Experimental backcast
+   Revision 1.216  2015/12/18 17:32:11  brouard
+   Summary: 0.98r4 Warning and status=-2
+   Version 0.98r4 is now:
+    - displaying an error when status is -1, date of interview unknown and date of death known;
+    - permitting a status -2 when the vital status is unknown at a known date of right truncation.
+   Older changes concerning s=-2, dating from 2005 have been supersed.
+   Revision 1.215  2015/12/16 08:52:24  brouard
+   Summary: 0.98r4 working
    Revision 1.214  2015/12/16 06:57:54  brouard
    Summary: temporary not working
- Line 16
+ Line 163
    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 601
+ Line 746
    Short summary of the programme:
-   This program computes Healthy Life Expectancies from
+   This program computes Healthy Life Expectancies or State-specific
-   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
+   (if states aren't health statuses) Expectancies from
-   first survey ("cross") where individuals from different ages are
+   cross-longitudinal data. Cross-longitudinal data consist in:
-   interviewed on their health status or degree of disability (in the
-   case of a health survey which is our main interest) -2- at least a
+   -1- a first survey ("cross") where individuals from different ages
-   second wave of interviews ("longitudinal") which measure each change
+   are interviewed on their health status or degree of disability (in
-   (if any) in individual health status.  Health expectancies are
+   the case of a health survey which is our main interest)
-   computed from the time spent in each health state according to a
-   model. More health states you consider, more time is necessary to reach the
+   -2- at least a second wave of interviews ("longitudinal") which
-   Maximum Likelihood of the parameters involved in the model.  The
+   measure each change (if any) in individual health status.  Health
-   simplest model is the multinomial logistic model where pij is the
+   expectancies are computed from the time spent in each health state
-   probability to be observed in state j at the second wave
+   according to a model. More health states you consider, more time is
-   conditional to be observed in state i at the first wave. Therefore
+   necessary to reach the Maximum Likelihood of the parameters involved
-   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
+   in the model.  The simplest model is the multinomial logistic model
-   'age' is age and 'sex' is a covariate. If you want to have a more
+   where pij is the probability to be observed in state j at the second
-   complex model than "constant and age", you should modify the program
+   wave conditional to be observed in state i at the first
-   where the markup *Covariates have to be included here again* invites
+   wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
-   you to do it.  More covariates you add, slower the
+   etc , where 'age' is age and 'sex' is a covariate. If you want to
+   have a more complex model than "constant and age", you should modify
+   the program where the markup *Covariates have to be included here
+   again* invites you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
- Line 637
+ Line 785
    hPijx.
    Also this programme outputs the covariance matrix of the parameters but also
    of the life expectancies. It also computes the period (stable) prevalence.
+ Back prevalence and projections:
+  - 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)
+     Computes the back prevalence limit for any combination of
+     covariate values k at any age between ageminpar and agemaxpar and
+     returns it in **bprlim. In the loops,
+    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
+        **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
+    - hBijx Back Probability to be in state i at age x-h being in j at x
+    Computes for any combination of covariates k and any age between bage and fage
+    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);
+      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.
+      Returns p3mat[i][j][h] after calling
+      p3mat[i][j][h]=matprod2(newm,
+      bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
+      dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+      oldm);
+ Important routines
+ - func (or funcone), computes logit (pij) distinguishing
+   o fixed variables (single or product dummies or quantitative);
+   o varying variables by:
+    (1) wave (single, product dummies, quantitative),
+    (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
+        % fixed dummy (treated) or quantitative (not done because time-consuming);
+        % varying dummy (not done) or quantitative (not done);
+ - 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
+     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).
             Institut national d'études démographiques, Paris.
- Line 699
+ Line 895
  /* #define DEBUGLINMIN */
  /* #define DEBUGHESS */
  #define DEBUGHESSIJ
- /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
+ /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan) *\/ */
  #define POWELL /* Instead of NLOPT */
- #define POWELLF1F3 /* Skip test */
+ #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 *\/ */
- Line 709
+ Line 905
  #include <stdio.h>
  #include <stdlib.h>
  #include <string.h>
+ #include <ctype.h>
  #ifdef _WIN32
  #include <io.h>
- Line 754  typedef struct {
+ Line 951  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"*/
- Line 775  typedef struct {
+ Line 972  typedef struct {
  #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
  #define MAXN 20000
  #define YEARM 12. /**< Number of months per year */
- #define AGESUP 130
+ /* #define AGESUP 130 */
+ #define AGESUP 150
+ #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
  #define AGEBASE 40
  #define AGEOVERFLOW 1.e20
  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
- Line 793  typedef struct {
+ Line 992  typedef struct {
  /* $State$ */
  #include "version.h"
  char version[]=__IMACH_VERSION__;
- char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+ 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 fullversion[]="$Revision$ $Date$";
  char strstart[80];
  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
- Line 802  int nagesqr=0, nforce=0; /* nagesqr=1 if
+ Line 1001  int nagesqr=0, nforce=0; /* nagesqr=1 if
  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
- int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
+ int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
+ 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 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 */
+ int nsd=0; /**< Total number of single dummy variables (output) */
+ int nsq=0; /**< Total number of single quantitative variables (output) */
+ int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
+ int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
+ 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 ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
  int npar=NPARMAX;
  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 */
+ int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
  int popbased=0;
  int *wav; /* Number of waves for this individuual 0 is possible */
- Line 825  int **dh; /* dh[mi][i] is number of step
+ Line 1036  int **dh; /* dh[mi][i] is number of step
  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  int countcallfunc=0;  /* Count the number of calls to func */
+ int selected(int kvar); /* Is covariate kvar selected for printing results */
  double jmean=1; /* Mean space between 2 waves */
  double **matprod2(); /* test */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+ double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
  /*FILE *fic ; */ /* Used in readdata only */
- FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+ FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
  FILE *ficlog, *ficrespow;
  int globpr=0; /* Global variable for printing or not */
  double fretone; /* Only one call to likelihood */
- Line 853  char fileresv[FILENAMELENGTH];
+ Line 1068  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
- char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+ char model[MAXLINE]; /**< The model line */
+ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
  char command[FILENAMELENGTH];
  int  outcmd=0;
- char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+ char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
  char fileresu[FILENAMELENGTH]; /* fileres without r in front */
  char filelog[FILENAMELENGTH]; /* Log file */
  char filerest[FILENAMELENGTH];
- Line 890  double dval;
+ Line 1106  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 936  int *ncodemaxwundef;  /* ncodemax[j]= Nu
+ Line 1153  int *ncodemaxwundef;  /* ncodemax[j]= Nu
                               covariate for which somebody answered including
                               undefined. Usually 3: -1, 0 and 1. */
  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
- double **pmmij, ***probs;
+ double **pmmij, ***probs; /* Global pointer */
+ double ***mobaverage, ***mobaverages; /* New global variable */
  double *ageexmed,*agecens;
  double dateintmean=0;
- Line 946  double *agedc;
+ Line 1164  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 ***cotvar; /* Time varying covariate itv */
+ 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 */
+ /*k          1  2   3   4     5    6    7     8    9 */
+ /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
+ /* Tndvar[k]    1   2   3               4          5 */
+ /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
+ /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
+ /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
+ /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
+ /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
+ /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
+ /* Tprod[i]=k           4               7            */
+ /* Tage[i]=k                  5               8      */
+ /* */
+ /* Type                    */
+ /* V         1  2  3  4  5 */
+ /*           F  F  V  V  V */
+ /*           D  Q  D  D  Q */
+ /*                         */
+ int *TvarsD;
+ int *TvarsDind;
+ int *TvarsQ;
+ int *TvarsQind;
+ #define MAXRESULTLINES 10
+ int nresult=0;
+ int parameterline=0; /* # of the parameter (type) line */
+ int TKresult[MAXRESULTLINES];
+ int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
+ double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
+ /* 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 */
+ int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *Tvarsel; /**< Selected covariates for output */
+ double *Tvalsel; /**< Selected modality value of covariate for output */
+ 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*/
+ int *TmodelInvind; /** 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*/
+ int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) 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  */
  int *Ndum; /** Freq of modality (tricode */
  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
- int **Tvard, *Tprod, cptcovprod, *Tvaraff;
+ int **Tvard;
+ 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 */
+    /* 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) */
+ int cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
+ #define FD 1; /* Fixed dummy covariate */
+ #define FQ 2; /* Fixed quantitative covariate */
+ #define FP 3; /* Fixed product covariate */
+ #define FPDD 7; /* Fixed product dummy*dummy covariate */
+ #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
+ #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
+ #define VD 10; /* Varying dummy covariate */
+ #define VQ 11; /* Varying quantitative covariate */
+ #define VP 12; /* Varying product covariate */
+ #define VPDD 13; /* Varying product dummy*dummy covariate */
+ #define VPDQ 14; /* Varying product dummy*quantitative covariate */
+ #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
+ #define APFD 16; /* Age product * fixed dummy covariate */
+ #define APFQ 17; /* Age product * fixed quantitative covariate */
+ #define APVD 18; /* Age product * varying dummy covariate */
+ #define APVQ 19; /* Age product * varying quantitative covariate */
+ #define FTYPE 1; /* Fixed covariate */
+ #define VTYPE 2; /* Varying covariate (loop in wave) */
+ #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
+ struct kmodel{
+         int maintype; /* main type */
+         int subtype; /* subtype */
+ };
+ struct kmodel modell[NCOVMAX];
  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
  double ftolhess; /**< Tolerance for computing hessian */
- Line 1149  int nbocc(char *s, char occ)
+ Line 1464  int nbocc(char *s, char occ)
    i=0;
    lg=strlen(s);
    for(i=0; i<= lg; i++) {
-   if  (s[i] == occ ) j++;
+     if  (s[i] == occ ) j++;
    }
    return j;
  }
- Line 1493  double brent(double ax, double bx, doubl
+ Line 1808  double brent(double ax, double bx, doubl
        etemp=e;
        e=d;
        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
-         d=CGOLD*(e=(x >= xm ? a-x : b-x));
+                                 d=CGOLD*(e=(x >= xm ? a-x : b-x));
        else {
-         d=p/q;
+                                 d=p/q;
-         u=x+d;
+                                 u=x+d;
-         if (u-a < tol2 || b-u < tol2)
+                                 if (u-a < tol2 || b-u < tol2)
-           d=SIGN(tol1,xm-x);
+                                         d=SIGN(tol1,xm-x);
        }
      } else {
        d=CGOLD*(e=(x >= xm ? a-x : b-x));
- Line 1512  double brent(double ax, double bx, doubl
+ Line 1827  double brent(double ax, double bx, doubl
      } else {
        if (u < x) a=u; else b=u;
        if (fu <= fw || w == x) {
-         v=w;
+                                 v=w;
-         w=u;
+                                 w=u;
-         fv=fw;
+                                 fv=fw;
-         fw=fu;
+                                 fw=fu;
        } else if (fu <= fv || v == x || v == w) {
-         v=u;
+                                 v=u;
-         fv=fu;
+                                 fv=fu;
        }
      }
    }
- Line 1559  values at the three points, fa, fb , and
+ Line 1874  values at the three points, fa, fb , and
    *cx=(*bx)+GOLD*(*bx-*ax);
    *fc=(*func)(*cx);
  #ifdef DEBUG
-   printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
+   printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
-   fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
+   fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
  #endif
-   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
+   while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
      r=(*bx-*ax)*(*fb-*fc);
-     q=(*bx-*cx)*(*fb-*fa);
+     q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
- Line 1575  values at the three points, fa, fb , and
+ Line 1890  values at the three points, fa, fb , and
        double A, fparabu;
        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
        fparabu= *fa - A*(*ax-u)*(*ax-u);
-       printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
-       fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
+       fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
        /* And thus,it can be that fu > *fc even if fparabu < *fc */
        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
- Line 1609  values at the three points, fa, fb , and
+ Line 1924  values at the three points, fa, fb , and
  /*      fu = *fc; */
  /*      *fc =dum; */
  /*       } */
- #ifdef DEBUG
+ #ifdef DEBUGMNBRAK
-       printf("mnbrak34  fu < or >= fc \n");
+                  double A, fparabu;
-       fprintf(ficlog, "mnbrak34 fu < fc\n");
+      A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
+      fparabu= *fa - A*(*ax-u)*(*ax-u);
+      printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
+      fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
  #endif
        dum=u; /* Shifting c and u */
        u = *cx;
- Line 1622  values at the three points, fa, fb , and
+ Line 1940  values at the three points, fa, fb , and
  #endif
      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
  #ifdef DEBUG
-       printf("mnbrak2  u after c but before ulim\n");
+       printf("\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
-       fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
+       fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim\n",u,*cx);
  #endif
        fu=(*func)(u);
        if (fu < *fc) {
  #ifdef DEBUG
-       printf("mnbrak2  u after c but before ulim AND fu < fc\n");
+                                 printf("\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
-       fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
+                           fprintf(ficlog,"\nmnbrak2  u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
+ #endif
+                           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+                                 SHFT(*fb,*fc,fu,(*func)(u))
+ #ifdef DEBUG
+                                         printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
  #endif
-         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
-         SHFT(*fb,*fc,fu,(*func)(u))
        }
      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
  #ifdef DEBUG
-       printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
+       printf("\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
-       fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
+       fprintf(ficlog,"\nmnbrak2  u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
  #endif
        u=ulim;
        fu=(*func)(u);
      } else { /* u could be left to b (if r > q parabola has a maximum) */
  #ifdef DEBUG
-       printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+       printf("\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
-       fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
+       fprintf(ficlog,"\nmnbrak2  u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
  #endif
        u=(*cx)+GOLD*(*cx-*bx);
        fu=(*func)(u);
+ #ifdef DEBUG
+       printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
+       fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
+ #endif
      } /* end tests */
      SHFT(*ax,*bx,*cx,u)
      SHFT(*fa,*fb,*fc,fu)
  #ifdef DEBUG
-       printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
+       printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
-       fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
+       fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
  #endif
    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
  }
- Line 1668  int ncom;
+ Line 1993  int ncom;
  double *pcom,*xicom;
  double (*nrfunc)(double []);
+ #ifdef LINMINORIGINAL
  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)
+ #endif
  {
    double brent(double ax, double bx, double cx,
                 double (*f)(double), double tol, double *xmin);
- Line 1712  void linmin(double p[], double xi[], int
+ Line 2041  void linmin(double p[], double xi[], int
  #ifdef LINMINORIGINAL
  #else
      if (fx != fx){
-         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
+                         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
-         printf("|");
+                         printf("|");
-         fprintf(ficlog,"|");
+                         fprintf(ficlog,"|");
  #ifdef DEBUGLINMIN
-         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
+                         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);
  #endif
      }
-   }while(fx != fx);
+   }while(fx != fx && xxs > 1.e-5);
  #endif
  #ifdef DEBUGLINMIN
    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
    fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
  #endif
+ #ifdef LINMINORIGINAL
+ #else
+         if(fb == fx){ /* Flat function in the direction */
+                 xmin=xx;
+     *flat=1;
+         }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) */
    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
    /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
    /* fmin = f(p[j] + xmin * xi[j]) */
    /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
    /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
  #ifdef DEBUG
-   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
-   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+   fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
+ #endif
+ #ifdef LINMINORIGINAL
+ #else
+                         }
  #endif
  #ifdef DEBUGLINMIN
    printf("linmin end ");
- Line 1783  such that failure to decrease by more th
+ Line 2125  such that failure to decrease by more th
  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.
   */
+ #ifdef LINMINORIGINAL
+ #else
+         int *flatdir; /* Function is vanishing in that direction */
+         int flat=0, flatd=0; /* Function is vanishing in that direction */
+ #endif
  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
              double (*func)(double []))
  {
-   void linmin(double p[], double xi[], int n, double *fret,
+ #ifdef LINMINORIGINAL
+  void linmin(double p[], double xi[], int n, double *fret,
                double (*func)(double []));
-   int i,ibig,j;
+ #else
+  void linmin(double p[], double xi[], int n, double *fret,
+              double (*func)(double []),int *flat);
+ #endif
+  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 1814  void powell(double p[], double **xi, int
+ Line 2172  void powell(double p[], double **xi, int
      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(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
      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;
- Line 1836  void powell(double p[], double **xi, int
+ Line 2227  void powell(double p[], double **xi, int
          strcpy(strfor,asctime(&forecast_time));
          itmp = strlen(strfor);
          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);
          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);
        }
- Line 1850  void powell(double p[], double **xi, int
+ Line 2241  void powell(double p[], double **xi, int
  #endif
        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
        fprintf(ficlog,"%d",i);fflush(ficlog);
+ #ifdef LINMINORIGINAL
        linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
-                                     /* Outputs are fret(new point p) p is updated and xit rescaled */
+ #else
+       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
+                         flatdir[i]=flat; /* Function is vanishing in that direction i */
+ #endif
+                         /* Outputs are fret(new point p) p is updated and xit rescaled */
        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
-         /* because that direction will be replaced unless the gain del is small */
+                                 /* because that direction will be replaced unless the gain del is small */
-         /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
+                                 /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
-         /* Unless the n directions are conjugate some gain in the determinant may be obtained */
+                                 /* Unless the n directions are conjugate some gain in the determinant may be obtained */
-         /* with the new direction. */
+                                 /* with the new direction. */
-         del=fabs(fptt-(*fret));
+                                 del=fabs(fptt-(*fret));
-         ibig=i;
+                                 ibig=i;
        }
  #ifdef DEBUG
        printf("%d %.12e",i,(*fret));
        fprintf(ficlog,"%d %.12e",i,(*fret));
        for (j=1;j<=n;j++) {
-         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+                                 xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
-         printf(" x(%d)=%.12e",j,xit[j]);
+                                 printf(" x(%d)=%.12e",j,xit[j]);
-         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+                                 fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        }
        for(j=1;j<=n;j++) {
-         printf(" p(%d)=%.12e",j,p[j]);
+                                 printf(" p(%d)=%.12e",j,p[j]);
-         fprintf(ficlog," p(%d)=%.12e",j,p[j]);
+                                 fprintf(ficlog," p(%d)=%.12e",j,p[j]);
        }
        printf("\n");
        fprintf(ficlog,"\n");
- Line 1879  void powell(double p[], double **xi, int
+ Line 2275  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) */
-     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
+       for(j=1;j<=n;j++) {
+                                 if(flatdir[j] >0){
+                                         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+                                         fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
+                                 }
+                                 /* printf("\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) { /* 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 1887  void powell(double p[], double **xi, int
+ Line 2292  void powell(double p[], double **xi, int
        /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
        /* By using V1+V2+V3, the gain should be  7.82, compared with basic 1+age. */
        /* By adding 10 parameters more the gain should be 18.31 */
        /* Starting the program with initial values given by a former maximization will simply change */
        /* the scales of the directions and the directions, because the are reset to canonical directions */
        /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
- Line 1915  void powell(double p[], double **xi, int
+ Line 2320  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];
        pt[j]=p[j];
      }
      fptt=(*func)(ptt); /* f_3 */
- #ifdef POWELLF1F3
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
+                 if (*iter <=4) {
+ #else
+ #endif
+ #ifdef POWELLNOF3INFF1TEST    /* skips test F3 <F1 */
  #else
      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
  #endif
- Line 1938  void powell(double p[], double **xi, int
+ Line 2350  void powell(double p[], double **xi, int
        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
-       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
+       /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
+       /* also  lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
+       /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
+       /*  Even if f3 <f1, directest can be negative and t >0 */
+       /* mu² and del² are equal when f3=f1 */
+                         /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
+                         /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
+                         /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
+                         /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
  #ifdef NRCORIGINAL
        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
  #else
- Line 1961  void powell(double p[], double **xi, int
+ Line 2381  void powell(double p[], double **xi, int
        if (t < 0.0) { /* Then we use it for new direction */
  #else
        if (directest*t < 0.0) { /* Contradiction between both tests */
-         printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
+                                 printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
-         fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
+         fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
        }
        if (directest < 0.0) { /* Then we use it for new direction */
  #endif
  #ifdef DEBUGLINMIN
          printf("Before linmin in direction P%d-P0\n",n);
          for (j=1;j<=n;j++) {
            printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
            fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
            if(j % ncovmodel == 0){
- Line 1979  void powell(double p[], double **xi, int
+ Line 2399  void powell(double p[], double **xi, int
            }
          }
  #endif
+ #ifdef LINMINORIGINAL
          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+ #else
+         linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+         flatdir[i]=flat; /* Function is vanishing in that direction i */
+ #endif
  #ifdef DEBUGLINMIN
          for (j=1;j<=n;j++) {
            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
- Line 1994  void powell(double p[], double **xi, int
+ Line 2420  void powell(double p[], double **xi, int
            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
          }
+ #ifdef LINMINORIGINAL
+ #else
+         for (j=1, flatd=0;j<=n;j++) {
+           if(flatdir[j]>0)
+             flatd++;
+         }
+         if(flatd >0){
+           printf("%d flat directions: ",flatd);
+           fprintf(ficlog,"%d flat directions :",flatd);
+           for (j=1;j<=n;j++) {
+             if(flatdir[j]>0){
+               printf("%d ",j);
+               fprintf(ficlog,"%d ",j);
+             }
+           }
+           printf("\n");
+           fprintf(ficlog,"\n");
+         }
+ #endif
          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
  #ifdef DEBUG
          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
          for(j=1;j<=n;j++){
-           printf(" %.12e",xit[j]);
+           printf(" %lf",xit[j]);
-           fprintf(ficlog," %.12e",xit[j]);
+           fprintf(ficlog," %lf",xit[j]);
          }
          printf("\n");
          fprintf(ficlog,"\n");
  #endif
        } /* end of t or directest negative */
- #ifdef POWELLF1F3
+ #ifdef POWELLNOF3INFF1TEST
  #else
-     } /* end if (fptt < fp)  */
+       } /* end if (fptt < fp)  */
  #endif
-   } /* loop iteration */
+ #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
+     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
+ #else
+ #endif
+                 } /* loop iteration */
  }
  /**** 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 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)
+        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 */
    /* or prevalence in state 1, prevalence in state 2, 0 */
- Line 2038  double **prevalim(double **prlim, int nl
+ Line 2489  double **prevalim(double **prlim, int nl
    /* {0.51571254859325999, 0.4842874514067399, */
    /*  0.51326036147820708, 0.48673963852179264} */
    /* If we start from prlim again, prlim tends to a constant matrix */
    int i, ii,j,k;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
-   double **out, cov[NCOVMAX+1], **pmij();
+   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;
- Line 2051  double **prevalim(double **prlim, int nl
+ Line 2502  double **prevalim(double **prlim, int nl
    max=vector(1,nlstate);
    meandiff=vector(1,nlstate);
+         /* Starting with matrix unity */
    for (ii=1;ii<=nlstate+ndeath;ii++)
      for (j=1;j<=nlstate+ndeath;j++){
        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 2067  double **prevalim(double **prlim, int nl
+ Line 2519  double **prevalim(double **prlim, int nl
      cov[2]=agefin;
      if(nagesqr==1)
        cov[3]= agefin*agefin;;
-     for (k=1; k<=cptcovn;k++) {
+     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
-       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[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])]); */
+       /* 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 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++){  /* For product with age */
+       if(Dummy[Tvar[Tage[k]]]){
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       } else{
+         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,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=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,k)] * Tqinvresult[nres][Tvard[k][1]];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
+         }
+       }
      }
-     /*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]; */
-     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)];
      /*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' */
      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      savm=oldm;
- Line 2130  Earliest age to start was %d-%d=%d, ncvl
+ Line 2605  Earliest age to start was %d-%d=%d, ncvl
    return prlim; /* should not reach here */
  }
- /*************** transition probabilities ***************/
- double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+  /**** Back Prevalence limit (stable or period prevalence)  ****************/
+  /* 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, int nres)
  {
-   /* According to parameters values stored in x and the covariate's values stored in cov,
+   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
-      computes the probability to be observed in state j being in state i by appying the
+      matrix by transitions matrix until convergence is reached with precision ftolpl */
-      model to the ncovmodel covariates (including constant and age).
+   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
-      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+   /* Wx is row vector: population in state 1, population in state 2, population dead */
-      and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+   /* or prevalence in state 1, prevalence in state 2, 0 */
-      ncth covariate in the global vector x is given by the formula:
+   /* newm is the matrix after multiplications, its rows are identical at a factor */
-      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+   /* Initial matrix pimij */
-      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
-      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
-      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+   /*  0,                   0                  , 1} */
-      Outputs ps[i][j] the probability to be observed in j being in j according to
+   /*
-      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+    * and after some iteration: */
-   */
+   /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
-   double s1, lnpijopii;
+   /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
-   /*double t34;*/
+   /*  0,                   0                  , 1} */
-   int i,j, nc, ii, jj;
+   /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
+   /* {0.51571254859325999, 0.4842874514067399, */
+   /*  0.51326036147820708, 0.48673963852179264} */
+   /* If we start from prlim again, prlim tends to a constant matrix */
-     for(i=1; i<= nlstate; i++){
+   int i, ii,j,k;
-       for(j=1; j<i;j++){
+   int first=0;
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+   double *min, *max, *meandiff, maxmax,sumnew=0.;
-           /*lnpijopii += param[i][j][nc]*cov[nc];*/
+   /* double **matprod2(); */ /* test */
-           lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+   double **out, cov[NCOVMAX+1], **bmij();
- /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+   double **newm;
-         }
+   double         **dnewm, **doldm, **dsavm;  /* for use */
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+   double         **oldm, **savm;  /* for use */
- /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-       }
+   double agefin, delaymax=200. ; /* 100 Max number of years to converge */
-       for(j=i+1; j<=nlstate+ndeath;j++){
+   int ncvloop=0;
-         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+   min=vector(1,nlstate);
-           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+   max=vector(1,nlstate);
- /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+   meandiff=vector(1,nlstate);
-         }
-         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
+         oldm=oldms; savm=savms;
+         /* Starting with matrix unity */
+         for (ii=1;ii<=nlstate+ndeath;ii++)
+                 for (j=1;j<=nlstate+ndeath;j++){
+       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+     }
+   cov[1]=1.;
+   /* 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 */
+     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)
+       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 */
+       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
+       /* printf("bprevalim 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<=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]]]){
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       } else{
+         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 */
-     for(i=1; i<= nlstate; i++){
+       /* 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]); */
-       s1=0;
+       if(Dummy[Tvard[k][1]==0]){
-       for(j=1; j<i; j++){
+         if(Dummy[Tvard[k][2]==0]){
-         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
-         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+         }else{
-       }
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
-       for(j=i+1; j<=nlstate+ndeath; j++){
+         }
-         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       }else{
-         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+         if(Dummy[Tvard[k][2]==0]){
-       }
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
-       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+         }else{
-       ps[i][i]=1./(s1+1.);
+           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
-       /* Computing other pijs */
+         }
-       for(j=1; j<i; j++)
-         ps[i][j]= exp(ps[i][j])*ps[i][i];
-       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 */
-     } /* end i */
-     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-       for(jj=1; jj<= nlstate+ndeath; jj++){
-         ps[ii][jj]=0;
-         ps[ii][ii]=1;
        }
      }
+     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
-     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
-     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
-     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+     /* 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 *\/ */
-     /*   printf("\n "); */
+                 /* ij should be linked to the correct index of cov */
-     /* } */
+                 /* age and covariate values ij are in 'cov', but we need to pass
-     /* printf("\n ");printf("%lf ",cov[2]);*/
+                  * ij for the observed prevalence at age and status and covariate
-     /*
+                  * number:  prevacurrent[(int)agefin][ii][ij]
-       for(i=1; i<= npar; i++) printf("%f ",x[i]);
+                  */
-       goto end;*/
+     /* 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 *\/ */
-     return ps;
+     /* 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 */
+     savm=oldm;
- /**************** Product of 2 matrices ******************/
+     oldm=newm;
+     for(j=1; j<=nlstate; j++){
- double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
+       max[j]=0.;
- {
+       min[j]=1.;
-   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+     }
-      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+     for(j=1; j<=nlstate; j++){
-   /* in, b, out are matrice of pointers which should have been initialized
+       for(i=1;i<=nlstate;i++){
+         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
+         bprlim[i][j]= newm[i][j];
+         max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
+         min[i]=FMIN(min[i],bprlim[i][j]);
+       }
+     }
+     maxmax=0.;
+     for(i=1; i<=nlstate; i++){
+       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
+       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 */
+     *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);*/
+     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);
+       free_vector(max,1,nlstate);
+       free_vector(meandiff,1,nlstate);
+       return bprlim;
+     }
+   } /* age loop */
+     /* After some age loop it doesn't converge */
+   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);
+   free_vector(max,1,nlstate);
+   free_vector(meandiff,1,nlstate);
+   return bprlim; /* should not reach here */
+ }
+ /*************** transition probabilities ***************/
+ 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
+      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
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      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
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
+   /*double t34;*/
+   int i,j, nc, ii, jj;
+   for(i=1; i<= nlstate; i++){
+     for(j=1; j<i;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+         /*       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); */
+     }
+     for(j=i+1; j<=nlstate+ndeath;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+       }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+     }
+   }
+   for(i=1; i<= nlstate; i++){
+     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); */
+     }
+     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); */
+     }
+     /* 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];
+     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 */
+   } /* end i */
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(jj=1; jj<= nlstate+ndeath; jj++){
+       ps[ii][jj]=0;
+       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]); */
+   /*   } */
+   /*   printf("\n "); */
+   /* } */
+   /* printf("\n ");printf("%lf ",cov[2]);*/
+   /*
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
+                 goto end;*/
+   return ps;
+ }
+ /*************** backward transition probabilities ***************/
+  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
+ /* 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
+    * and returns in **ps as well as **bmij.
+    */
+   int i, ii, j,k;
+   double **out, **pmij();
+   double sumnew=0.;
+   double agefin;
+   double **dnewm, **dsavm, **doldm;
+   double **bbmij;
+   doldm=ddoldms; /* global pointers */
+   dnewm=ddnewms;
+   dsavm=ddsavms;
+   agefin=cov[2];
+   /* bmij *//* age is cov[2], ij is included in cov, but we need for
+      the observed prevalence (with this covariate ij) */
+   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
+   /* We do have the matrix Px in savm  and we need pij */
+   for (j=1;j<=nlstate+ndeath;j++){
+     sumnew=0.; /* w1 p11 + w2 p21 only on live states */
+     for (ii=1;ii<=nlstate;ii++){
+       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
+     } /* 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); */
+         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
+         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /* }else */
+         doldm[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)] */
+   /* 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 */
+   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
+   /* 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;
+ }
+ /*************** transition probabilities ***************/
+ double **bpmij(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
+      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
+      ncth covariate in the global vector x is given by the formula:
+      j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
+      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
+      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+   */
+   double s1, lnpijopii;
+   /*double t34;*/
+   int i,j, nc, ii, jj;
+   for(i=1; i<= nlstate; i++){
+     for(j=1; j<i;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+         /*       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); */
+     }
+     for(j=i+1; j<=nlstate+ndeath;j++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+       }
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+     }
+   }
+   for(i=1; i<= nlstate; i++){
+     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); */
+     }
+     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); */
+     }
+     /* 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];
+     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 */
+   } /* end i */
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+     for(jj=1; jj<= nlstate+ndeath; jj++){
+       ps[ii][jj]=0;
+       ps[ii][ii]=1;
+     }
+   }
+   /* Added for backcast */ /* Transposed matrix too */
+   for(jj=1; jj<= nlstate+ndeath; jj++){
+     s1=0.;
+     for(ii=1; ii<= nlstate+ndeath; ii++){
+       s1+=ps[ii][jj];
+     }
+     for(ii=1; ii<= nlstate; ii++){
+       ps[ii][jj]=ps[ii][jj]/s1;
+     }
+   }
+   /* Transposition */
+   for(jj=1; jj<= nlstate+ndeath; jj++){
+     for(ii=jj; ii<= nlstate+ndeath; ii++){
+       s1=ps[ii][jj];
+       ps[ii][jj]=ps[jj][ii];
+       ps[jj][ii]=s1;
+     }
+   }
+   /* 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]); */
+   /*   } */
+   /*   printf("\n "); */
+   /* } */
+   /* printf("\n ");printf("%lf ",cov[2]);*/
+   /*
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     goto end;*/
+   return ps;
+ }
+ /**************** Product of 2 matrices ******************/
+ double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
+ {
+   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+   /* in, b, out are matrice of pointers which should have been initialized
       before: only the contents of out is modified. The function returns
       a pointer to pointers identical to out */
    int i, j, k;
- Line 2234  double **matprod2(double **out, double *
+ Line 3039  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' over
+   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 2270  double ***hpxij(double ***po, int nhstep
+ Line 3075  double ***hpxij(double ***po, int nhstep
        cov[2]=agexact;
        if(nagesqr==1)
          cov[3]= agexact*agexact;
-       for (k=1; k<=cptcovn;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,k)];
+         /* printf("hpxij 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 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++){
+         if(Dummy[Tvar[Tage[k]]]){
+           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+         } else{
+           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]); */
+       }
+       for (k=1; k<=cptcovprod;k++){ /*  */
+         /* printf("hPxij 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]); */
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+       }
+       /* 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 */
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+       /* if((int)age == 70){ */
+       /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
+       /*        for(i=1; i<=nlstate+ndeath; i++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
+       savm=oldm;
+       oldm=newm;
+     }
+     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]);*/
+       }
+     /*printf("h=%d ",h);*/
+   } /* end 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 )
+ {
+   /* 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.
+      Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+      (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.
+   */
+   int i, j, d, h, k;
+   double **out, cov[NCOVMAX+1];
+   double **newm;
+   double agexact;
+   double agebegin, ageend;
+   double **oldm, **savm;
+   oldm=oldms;savm=savms;
+   /* Hstepm could be zero and should return the unit matrix */
+   for (i=1;i<=nlstate+ndeath;i++)
+     for (j=1;j<=nlstate+ndeath;j++){
+       oldm[i][j]=(i==j ? 1.0 : 0.0);
+       po[i][j][0]=(i==j ? 1.0 : 0.0);
+     }
+   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+   for(h=1; h <=nhstepm; h++){
+     for(d=1; d <=hstepm; d++){
+       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-1))*stepm/YEARM; /\* age just before transition *\/ */
+       cov[2]=agexact;
+       if(nagesqr==1)
+         cov[3]= agexact*agexact;
+       for (k=1; k<=cptcovn;k++)
          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
-         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
          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,Tvar[Tage[k]])]*cov[2]; */
+       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[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)];
-         /* 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,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,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]);*/
-       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+       /* Careful transposed matrix */
-                    pmij(pmmij,cov,ncovmodel,x,nlstate));
+       /* age is in cov[2] */
+       /* 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);
+       /* 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++) { */
+       /*          printf("%d pmmij ",i); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",pmmij[i][j]); */
+       /*          } */
+       /*          printf(" oldm "); */
+       /*          for(j=1;j<=nlstate+ndeath;j++) { */
+       /*            printf("%f ",oldm[i][j]); */
+       /*          } */
+       /*          printf("\n"); */
+       /*        } */
+       /* } */
        savm=oldm;
        oldm=newm;
      }
- Line 2296  double ***hpxij(double ***po, int nhstep
+ Line 3223  double ***hpxij(double ***po, int nhstep
        }
      /*printf("h=%d ",h);*/
    } /* end h */
- /*     printf("\n H=%d \n",h); */
+   /*     printf("\n H=%d \n",h); */
    return po;
  }
  #ifdef NLOPT
    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
    double fret;
- Line 2324  double ***hpxij(double ***po, int nhstep
+ Line 3252  double ***hpxij(double ***po, int nhstep
  double func( double *x)
  {
    int i, ii, j, k, mi, d, kk;
+   int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
-   double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
    int s1, s2;
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
    double bbh, survp;
    long ipmx;
    double agexact;
- Line 2344  double func( double *x)
+ Line 3273  double func( double *x)
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
+   ioffset=0;
    if(mle==1){
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        /* Computes the values of the ncovmodel covariates of the model
-          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
+          depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
           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.
-        */
+       */
-       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
+       ioffset=2+nagesqr ;
-           cov[2+nagesqr+k]=covar[Tvar[k]][i];
+    /* Fixed */
+       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
+         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)*/
        }
        /* 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]
           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
+          mw[mi][i] is real wave of the mi th effectve wave */
+       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
+          s2=s[mw[mi+1][i]][i];
+          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
+          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
+          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 )*/
+           /* 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 (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 2369  double func( double *x)
+ Line 3313  double func( double *x)
            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
            cov[2]=agexact;
            if(nagesqr==1)
-             cov[3]= agexact*agexact;
+             cov[3]= agexact*agexact;  /* Should be changed here */
            for (kk=1; kk<=cptcovage;kk++) {
+           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));
            savm=oldm;
            oldm=newm;
          } /* end mult */
          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          /* But now since version 0.9 we anticipate for bias at large stepm.
           * If stepm is larger than one month (smallest stepm) and if the exact delay
- Line 2387  double func( double *x)
+ Line 3334  double func( double *x)
           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
+                                  * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
+                                  * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
+                                  * For stepm > 1 the results are less biased than in previous versions.
-          */
+                                  */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
- Line 2406  double func( double *x)
+ Line 3353  double func( double *x)
               which is also equal to probability to die before dh
               minus probability to die before dh-stepm .
               In version up to 0.92 likelihood was computed
-         as if date of death was unknown. Death was treated as any other
+              as if date of death was unknown. Death was treated as any other
-         health state: the date of the interview describes the actual state
+              health state: the date of the interview describes the actual state
-         and not the date of a change in health state. The former idea was
+              and not the date of a change in health state. The former idea was
-         to consider that at each interview the state was recorded
+              to consider that at each interview the state was recorded
-         (healthy, disable or death) and IMaCh was corrected; but when we
+              (healthy, disable or death) and IMaCh was corrected; but when we
-         introduced the exact date of death then we should have modified
+              introduced the exact date of death then we should have modified
-         the contribution of an exact death to the likelihood. This new
+              the contribution of an exact death to the likelihood. This new
-         contribution is smaller and very dependent of the step unit
+              contribution is smaller and very dependent of the step unit
-         stepm. It is no more the probability to die between last interview
+              stepm. It is no more the probability to die between last interview
-         and month of death but the probability to survive from last
+              and month of death but the probability to survive from last
-         interview up to one month before death multiplied by the
+              interview up to one month before death multiplied by the
-         probability to die within a month. Thanks to Chris
+              probability to die within a month. Thanks to Chris
-         Jackson for correcting this bug.  Former versions increased
+              Jackson for correcting this bug.  Former versions increased
-         mortality artificially. The bad side is that we add another loop
+              mortality artificially. The bad side is that we add another loop
-         which slows down the processing. The difference can be up to 10%
+              which slows down the processing. The difference can be up to 10%
-         lower mortality.
+              lower mortality.
+           */
+           /* If, at the beginning of the maximization mostly, the
+              cumulative probability or probability to be dead is
+              constant (ie = 1) over time d, the difference is equal to
+.  out[s1][3] = savm[s1][3]: probability, being at state
+              s1 at precedent wave, to be dead a month before current
+              wave is equal to probability, being at state s1 at
+              precedent wave, to be dead at mont of the current
+              wave. Then the observed probability (that this person died)
+              is null according to current estimated parameter. In fact,
+              it should be very low but not zero otherwise the log go to
+              infinity.
            */
-         /* If, at the beginning of the maximization mostly, the
-            cumulative probability or probability to be dead is
-            constant (ie = 1) over time d, the difference is equal to
-.  out[s1][3] = savm[s1][3]: probability, being at state
-            s1 at precedent wave, to be dead a month before current
-            wave is equal to probability, being at state s1 at
-            precedent wave, to be dead at mont of the current
-            wave. Then the observed probability (that this person died)
-            is null according to current estimated parameter. In fact,
-            it should be very low but not zero otherwise the log go to
-            infinity.
-         */
  /* #ifdef INFINITYORIGINAL */
  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
  /* #else */
- Line 2443  double func( double *x)
+ Line 3390  double func( double *x)
  /*        else */
  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
  /* #endif */
-             lli=log(out[s1][s2] - savm[s1][s2]);
+           lli=log(out[s1][s2] - savm[s1][s2]);
-         } else if  (s2==-2) {
+         } else if  ( s2==-1 ) { /* alive */
            for (j=1,survp=0. ; j<=nlstate; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            /*survp += out[s1][j]; */
            lli= log(survp);
          }
+         else if  (s2==-4) {
-         else if  (s2==-4) {
            for (j=3,survp=0. ; j<=nlstate; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
          }
+         else if  (s2==-5) {
-         else if  (s2==-5) {
+           for (j=1,survp=0. ; j<=2; j++)
-           for (j=1,survp=0. ; j<=2; j++)
              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
          }
          else{
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[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 */
- Line 2471  double func( double *x)
+ Line 3415  double func( double *x)
          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
          /*if(lli ==000.0)*/
          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          ipmx +=1;
          sw += weight[i];
          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          /* if (lli < log(mytinydouble)){ */
- Line 2575  double func( double *x)
+ Line 3519  double func( double *x)
          s2=s[mw[mi+1][i]][i];
          if( s2 > nlstate){
            lli=log(out[s1][s2] - savm[s1][s2]);
+         } else if  ( s2==-1 ) { /* alive */
+           for (j=1,survp=0. ; j<=nlstate; j++)
+             survp += out[s1][j];
+           lli= log(survp);
          }else{
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          }
- Line 2628  double func( double *x)
+ Line 3576  double func( double *x)
  /*************** log-likelihood *************/
  double funcone( double *x)
  {
-   /* Same as likeli but slower because of a lot of printf and if */
+   /* Same as func but slower because of a lot of printf and if */
    int i, ii, j, k, mi, d, kk;
+   int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    double llt;
    int s1, s2;
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
    double bbh, survp;
    double agexact;
    double agebegin, ageend;
- Line 2647  double funcone( double *x)
+ Line 3598  double funcone( double *x)
    cov[1]=1.;
    for(k=1; k<=nlstate; k++) ll[k]=0.;
+   ioffset=0;
    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+cptcovage; */
-     for(mi=1; mi<= wav[i]-1; mi++){
+     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 */
+       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];  */
+ /*    cov[2+6]=covar[2][i]; V2  */
+ /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
+ /*    cov[2+7]=covar[Tvar[7]][i];  */
+ /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
+ /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
+ /*    cov[2+9]=covar[Tvar[9]][i];  */
+ /*    cov[2+9]=covar[1][i]; V1  */
+     }
+     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
+     /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
+     /* } */
+     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
+     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
+     /* } */
+     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]]-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 *\/ */
+       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
+       /* 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]); */
+       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
+       /*        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]); *\/ */
+       /*        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++){
            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 2660  double funcone( double *x)
+ Line 3651  double funcone( double *x)
        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 */
+       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
          /*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.*/
          newm=savm;
-         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
          cov[2]=agexact;
          if(nagesqr==1)
            cov[3]= agexact*agexact;
          for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           if(!FixedV[Tvar[Tage[kk]]])
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           else
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
          }
+         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 2682  double funcone( double *x)
+ Line 3677  double funcone( double *x)
        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); */
+       /*        /\* exit(1); *\/ */
+       /* } */
        bbh=(double)bh[mi][i]/(double)stepm;
        /* bias is positive if real duration
         * is higher than the multiple of stepm and negative otherwise.
         */
        if( s2 > nlstate && (mle <5) ){  /* Jackson */
          lli=log(out[s1][s2] - savm[s1][s2]);
-       } else if  (s2==-2) {
+       } else if  ( s2==-1 ) { /* alive */
          for (j=1,survp=0. ; j<=nlstate; j++)
            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
          lli= log(survp);
- Line 2709  double funcone( double *x)
+ Line 3708  double funcone( double *x)
        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 %11.6f %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,
 *weight[i]*lli,out[s1][s2],savm[s1][s2]);
- Line 2719  double funcone( double *x)
+ Line 3718  double funcone( double *x)
          }
          fprintf(ficresilk," %10.6f\n", -llt);
        }
-     } /* end of wave */
+         } /* end of wave */
-   } /* end of individual */
+ } /* end of individual */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   if(globpr==0){ /* First time we count the contributions and weights */
+ if(globpr==0){ /* First time we count the contributions and weights */
-     gipmx=ipmx;
+         gipmx=ipmx;
-     gsw=sw;
+         gsw=sw;
-   }
+ }
-   return -l;
+ return -l;
  }
- Line 3067  double hessij( double x[], double **hess
+ Line 4066  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; 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; 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 3157  void ludcmp(double **a, int n, int *indx
+ Line 4156  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 3223  void pstamp(FILE *fichier)
+ Line 4231  void pstamp(FILE *fichier)
    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
  }
+ 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; /* 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/(ne-2)/(sumx2 - sumx * sumx /ne));
+   *sa= *sb * sqrt(sumx2/ne);
+   return 0;
+ }
  /************ 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 **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\
+                   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 */
-   int i, m, jk, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0;
+   int iind=0, iage=0;
    int mi; /* Effective wave */
    int first;
    double ***freq; /* Frequencies */
-   double *pp, **prop;
+   double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */
-   double pos,posprop, k2, dateintsum=0,k2cpt=0;
+   int no;
+   double *meanq;
+   double **meanqt;
+   double *pp, **prop, *posprop, *pospropt;
+   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
    char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
    double agebegin, ageend;
    pp=vector(1,nlstate);
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   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 */
+   meanqt=matrix(1,lastpass,1,nqtveff);
    strcpy(fileresp,"P_");
    strcat(fileresp,fileresu);
    /*strcat(fileresphtm,fileresu);*/
- Line 3248  void  freqsummary(char fileres[], int ia
+ Line 4331  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 3258  void  freqsummary(char fileres[], int ia
+ Line 4341  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);
+             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 and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
    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);
+             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>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);
-   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
+   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=cptcoveff;
+   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
+   j=cptcoveff;  /* Only dummy covariates of the model */
    if (cptcovn<1) {j=1;ncodemax[1]=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
+   */
+   dateintsum=0;
+   k2cpt=0;
-   first=1;
+   if(cptcoveff == 0 )
+     nl=1;  /* Constant model only */
-   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
+   else
+     nl=2;
+   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
+     if(nj==1)
+       j=0;  /* First pass for the constant */
+     else
+       j=cptcoveff; /* Other passes for the covariate values */
+     first=1;
+     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 */
+       posproptt=0.;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          scanf("%d", i);*/
        for (i=-5; i<=nlstate+ndeath; i++)
- Line 3295  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4399  Title=%s <br>Datafile=%s Firstpass=%d La
            for(m=iagemin; m <= iagemax+3; m++)
              freq[i][jk][m]=0;
-       for (i=1; i<=nlstate; i++)
+       for (i=1; i<=nlstate; i++)  {
          for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=0;
+         posprop[i]=0;
+         pospropt[i]=0;
+       }
+       /* for (z1=1; z1<= nqfveff; z1++) {   */
+       /*   meanq[z1]+=0.; */
+       /*   for(m=1;m<=lastpass;m++){ */
+       /*        meanqt[m][z1]=0.; */
+       /*   } */
+       /* } */
+       /* dateintsum=0; */
+       /* k2cpt=0; */
-       dateintsum=0;
+       /* For that combination of covariate j1, we count and print the frequencies in one pass */
-       k2cpt=0;
+       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
-       for (i=1; i<=imx; i++) { /* For each individual i */
          bool=1;
-         if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+         if(j !=0){
-           for (z1=1; z1<=cptcoveff; z1++)
+           if(anyvaryingduminmodel==0){ /* If All fixed covariates */
-             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
+             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
+               /* for (z1=1; z1<= nqfveff; z1++) {   */
-               bool=0;
+               /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
-               /* 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),
+               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
-                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+                 /* if(Tvaraff[z1] ==-20){ */
-               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-             }
+                 /* }else  if(Tvaraff[z1] ==-10){ */
-         } /* cptcovn > 0 */
+                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
+                 /* }else  */
-         if (bool==1){
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
+                   /* Tests if 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 or all fixed */
            /* for(m=firstpass; m<=lastpass; m++){ */
-           for(mi=1; mi<wav[i];mi++){
+           for(mi=1; mi<wav[iind];mi++){ /* For that wave */
-             m=mw[mi][i];
+             m=mw[mi][iind];
-             /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
+             if(j!=0){
-                and mw[mi+1][i]. dh depends on stepm. */
+               if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+                 for (z1=1; z1<=cptcoveff; z1++) {
-             ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
+                   if( Fixed[Tmodelind[z1]]==1){
-             if(m >=firstpass && m <=lastpass){
+                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-               k2=anint[m][i]+(mint[m][i]/12.);
+                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
-               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+                                                                                       value is -1, we don't select. It differs from the
-               if(agev[m][i]==0) agev[m][i]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+                                                                                       constant and age model which counts them. */
-               if(agev[m][i]==1) agev[m][i]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+                       bool=0; /* not selected */
-               if (s[m][i]>0 && s[m][i]<=nlstate)  /* If status at wave m is known and a live state */
+                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-                 prop[s[m][i]][(int)agev[m][i]] += weight[i];  /* At age of beginning of transition, where status is known */
+                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-               if (m<lastpass) {
+                       bool=0;
-                 /* if(s[m][i]==4 && s[m+1][i]==4) */
+                     }
-                 /*   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
+                   }
-                 if(s[m][i]==-1)
+                 }
-                   printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
+               }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
-                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
+             } /* end j==0 */
-                 /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
+             /* bool =0 we keep that guy which corresponds to the combination of dummy values */
-                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
+             if(bool==1){
+               /* 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 */
+                   /* 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{
-             if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
+               bool=1;
-               dateintsum=dateintsum+k2;
+             }/* end bool 2 */
-               k2cpt++;
-               /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
-             }
-             /*}*/
            } /* end m */
          } /* end bool */
-       } /* end i = 1 to imx */
+       } /* end iind = 1 to imx */
+       /* prop[s][age] is feeded 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);*/
        pstamp(ficresp);
-       if  (cptcovn>0) {
+       if  (cptcoveff>0 && j!=0){
+         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<=cptcoveff; z1++){
-           fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           if(!FixedV[Tvaraff[z1]]){
-           fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           }else{
+             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           }
          }
-           fprintf(ficresp, "**********\n#");
+         printf( "**********\n#");
+         fprintf(ficresp, "**********\n#");
          fprintf(ficresphtm, "**********</h3>\n");
          fprintf(ficresphtmfr, "**********</h3>\n");
-         fprintf(ficlog, "\n#********** Variable ");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          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(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");
- Line 3386  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4550  Title=%s <br>Datafile=%s Firstpass=%d La
          }
        }
        fprintf(ficresphtmfr, "\n");
        /* For each age */
-       for(i=iagemin; i <= iagemax+3; i++){
+       for(iage=iagemin; iage <= iagemax+3; iage++){
          fprintf(ficresphtm,"<tr>");
-         if(i==iagemax+1){
+         if(iage==iagemax+1){
            fprintf(ficlog,"1");
            fprintf(ficresphtmfr,"<tr><th>0</th> ");
-         }else if(i==iagemax+2){
+         }else if(iage==iagemax+2){
            fprintf(ficlog,"0");
            fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-         }else if(i==iagemax+3){
+         }else if(iage==iagemax+3){
            fprintf(ficlog,"Total");
            fprintf(ficresphtmfr,"<tr><th>Total</th> ");
          }else{
- Line 3404  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4568  Title=%s <br>Datafile=%s Firstpass=%d La
              first=0;
              printf("See log file for details...\n");
            }
-           fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
-           fprintf(ficlog,"Age %d", i);
+           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][i];
+             pp[jk] += freq[jk][m][iage];
          }
          for(jk=1; jk <=nlstate ; jk++){
            for(m=-1, pos=0; m <=0 ; m++)
-             pos += freq[jk][m][i];
+             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]);
- Line 3425  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4589  Title=%s <br>Datafile=%s Firstpass=%d La
              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
            }
          }
          for(jk=1; jk <=nlstate ; jk++){
-           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+           /* posprop[jk]=0; */
-             pp[jk] += freq[jk][m][i];
+           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-         }
+             pp[jk] += freq[jk][m][iage];
-         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
+         }       /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
-           pos += pp[jk];
-           posprop += prop[jk][i];
+         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){
- Line 3444  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4613  Title=%s <br>Datafile=%s Firstpass=%d La
                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            }
-           if( i <= iagemax){
+           if( iage <= iagemax){
              if(pos>=1.e-5){
-               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+               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>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
+               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-               /*probs[i][jk][j1]= pp[jk]/pos;*/
+               /*probs[iage][jk][j1]= pp[jk]/pos;*/
-               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+               /*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",i,prop[jk][i],posprop);
+               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>",i, prop[jk][i],posprop);
+               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][i] !=0 ) { /* minimizing output */
+             if(freq[jk][m][iage] !=0 ) { /* minimizing output */
                if(first==1){
-                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
                }
-               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+               /* 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][i]);
+               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(i <= iagemax){
+         if(iage <= iagemax){
            fprintf(ficresp,"\n");
            fprintf(ficresphtm,"</tr>\n");
          }
          if(first==1)
            printf("Others in log...\n");
          fprintf(ficlog,"\n");
-       } /* end loop i */
+       } /* end loop age iage */
+       fprintf(ficresphtm,"<tr><th>Tot</th>");
+       for(jk=1; jk <=nlstate ; jk++){
+         if(posproptt < 1.e-5){
+           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+         }else{
+           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+         }
+       }
+       fprintf(ficresphtm,"</tr>\n");
        fprintf(ficresphtm,"</table>\n");
        fprintf(ficresphtmfr,"</table>\n");
-       /*}*/
+       if(posproptt < 1.e-5){
-   } /* end j1 */
+         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(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
+         printf("#  This combination (%d) is not valid and no result will be produced\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");
+       fprintf(ficlog,"\n");
+       if(j!=0){
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
+         for(i=1,jk=1; i <=nlstate; i++){
+           for(k=1; k <=(nlstate+ndeath); k++){
+             if (k != i) {
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */
+                 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[jk],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[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                     pstart[jk]= 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, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */
+                   }
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
+                   pstart[jk]=b;
+                   pstart[jk-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[jk]= 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("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],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]); */
+                 jk++;
+               } /* end jj */
+             } /* end k!= i */
+           } /* end k */
+         } /* end i, jk */
+       } /* 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,jk=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[jk]=p[jk]; /* Setting pstart to p values by default */
+               if(jj==1){ /* Age has to be done */
+                 pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
+                 printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],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[jk],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]); */
+               jk++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       }
+       printf("#Freqsummary\n");
+       fprintf(ficlog,"\n");
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
+         for(m=-1; m <=nlstate+ndeath; m++){
+           /* param[i]|j][k]= freq[jk][m][iagemax+3] */
+           printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
+           fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
+           /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */
+           /*   printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
+           /*   fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
+           /* } */
+         }
+       } /* end loop jk */
+       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");
+         }
+       }
+     }
+   } /* end mle=-2 */
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
    fclose(ficresphtm);
    fclose(ficresphtmfr);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
+   free_vector(meanq,1,nqfveff);
+   free_matrix(meanqt,1,lastpass,1,nqtveff);
+   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+4+AGEMARGE);
    free_vector(pp,1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin, iagemax+3);
+   /* End of freqsummary */
-   /* End of Freq */
  }
  /************ Prevalence ********************/
- Line 3502  void prevalence(double ***probs, double
+ Line 4810  void prevalence(double ***probs, double
       We still use firstpass and lastpass as another selection.
    */
-   int i, m, jk, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, iv;
    int mi; /* Effective wave */
    int iage;
    double agebegin, ageend;
- Line 3516  void prevalence(double ***probs, double
+ Line 4824  void prevalence(double ***probs, double
    iagemin= (int) agemin;
    iagemax= (int) agemax;
    /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin,iagemax+3);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
- Line 3524  void prevalence(double ***probs, double
+ Line 4832  void prevalence(double ***probs, double
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    first=1;
-   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
      for (i=1; i<=nlstate; i++)
-       for(iage=iagemin; iage <= iagemax+3; 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)]); */
+     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
      for (i=1; i<=imx; i++) { /* Each individual */
        bool=1;
-       if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-         for (z1=1; z1<=cptcoveff; z1++)
+       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
-           if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
+         m=mw[mi][i];
-             bool=0;
+         /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
-       }
+         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
-       if (bool==1) {
+         for (z1=1; z1<=cptcoveff; z1++){
-         /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
+           if( Fixed[Tmodelind[z1]]==1){
-         for(mi=1; mi<wav[i];mi++){
+             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-           m=mw[mi][i];
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,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)]) {
+               bool=0;
+             }
+         }
+         if(bool==1){ /* Otherwise we skip that wave/person */
            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
            /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
            if(m >=firstpass && m <=lastpass){
- Line 3547  void prevalence(double ***probs, double
+ Line 4865  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 || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
+               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);
+               }
                if (s[m][i]>0 && s[m][i]<=nlstate) {
                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
- Line 3555  void prevalence(double ***probs, double
+ Line 4876  void prevalence(double ***probs, double
                } /* end valid statuses */
              } /* end selection of dates */
            } /* end selection of waves */
-         } /* end effective waves */
+         } /* end bool */
-       } /* end bool */
+       } /* end wave */
-     }
+     } /* end individual */
      for(i=iagemin; i <= iagemax+3; i++){
        for(jk=1,posprop=0; jk <=nlstate ; jk++) {
          posprop += prop[jk][i];
- Line 3570  void prevalence(double ***probs, double
+ Line 4891  void prevalence(double ***probs, double
            } else{
              if(first==1){
                first=0;
-               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
+               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]);
              }
            }
          }
        }/* end jk */
      }/* end i */
-     /*} *//* end i1 */
+      /*} *//* end i1 */
    } /* end j1 */
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
-   free_matrix(prop,1,nlstate, iagemin,iagemax+3);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
  }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- Line 3593  void  concatwav(int wav[], int **dh, int
+ Line 4914  void  concatwav(int wav[], int **dh, int
       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.
-      */
+   */
-   int i, mi, m;
+   int i=0, mi=0, m=0, mli=0;
    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       double sum=0., jmean=0.;*/
-   int first, firstwo;
+   int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
    int j, k=0,jk, ju, jl;
    double sum=0.;
    first=0;
    firstwo=0;
+   firsthree=0;
+   firstfour=0;
    jmin=100000;
    jmax=-1;
    jmean=0.;
+ /* Treating live states */
    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
-     mi=0;
+     mi=0;  /* First valid wave */
+     mli=0; /* Last valid wave */
      m=firstpass;
      while(s[m][i] <= nlstate){  /* a live state */
-       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
+       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;
-       if(m >=lastpass)
+         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 */
+ #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
          break;
-       else
+ #else
-         m++;
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+           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 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;
+           }
+           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);
+           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? */
+             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);
+           }
+           break;
+         }
+         break;
+ #endif
+       }/* End m >= lastpass */
      }/* end while */
+     /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
+     /* After last pass */
+ /* Treating death states */
      if (s[m][i] > nlstate){  /* In a death state */
+       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
+       /* } */
        mi++;     /* Death is another wave */
        /* if(mi==0)  never been interviewed correctly before death */
-          /* Only death is a correct wave */
+       /* Only death is a correct wave */
-       mw[mi][i]=m;
-     }else if (andc[i] != 9999) { /* A death occured after lastpass */
-       m++;
-       mi++;
-       s[m][i]=nlstate+1;  /* We are setting the status to the last of non live state */
        mw[mi][i]=m;
-       nbwarn++;
+     } /* else not in a death state */
-       if(firstwo==0){
+ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-         printf("Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m);
+     else if ((int) andc[i] != 9999) {  /* Date of death is known */
-         fprintf(ficlog,"Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
+       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-         firstwo=1;
+         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 */
-       }
+           nbwarn++;
-       if(firstwo==1){
+           if(firstfiv==0){
-         fprintf(ficlog,"Warning! Death for individual %ld line=%d  occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
+             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 );
+             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 );
+           }
+         }else{ /* Death occured afer last wave 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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). 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], 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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+         }
+       }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 );
+           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 );
        }
-     }
+     } /* end if date of death is known */
-     wav[i]=mi;
+ #endif
+     wav[i]=mi; /* mi should be the last effective wave (or mli) */
+     /* wav[i]=mw[mi][i]; */
      if(mi==0){
        nbwarn++;
        if(first==0){
- Line 3650  void  concatwav(int wav[], int **dh, int
+ Line 5025  void  concatwav(int wav[], int **dh, int
      } /* end mi==0 */
    } /* End individuals */
    /* wav and mw are no more changed */
    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 3686  void  concatwav(int wav[], int **dh, int
+ Line 5061  void  concatwav(int wav[], int **dh, int
          else{
            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
            k=k+1;
            if (j >= jmax) {
              jmax=j;
- Line 3740  void  concatwav(int wav[], int **dh, int
+ Line 5115  void  concatwav(int wav[], int **dh, int
    jmean=sum/k;
    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-  }
+ }
  /*********** Tricode ****************************/
- void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
+  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 2 (V2)
+     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
-    * nbcode[Tvar[j]][1]=
+     * 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; */
-   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 */
-   /* Loop on covariates without age and products */
+    /* Loop on covariates without age and products and no quantitative variable */
-   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
+    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
-     for (k=-1; k < maxncov; k++) Ndum[k]=0;
+    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
+      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-                                modality of this covariate Vj*/
+      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+        switch(Fixed[k]) {
-                                     * If product of Vn*Vm, still boolean *:
+        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-                                     * 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 < -1) && (ij > NCOVMAX)){
-       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+              exit(1);
-       /* getting the maximum value of the modality of the covariate
+            }else
-          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-          female is 1, then modmaxcovj=1.*/
+            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-     } /* end for loop on individuals i */
+            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+            /* getting the maximum value of the modality of the covariate
-     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-     cptcode=modmaxcovj;
+               female ies 1, then modmaxcovj=1.
-     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+            */
-    /*for (i=0; i<=cptcode; i++) {*/
+          } /* end for loop on individuals i */
-     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
+          printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+          fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+          cptcode=modmaxcovj;
-       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
+          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-         if( k != -1){
+          /*for (i=0; i<=cptcode; i++) {*/
-           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
+          for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
-                              covariate for which somebody answered excluding
+            printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-                              undefined. Usually 2: 0 and 1. */
+            fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-         }
+            if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
+              if( j != -1){
-                              covariate for which somebody answered including
+                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
-                              undefined. Usually 3: -1, 0 and 1. */
+                                   covariate for which somebody answered excluding
-       }
+                                   undefined. Usually 2: 0 and 1. */
-       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
+              }
-          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
-     } /* Ndum[-1] number of undefined modalities */
+                                      covariate for which somebody answered including
+                                      undefined. Usually 3: -1, 0 and 1. */
-     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+            }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
-     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
+                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
+          } /* Ndum[-1] number of undefined modalities */
-        modmincovj=3; modmaxcovj = 7;
-        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
+          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-        which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
+          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
-        defining two dummy variables: variables V1_1 and V1_2.
+          /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
-        nbcode[Tvar[j]][ij]=k;
+          /* modmincovj=3; modmaxcovj = 7; */
-        nbcode[Tvar[j]][1]=0;
+          /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
-        nbcode[Tvar[j]][2]=1;
+          /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
-        nbcode[Tvar[j]][3]=2;
+          /*              defining two dummy variables: variables V1_1 and V1_2.*/
-        To be continued (not working yet).
+          /* nbcode[Tvar[j]][ij]=k; */
-     */
+          /* nbcode[Tvar[j]][1]=0; */
-     ij=0; /* ij is similar to i but can jump over null modalities */
+          /* nbcode[Tvar[j]][2]=1; */
-     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*/
+          /* nbcode[Tvar[j]][3]=2; */
-         if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+          /* To be continued (not working yet). */
-           break;
+          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*/
-         ij++;
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-         nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
+              break;
-         cptcode = ij; /* New max modality for covar j */
+            }
-     } /* end of loop on modality i=-1 to 1 or more */
+            ij++;
+            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*/
-     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+            cptcode = ij; /* New max modality for covar j */
-     /*  /\*recode from 0 *\/ */
+          } /* end of loop on modality i=-1 to 1 or more */
-     /*                               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; */
+        case 1: /* Testing on varying covariate, could be simple and
-     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+                 * should look at waves or product of fixed *
-     /*  } */
+                 * varying. No time to test -1, assuming 0 and 1 only */
-     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+          ij=0;
-     /*  if (ij > ncodemax[j]) { */
+          for(i=0; i<=1;i++){
-     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+            nbcode[Tvar[k]][++ij]=i;
-     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+          }
-     /*    break; */
+          break;
-     /*  } */
+        default:
-     /*   }  /\* end of loop on modality k *\/ */
+          break;
-   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+        } /* end switch */
+      } /* end dummy test */
-  for (k=-1; k< maxncov; k++) Ndum[k]=0;
+      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
+      /*         /\*recode from 0 *\/ */
-    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+      /*                                      k is a modality. If we have model=V1+V1*sex  */
-    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
+      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-    Ndum[ij]++; /* Might be supersed V1 + V1*age */
+      /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
-  }
+      /*         } */
+      /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
-  ij=0;
+      /*         if (ij > ncodemax[j]) { */
-  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-    if((Ndum[i]!=0) && (i<=ncovcol)){
+      /*           break; */
-      ij++;
+      /*         } */
-      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+      /*   }  /\* end of loop on modality k *\/ */
-      Tvaraff[ij]=i; /*For printing (unclear) */
+    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-    }else{
-        /* Tvaraff[ij]=0; */
+    for (k=-1; k< maxncov; k++) Ndum[k]=0;
+    /* 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 */
+      /* 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 */
+      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} */
+    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+    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 (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]);*/
+      /* 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 product not in single variable we don't print results */
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        ++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*/
+        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 */
+        if(Fixed[k]!=0)
+          anyvaryingduminmodel=1;
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
+        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
+        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
+        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+      }
+    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+    /* ij--; */
+    /* cptcoveff=ij; /\*Number of total covariates*\/ */
+    *cptcov=ij; /*Number of total real effective covariates: effective
+                 * 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?*/
+    for(j=ij+1; j<= cptcovt; j++){
+      Tvaraff[j]=0;
+      Tmodelind[j]=0;
+    }
+    for(j=ntveff+1; j<= cptcovt; j++){
+      TmodelInvind[j]=0;
     }
+    /* To be sorted */
+    ;
   }
-  /* ij--; */
-  cptcoveff=ij; /*Number of total covariates*/
- }
  /*********** 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 */
- Line 3885  void evsij(double ***eij, double x[], in
+ Line 5300  void evsij(double ***eij, double x[], in
    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 3948  void evsij(double ***eij, double x[], in
+ Line 5363  void evsij(double ***eij, double x[], in
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     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 3983  void evsij(double ***eij, double x[], in
+ Line 5398  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
-    to initial status i, ei. .
+      to initial status i, ei. .
    */
    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    int nhstepma, nstepma; /* Decreasing with age */
- Line 4081  void cvevsij(double ***eij, double x[],
+ Line 5496  void cvevsij(double ***eij, double x[],
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
      /* if (stepm >= YEARM) hstepm=1;*/
      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      /* 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 */
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      /* Computing  Variances of health expectancies */
      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         decrease memory allocation */
- Line 4096  void cvevsij(double ***eij, double x[],
+ Line 5511  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++){
            for(h=0; h<=nhstepm-1; h++){
- Line 4107  void cvevsij(double ***eij, double x[],
+ Line 5522  void cvevsij(double ***eij, double x[],
            }
          }
        }
        for(ij=1; ij<= nlstate*nlstate; ij++)
          for(h=0; h<=nhstepm-1; h++){
            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- Line 4120  void cvevsij(double ***eij, double x[],
+ Line 5535  void cvevsij(double ***eij, double x[],
          for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];
-      for(ij=1;ij<=nlstate*nlstate;ij++)
+     for(ij=1;ij<=nlstate*nlstate;ij++)
        for(ji=1;ji<=nlstate*nlstate;ji++)
          varhe[ij][ji][(int)age] =0.;
-      printf("%d|",(int)age);fflush(stdout);
+     printf("%d|",(int)age);fflush(stdout);
-      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-      for(h=0;h<=nhstepm-1;h++){
+     for(h=0;h<=nhstepm-1;h++){
        for(k=0;k<=nhstepm-1;k++){
          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- Line 4136  void cvevsij(double ***eij, double x[],
+ Line 5551  void cvevsij(double ***eij, double x[],
              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
        }
      }
      /* 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++){
            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
            /* 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]);*/
          }
      fprintf(ficresstdeij,"%3.0f",age );
      for(i=1; i<=nlstate;i++){
        eip=0.;
- Line 4161  void cvevsij(double ***eij, double x[],
+ Line 5576  void cvevsij(double ***eij, double x[],
        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
      }
      fprintf(ficresstdeij,"\n");
      fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
- Line 4174  void cvevsij(double ***eij, double x[],
+ Line 5589  void cvevsij(double ***eij, double x[],
            }
        }
      fprintf(ficrescveij,"\n");
    }
    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- Line 4184  void cvevsij(double ***eij, double x[],
+ Line 5599  void cvevsij(double ***eij, double x[],
    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    printf("\n");
    fprintf(ficlog,"\n");
    free_vector(xm,1,npar);
    free_vector(xp,1,npar);
    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  }
- /************ 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[])
- {
-   /* Variance of health expectancies */
-   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-   /* double **newm;*/
-   /* 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 k;
-   double *xp;
-   double **gp, **gm;  /* for var eij */
-   double ***gradg, ***trgradg; /*for var eij */
-   double **gradgp, **trgradgp; /* 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 ***p3mat;
-   double age,agelim, hf;
-   double ***mobaverage;
-   int theta;
-   char digit[4];
-   char digitp[25];
-   char fileresprobmorprev[FILENAMELENGTH];
-   if(popbased==1){
-     if(mobilav!=0)
-       strcpy(digitp,"-POPULBASED-MOBILAV_");
-     else strcpy(digitp,"-POPULBASED-NOMOBIL_");
-   }
-   else
-     strcpy(digitp,"-STABLBASED_");
-   if (mobilav!=0) {
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
-     }
-   }
-   strcpy(fileresprobmorprev,"PRMORPREV-");
-   sprintf(digit,"%-d",ij);
-   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
-   strcat(fileresprobmorprev,digit); /* Tvar to be done */
-   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
-   strcat(fileresprobmorprev,fileresu);
-   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobmorprev);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
-   }
-   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-   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,"# Age cov=%-d",ij);
-   for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-     fprintf(ficresprobmorprev," p.%-d SE",j);
-     for(i=1; i<=nlstate;i++)
-       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
-   }
-   fprintf(ficresprobmorprev,"\n");
-   fprintf(ficgp,"\n# Routine varevsij");
-   fprintf(ficgp,"\nunset title \n");
- /* 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 ");
-   if(popbased==1)
-     fprintf(ficresvij,"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(ficresvij,"the age specific period (stable) prevalences in each health state \n");
-   fprintf(ficresvij,"# Age");
-   for(i=1; i<=nlstate;i++)
-     for(j=1; j<=nlstate;j++)
-       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
-   fprintf(ficresvij,"\n");
-   xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
-   doldm=matrix(1,nlstate,1,nlstate);
-   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
-   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
-   gpp=vector(nlstate+1,nlstate+ndeath);
-   gmp=vector(nlstate+1,nlstate+ndeath);
-   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   if(estepm < stepm){
-     printf ("Problem %d lower than %d\n",estepm, stepm);
-   }
-   else  hstepm=estepm;
-   /* For example we decided to compute the life expectancy with the smallest unit */
-   /* 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 agelim.
-      Look at function hpijx to understand why because of memory size limitations,
-      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
-      means that if the survival funtion is printed every two years of age and if
-      you sum them up and add 1 year (area under the trapezoids) you won't get the same
-      results. So we changed our mind and took the option of the best precision.
-   */
-   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-   agelim = AGESUP;
-   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-     gp=matrix(0,nhstepm,1,nlstate);
-     gm=matrix(0,nhstepm,1,nlstate);
-     for(theta=1; theta <=npar; theta++){
-       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);
-       if (popbased==1) {
-         if(mobilav ==0){
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=probs[(int)age][i][ij];
-         }else{ /* mobilav */
-           for(i=1; i<=nlstate;i++)
-             prlim[i][i]=mobaverage[(int)age][i][ij];
-         }
-       }
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
-       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
-          computed over hstepm matrices product = hstepm*stepm months)
-          as a weighted average of prlim.
-       */
-       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 */
-       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);
-       if (popbased==1) {
+ /************ Variance ******************/
-         if(mobilav ==0){
+  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)
-           for(i=1; i<=nlstate;i++)
+  {
-             prlim[i][i]=probs[(int)age][i][ij];
+    /* Variance of health expectancies */
-         }else{ /* mobilav */
+    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
-           for(i=1; i<=nlstate;i++)
+    /* double **newm;*/
-             prlim[i][i]=mobaverage[(int)age][i][ij];
+    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
-         }
-       }
+    /* int movingaverage(); */
+    double **dnewm,**doldm;
-       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+    double **dnewmp,**doldmp;
+    int i, j, nhstepm, hstepm, h, nstepm ;
-       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
+    int k;
-         for(h=0; h<=nhstepm; h++){
+    double *xp;
-           for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+    double **gp, **gm;  /* for var eij */
-             gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+    double ***gradg, ***trgradg; /*for var eij */
-         }
+    double **gradgp, **trgradgp; /* for var p point j */
-       }
+    double *gpp, *gmp; /* for var p point j */
-       /* This for computing probability of death (h=1 means
+    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
-          computed over hstepm matrices product = hstepm*stepm months)
+    double ***p3mat;
-          as a weighted average of prlim.
+    double age,agelim, hf;
-       */
+    /* double ***mobaverage; */
-       for(j=nlstate+1;j<=nlstate+ndeath;j++){
+    int theta;
-         for(i=1,gmp[j]=0.; i<= nlstate; i++)
+    char digit[4];
-          gmp[j] += prlim[i][i]*p3mat[i][j][1];
+    char digitp[25];
-       }
-       /* end probability of death */
+    char fileresprobmorprev[FILENAMELENGTH];
-       for(j=1; j<= nlstate; j++) /* vareij */
+    if(popbased==1){
-         for(h=0; h<=nhstepm; h++){
+      if(mobilav!=0)
-           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+        strcpy(digitp,"-POPULBASED-MOBILAV_");
-         }
+      else strcpy(digitp,"-POPULBASED-NOMOBIL_");
+    }
-       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+    else
-         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+      strcpy(digitp,"-STABLBASED_");
-       }
-     } /* End theta */
-     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-     for(h=0; h<=nhstepm; h++) /* veij */
-       for(j=1; j<=nlstate;j++)
-         for(theta=1; theta <=npar; theta++)
-           trgradg[h][j][theta]=gradg[h][theta][j];
-     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
-       for(theta=1; theta <=npar; theta++)
-         trgradgp[j][theta]=gradgp[theta][j];
-     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.;
-     for(h=0;h<=nhstepm;h++){
+    /* if (mobilav!=0) { */
-       for(k=0;k<=nhstepm;k++){
+    /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+    /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
-         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+    /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
-         for(i=1;i<=nlstate;i++)
+    /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
-           for(j=1;j<=nlstate;j++)
+    /*   } */
-             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+    /* } */
-       }
-     }
+    strcpy(fileresprobmorprev,"PRMORPREV-");
+    sprintf(digit,"%-d",ij);
+    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+    strcat(fileresprobmorprev,digit); /* Tvar to be done */
+    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+    strcat(fileresprobmorprev,fileresu);
+    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+      printf("Problem with resultfile: %s\n", fileresprobmorprev);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+    }
+    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+    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][j]);
+    }
+    for(j=1;j<=cptcoveff;j++)
+      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
+    fprintf(ficresprobmorprev,"\n");
+    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+      fprintf(ficresprobmorprev," p.%-d SE",j);
+      for(i=1; i<=nlstate;i++)
+        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+    }
+    fprintf(ficresprobmorprev,"\n");
+    fprintf(ficgp,"\n# Routine varevsij");
+    fprintf(ficgp,"\nunset title \n");
+    /* 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 ");
+    if(popbased==1)
+      fprintf(ficresvij,"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(ficresvij,"the age specific period (stable) prevalences in each health state \n");
+    fprintf(ficresvij,"# Age");
+    for(i=1; i<=nlstate;i++)
+      for(j=1; j<=nlstate;j++)
+        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
+    fprintf(ficresvij,"\n");
+    xp=vector(1,npar);
+    dnewm=matrix(1,nlstate,1,npar);
+    doldm=matrix(1,nlstate,1,nlstate);
+    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+    gpp=vector(nlstate+1,nlstate+ndeath);
+    gmp=vector(nlstate+1,nlstate+ndeath);
+    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-     /* pptj */
+    if(estepm < stepm){
-     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+      printf ("Problem %d lower than %d\n",estepm, stepm);
-     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+    }
-     for(j=nlstate+1;j<=nlstate+ndeath;j++)
+    else  hstepm=estepm;
-       for(i=nlstate+1;i<=nlstate+ndeath;i++)
+    /* For example we decided to compute the life expectancy with the smallest unit */
-         varppt[j][i]=doldmp[j][i];
+    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
-     /* end ppptj */
+       nhstepm is the number of hstepm from age to agelim
-     /*  x centered again */
+       nstepm is the number of stepm from age to agelim.
+       Look at function hpijx to understand why because of memory size limitations,
-     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
+       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
-     if (popbased==1) {
+       means that if the survival funtion is printed every two years of age and if
-       if(mobilav ==0){
+       you sum them up and add 1 year (area under the trapezoids) you won't get the same
-         for(i=1; i<=nlstate;i++)
+       results. So we changed our mind and took the option of the best precision.
-           prlim[i][i]=probs[(int)age][i][ij];
+    */
-       }else{ /* mobilav */
+    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-         for(i=1; i<=nlstate;i++)
+    agelim = AGESUP;
-           prlim[i][i]=mobaverage[(int)age][i][ij];
+    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
-       }
+      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-     }
+      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-     /* This for computing probability of death (h=1 means
+      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
-        computed over hstepm (estepm) matrices product = hstepm*stepm months)
+      gp=matrix(0,nhstepm,1,nlstate);
-        as a weighted average of prlim.
+      gm=matrix(0,nhstepm,1,nlstate);
+      for(theta=1; theta <=npar; theta++){
+        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, nres);
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][ij];
+          }
+        }
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
+        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
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim.
+        */
+        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 */
+        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, nres);
+        if (popbased==1) {
+          if(mobilav ==0){
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=probs[(int)age][i][ij];
+          }else{ /* mobilav */
+            for(i=1; i<=nlstate;i++)
+              prlim[i][i]=mobaverage[(int)age][i][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++){
+            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+          }
+        }
+        /* This for computing probability of death (h=1 means
+           computed over hstepm matrices product = hstepm*stepm months)
+           as a weighted average of prlim.
+        */
+        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];
+        }
+        /* end probability of death */
+        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];
+          }
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+        }
+      } /* End theta */
+      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+      for(h=0; h<=nhstepm; h++) /* veij */
+        for(j=1; j<=nlstate;j++)
+          for(theta=1; theta <=npar; theta++)
+            trgradg[h][j][theta]=gradg[h][theta][j];
+      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+        for(theta=1; theta <=npar; theta++)
+          trgradgp[j][theta]=gradgp[theta][j];
+      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.;
+      for(h=0;h<=nhstepm;h++){
+        for(k=0;k<=nhstepm;k++){
+          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+          for(i=1;i<=nlstate;i++)
+            for(j=1;j<=nlstate;j++)
+              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+        }
+      }
+      /* pptj */
+      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++)
+        for(i=nlstate+1;i<=nlstate+ndeath;i++)
+          varppt[j][i]=doldmp[j][i];
+      /* end ppptj */
+      /*  x centered again */
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
+      if (popbased==1) {
+        if(mobilav ==0){
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=probs[(int)age][i][ij];
+        }else{ /* mobilav */
+          for(i=1; i<=nlstate;i++)
+            prlim[i][i]=mobaverage[(int)age][i][ij];
+        }
+      }
+      /* This for computing probability of death (h=1 means
+         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, 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];
+      }
+      /* end probability of death */
+      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+        for(i=1; i<=nlstate;i++){
+          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+        }
+      }
+      fprintf(ficresprobmorprev,"\n");
+      fprintf(ficresvij,"%.0f ",age );
+      for(i=1; i<=nlstate;i++)
+        for(j=1; j<=nlstate;j++){
+          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+        }
+      fprintf(ficresvij,"\n");
+      free_matrix(gp,0,nhstepm,1,nlstate);
+      free_matrix(gm,0,nhstepm,1,nlstate);
+      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+    } /* End age */
+    free_vector(gpp,nlstate+1,nlstate+ndeath);
+    free_vector(gmp,nlstate+1,nlstate+ndeath);
+    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+    /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
+    fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
+    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+    fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
+    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
+    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
+    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
+    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
+    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
+    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
+    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
      */
-     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-     for(j=nlstate+1;j<=nlstate+ndeath;j++){
+    fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-       for(i=1,gmp[j]=0.;i<= nlstate; i++)
-         gmp[j] += prlim[i][i]*p3mat[i][j][1];
-     }
-     /* end probability of death */
-     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
-     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
-       for(i=1; i<=nlstate;i++){
-         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
-       }
-     }
-     fprintf(ficresprobmorprev,"\n");
-     fprintf(ficresvij,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
-       for(j=1; j<=nlstate;j++){
-         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
-       }
-     fprintf(ficresvij,"\n");
-     free_matrix(gp,0,nhstepm,1,nlstate);
-     free_matrix(gm,0,nhstepm,1,nlstate);
-     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
-     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
-     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-   } /* End age */
-   free_vector(gpp,nlstate+1,nlstate+ndeath);
-   free_vector(gmp,nlstate+1,nlstate+ndeath);
-   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
-   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-   /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
-   fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
-   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
-   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-   fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
- /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
- /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
-   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
-   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
- */
- /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
-   fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
-   free_vector(xp,1,npar);
+    free_vector(xp,1,npar);
-   free_matrix(doldm,1,nlstate,1,nlstate);
+    free_matrix(doldm,1,nlstate,1,nlstate);
-   free_matrix(dnewm,1,nlstate,1,npar);
+    free_matrix(dnewm,1,nlstate,1,npar);
-   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
-   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   fclose(ficresprobmorprev);
+    fclose(ficresprobmorprev);
-   fflush(ficgp);
+    fflush(ficgp);
-   fflush(fichtm);
+    fflush(fichtm);
- }  /* end varevsij */
+  }  /* 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 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[], 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);*/
- Line 4523  void cvevsij(double ***eij, double x[],
+ Line 5946  void cvevsij(double ***eij, double x[],
    pstamp(ficresvpl);
    fprintf(ficresvpl,"# Standard deviation of period (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");
- Line 4550  void cvevsij(double ***eij, double x[],
+ Line 5975  void cvevsij(double ***eij, double x[],
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
        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
-         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];
- Line 4560  void cvevsij(double ***eij, double x[],
+ Line 5985  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 )
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        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 4609  void cvevsij(double ***eij, double x[],
+ Line 6034  void cvevsij(double ***eij, double x[],
        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      fprintf(ficresvpl,"%.0f ",age );
+     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]));
      fprintf(ficresvpl,"\n");
- Line 4628  void cvevsij(double ***eij, double x[],
+ Line 6055  void cvevsij(double ***eij, double x[],
  /************ Variance of one-step probabilities  ******************/
  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
- {
+  {
-   int i, j=0,  k1, l1, tj;
+    int i, j=0,  k1, l1, tj;
-   int k2, l2, j1,  z1;
+    int k2, l2, j1,  z1;
-   int k=0, l;
+    int k=0, l;
-   int first=1, first1, first2;
+    int first=1, first1, first2;
-   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
-   double **dnewm,**doldm;
+    double **dnewm,**doldm;
-   double *xp;
+    double *xp;
-   double *gp, *gm;
+    double *gp, *gm;
-   double **gradg, **trgradg;
+    double **gradg, **trgradg;
-   double **mu;
+    double **mu;
-   double age, cov[NCOVMAX+1];
+    double age, cov[NCOVMAX+1];
-   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
-   int theta;
+    int theta;
-   char fileresprob[FILENAMELENGTH];
+    char fileresprob[FILENAMELENGTH];
-   char fileresprobcov[FILENAMELENGTH];
+    char fileresprobcov[FILENAMELENGTH];
-   char fileresprobcor[FILENAMELENGTH];
+    char fileresprobcor[FILENAMELENGTH];
-   double ***varpij;
+    double ***varpij;
-   strcpy(fileresprob,"PROB_");
+    strcpy(fileresprob,"PROB_");
-   strcat(fileresprob,fileres);
+    strcat(fileresprob,fileres);
-   if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprob);
+      printf("Problem with resultfile: %s\n", fileresprob);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
-   }
+    }
-   strcpy(fileresprobcov,"PROBCOV_");
+    strcpy(fileresprobcov,"PROBCOV_");
-   strcat(fileresprobcov,fileresu);
+    strcat(fileresprobcov,fileresu);
-   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobcov);
+      printf("Problem with resultfile: %s\n", fileresprobcov);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
-   }
+    }
-   strcpy(fileresprobcor,"PROBCOR_");
+    strcpy(fileresprobcor,"PROBCOR_");
-   strcat(fileresprobcor,fileresu);
+    strcat(fileresprobcor,fileresu);
-   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
-     printf("Problem with resultfile: %s\n", fileresprobcor);
+      printf("Problem with resultfile: %s\n", fileresprobcor);
-     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
-   }
+    }
-   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
-   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
-   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
-   pstamp(ficresprob);
+    pstamp(ficresprob);
-   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
-   fprintf(ficresprob,"# Age");
+    fprintf(ficresprob,"# Age");
-   pstamp(ficresprobcov);
+    pstamp(ficresprobcov);
-   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
-   fprintf(ficresprobcov,"# Age");
+    fprintf(ficresprobcov,"# Age");
-   pstamp(ficresprobcor);
+    pstamp(ficresprobcor);
-   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
-   fprintf(ficresprobcor,"# Age");
+    fprintf(ficresprobcor,"# Age");
-   for(i=1; i<=nlstate;i++)
+    for(i=1; i<=nlstate;i++)
-     for(j=1; j<=(nlstate+ndeath);j++){
+      for(j=1; j<=(nlstate+ndeath);j++){
-       fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
-       fprintf(ficresprobcov," p%1d-%1d ",i,j);
+        fprintf(ficresprobcov," p%1d-%1d ",i,j);
-       fprintf(ficresprobcor," p%1d-%1d ",i,j);
+        fprintf(ficresprobcor," p%1d-%1d ",i,j);
-     }
+      }
-  /* fprintf(ficresprob,"\n");
+    /* fprintf(ficresprob,"\n");
-   fprintf(ficresprobcov,"\n");
+       fprintf(ficresprobcov,"\n");
-   fprintf(ficresprobcor,"\n");
+       fprintf(ficresprobcor,"\n");
-  */
+    */
-   xp=vector(1,npar);
+    xp=vector(1,npar);
-   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
-   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
-   first=1;
+    first=1;
-   fprintf(ficgp,"\n# Routine varprob");
+    fprintf(ficgp,"\n# Routine varprob");
-   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
-   fprintf(fichtm,"\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.</li>\n",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,"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 \
+    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.\
   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
-   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
  standard deviations wide on each axis. <br>\
- Line 4715  standard deviations wide on each axis. <
+ Line 6142  standard deviations wide on each axis. <
   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-   cov[1]=1;
+    cov[1]=1;
-   /* tj=cptcoveff; */
+    /* tj=cptcoveff; */
-   tj = (int) pow(2,cptcoveff);
+    tj = (int) pow(2,cptcoveff);
-   if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
-   j1=0;
+    j1=0;
-   for(j1=1; j1<=tj;j1++){
+    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/
-     /*for(i1=1; i1<=ncodemax[t];i1++){ */
+      if  (cptcovn>0) {
-     /*j1++;*/
+        fprintf(ficresprob, "\n#********** Variable ");
-       if  (cptcovn>0) {
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         fprintf(ficresprob, "\n#********** Variable ");
+        fprintf(ficresprob, "**********\n#\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        fprintf(ficresprobcov, "\n#********** Variable ");
-         fprintf(ficresprob, "**********\n#\n");
+        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         fprintf(ficresprobcov, "\n#********** Variable ");
+        fprintf(ficresprobcov, "**********\n#\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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)]);
-         fprintf(ficgp, "\n#********** Variable ");
+        fprintf(ficgp, "**********\n#\n");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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)]);
-         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");
+        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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)]);
-         fprintf(ficresprobcor, "\n#********** Variable ");
+        fprintf(ficresprobcor, "**********\n#");
-         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+        if(invalidvarcomb[j1]){
-         fprintf(ficresprobcor, "**********\n#");
+          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
-       }
+          fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
+          continue;
-       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+        }
-       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+      }
-       gp=vector(1,(nlstate)*(nlstate+ndeath));
+      gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
-       gm=vector(1,(nlstate)*(nlstate+ndeath));
+      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
-       for (age=bage; age<=fage; age ++){
+      gp=vector(1,(nlstate)*(nlstate+ndeath));
-         cov[2]=age;
+      gm=vector(1,(nlstate)*(nlstate+ndeath));
-         if(nagesqr==1)
+      for (age=bage; age<=fage; age ++){
-           cov[3]= age*age;
+        cov[2]=age;
-         for (k=1; k<=cptcovn;k++) {
+        if(nagesqr==1)
-           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
+          cov[3]= age*age;
-           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
+        for (k=1; k<=cptcovn;k++) {
-                                                          * 1  1 1 1 1
+          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
-                                                          * 2  2 1 1 1
+          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
-                                                          * 3  1 2 1 1
+                                                                     * 1  1 1 1 1
-                                                          */
+                                                                     * 2  2 1 1 1
-           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
+                                                                     * 3  1 2 1 1
-         }
+                                                                     */
-         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
-         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+        }
-         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++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+        for (k=1; k<=cptcovprod;k++)
+          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
-         for(theta=1; theta <=npar; theta++){
-           for(i=1; i<=npar; i++)
-             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
+        for(theta=1; theta <=npar; theta++){
+          for(i=1; i<=npar; i++)
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+            xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-           k=0;
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-           for(i=1; i<= (nlstate); i++){
-             for(j=1; j<=(nlstate+ndeath);j++){
+          k=0;
-               k=k+1;
+          for(i=1; i<= (nlstate); i++){
-               gp[k]=pmmij[i][j];
+            for(j=1; j<=(nlstate+ndeath);j++){
-             }
+              k=k+1;
-           }
+              gp[k]=pmmij[i][j];
+            }
-           for(i=1; i<=npar; i++)
+          }
-             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
+          for(i=1; i<=npar; i++)
-           pmij(pmmij,cov,ncovmodel,xp,nlstate);
+            xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-           k=0;
-           for(i=1; i<=(nlstate); i++){
+          pmij(pmmij,cov,ncovmodel,xp,nlstate);
-             for(j=1; j<=(nlstate+ndeath);j++){
+          k=0;
-               k=k+1;
+          for(i=1; i<=(nlstate); i++){
-               gm[k]=pmmij[i][j];
+            for(j=1; j<=(nlstate+ndeath);j++){
-             }
+              k=k+1;
-           }
+              gm[k]=pmmij[i][j];
+            }
-           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+          }
-             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-         }
+          for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+            gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
-         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+        }
-           for(theta=1; theta <=npar; theta++)
-             trgradg[j][theta]=gradg[theta][j];
-         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-         pmij(pmmij,cov,ncovmodel,x,nlstate);
-         k=0;
-         for(i=1; i<=(nlstate); i++){
-           for(j=1; j<=(nlstate+ndeath);j++){
-             k=k+1;
-             mu[k][(int) age]=pmmij[i][j];
-           }
-         }
-         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-             varpij[i][j][(int)age] = doldm[i][j];
-         /*printf("\n%d ",(int)age);
-           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
-           }*/
-         fprintf(ficresprob,"\n%d ",(int)age);
-         fprintf(ficresprobcov,"\n%d ",(int)age);
-         fprintf(ficresprobcor,"\n%d ",(int)age);
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
-           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
-         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
-           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
-         }
-         i=0;
-         for (k=1; k<=(nlstate);k++){
-           for (l=1; l<=(nlstate+ndeath);l++){
-             i++;
-             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
-             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
-             for (j=1; j<=i;j++){
-               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
-               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
-               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
-             }
-           }
-         }/* end of loop for state */
-       } /* end of loop for age */
-       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
-       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
-       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-       /* Confidence intervalle of pij  */
-       /*
-         fprintf(ficgp,"\nunset parametric;unset label");
-         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
-         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
-         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
-         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
-         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
-       */
-       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
-       first1=1;first2=2;
-       for (k2=1; k2<=(nlstate);k2++){
-         for (l2=1; l2<=(nlstate+ndeath);l2++){
-           if(l2==k2) continue;
-           j=(k2-1)*(nlstate+ndeath)+l2;
-           for (k1=1; k1<=(nlstate);k1++){
-             for (l1=1; l1<=(nlstate+ndeath);l1++){
-               if(l1==k1) continue;
-               i=(k1-1)*(nlstate+ndeath)+l1;
-               if(i<=j) continue;
-               for (age=bage; age<=fage; age ++){
-                 if ((int)age %5==0){
-                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
-                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
-                   mu1=mu[i][(int) age]/stepm*YEARM ;
-                   mu2=mu[j][(int) age]/stepm*YEARM;
-                   c12=cv12/sqrt(v1*v2);
-                   /* Computing eigen value of matrix of covariance */
-                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
-                   if ((lc2 <0) || (lc1 <0) ){
-                     if(first2==1){
-                       first1=0;
-                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
-                     }
-                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
-                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
-                     /* lc2=fabs(lc2); */
-                   }
-                   /* Eigen vectors */
+        for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
-                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+          for(theta=1; theta <=npar; theta++)
-                   /*v21=sqrt(1.-v11*v11); *//* error */
+            trgradg[j][theta]=gradg[theta][j];
-                   v21=(lc1-v1)/cv12*v11;
-                   v12=-v21;
+        matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
-                   v22=v11;
+        matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
-                   tnalp=v21/v11;
-                   if(first1==1){
+        pmij(pmmij,cov,ncovmodel,x,nlstate);
-                     first1=0;
-                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+        k=0;
-                   }
+        for(i=1; i<=(nlstate); i++){
-                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+          for(j=1; j<=(nlstate+ndeath);j++){
-                   /*printf(fignu*/
+            k=k+1;
-                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+            mu[k][(int) age]=pmmij[i][j];
-                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+          }
-                   if(first==1){
+        }
-                     first=0;
+        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
-                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
+          for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
-                     fprintf(ficgp,"\nset parametric;unset label");
+            varpij[i][j][(int)age] = doldm[i][j];
-                     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");
+        /*printf("\n%d ",(int)age);
-                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
-  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
+          printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+          fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+          }*/
+        fprintf(ficresprob,"\n%d ",(int)age);
+        fprintf(ficresprobcov,"\n%d ",(int)age);
+        fprintf(ficresprobcor,"\n%d ",(int)age);
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+          fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+        for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+          fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+          fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+        }
+        i=0;
+        for (k=1; k<=(nlstate);k++){
+          for (l=1; l<=(nlstate+ndeath);l++){
+            i++;
+            fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+            fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+            for (j=1; j<=i;j++){
+              /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
+              fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+              fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+            }
+          }
+        }/* end of loop for state */
+      } /* end of loop for age */
+      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+      /* Confidence intervalle of pij  */
+      /*
+        fprintf(ficgp,"\nunset parametric;unset label");
+        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+        fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+        fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+      */
+      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+      first1=1;first2=2;
+      for (k2=1; k2<=(nlstate);k2++){
+        for (l2=1; l2<=(nlstate+ndeath);l2++){
+          if(l2==k2) continue;
+          j=(k2-1)*(nlstate+ndeath)+l2;
+          for (k1=1; k1<=(nlstate);k1++){
+            for (l1=1; l1<=(nlstate+ndeath);l1++){
+              if(l1==k1) continue;
+              i=(k1-1)*(nlstate+ndeath)+l1;
+              if(i<=j) continue;
+              for (age=bage; age<=fage; age ++){
+                if ((int)age %5==0){
+                  v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+                  v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+                  mu1=mu[i][(int) age]/stepm*YEARM ;
+                  mu2=mu[j][(int) age]/stepm*YEARM;
+                  c12=cv12/sqrt(v1*v2);
+                  /* Computing eigen value of matrix of covariance */
+                  lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+                  if ((lc2 <0) || (lc1 <0) ){
+                    if(first2==1){
+                      first1=0;
+                      printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+                    }
+                    fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+                    /* lc1=fabs(lc1); */ /* If we want to have them positive */
+                    /* lc2=fabs(lc2); */
+                  }
+                  /* Eigen vectors */
+                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                  /*v21=sqrt(1.-v11*v11); *//* error */
+                  v21=(lc1-v1)/cv12*v11;
+                  v12=-v21;
+                  v22=v11;
+                  tnalp=v21/v11;
+                  if(first1==1){
+                    first1=0;
+                    printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                  }
+                  fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+                  /*printf(fignu*/
+                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+                  /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+                  if(first==1){
+                    first=0;
+                    fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
+                    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>\
+  :<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,\
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
-                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                    fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+                    fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
-                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+                    fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+                    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,"\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",\
+                    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(lc1),v12,sqrt(lc2),                                                                         \
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-                   }else{
+                  }else{
-                     first=0;
+                    first=0;
-                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
+                    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,"\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,"\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",\
+                    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(lc2),                                 \
-                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
-                   }/* if first */
+                  }/* if first */
-                 } /* age mod 5 */
+                } /* age mod 5 */
-               } /* end loop age */
+              } /* end loop age */
-               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
+              fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
-               first=1;
+              first=1;
-             } /*l12 */
+            } /*l12 */
-           } /* k12 */
+          } /* k12 */
-         } /*l1 */
+        } /*l1 */
-       }/* k1 */
+      }/* k1 */
-       /* } */ /* loop covariates */
+    }  /* loop on combination of covariates j1 */
-   }
+    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
-   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(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
-   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
-   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
+    free_vector(xp,1,npar);
-   free_vector(xp,1,npar);
+    fclose(ficresprob);
-   fclose(ficresprob);
+    fclose(ficresprobcov);
-   fclose(ficresprobcov);
+    fclose(ficresprobcor);
-   fclose(ficresprobcor);
+    fflush(ficgp);
-   fflush(ficgp);
+    fflush(fichtmcov);
-   fflush(fichtmcov);
+  }
- }
  /******************* Printing html file ***********/
  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 estepm ,          \
+                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                    double jprev2, double mprev2,double anprev2, double dateprev2){
-   int jj1, k1, i1, cpt;
+   int jj1, k1, i1, cpt, k4, nres;
     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"));
- Line 4984  void printinghtml(char fileresu[], char
+ Line 6414  void printinghtml(char fileresu[], char
   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
             stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
     fprintf(fichtm,"\
+  - 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",
             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
     fprintf(fichtm,"\
+  - Period (stable) back 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): \
     <a href=\"%s\">%s</a> <br>\n",
             estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
- Line 4996  void printinghtml(char fileresu[], char
+ Line 6432  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>");
+    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+    m=pow(2,cptcoveff);
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    jj1=0;
-  m=pow(2,cptcoveff);
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
-  jj1=0;
+      /* for(i1=1; i1<=ncodemax[k1];i1++){ */
-  for(k1=1; k1<=m;k1++){
-    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         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\">");
+        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);
+          continue;
+        }
       }
       /* 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,\
+  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. Or probability to survive 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> \
- <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,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.\
-  Or probability to survive in various states (1 to %d) being in state %d at different ages.\
+  Or probability to survive in various states (1 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> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
       }
       /* Period (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 to be in state %d some years earlier, knowing that we will be in state (1 to %d) at different 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,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
       }
-     if(prevfcast==1){
+      if(backcast==1){
-       /* Projection of prevalence up to period (stable) prevalence in each health state */
+        /* Period (stable) back prevalence in each health state */
-       for(cpt=1; cpt<=nlstate;cpt++){
+        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- Convergence to mixed (stable) back prevalence in state %d. Or probability to be in state %d at a younger age, knowing that we will be 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\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),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 */
+        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) 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-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+ <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),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> <br> \
- <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
       }
-    /* } /\* end i1 *\/ */
+      /* } /\* end i1 *\/ */
-  }/* End k1 */
+    }/* End k1 */
-  fprintf(fichtm,"</ul>");
+    fprintf(fichtm,"</ul>");
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
- Line 5069  variances but at the covariance matrix.
+ Line 6530  variances but at the covariance matrix.
  covariance matrix of the one-step probabilities. \
  See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
-  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+    fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
+            subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
+            subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
-          subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
+            subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
     <a href=\"%s\">%s</a> <br>\n</li>",
             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
     <a href=\"%s\">%s</a> <br>\n</li>",
             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
-  fprintf(fichtm,"\
+    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",
-          estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
+            estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
-  fprintf(fichtm,"\
+    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_"));
+            estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
-  fprintf(fichtm,"\
+    fprintf(fichtm,"\
   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
-          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+            subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- Line 5102  See page 'Matrix of variance-covariance
+ Line 6563  See page 'Matrix of variance-covariance
  /*      <br>",fileres,fileres,fileres,fileres); */
  /*  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);
+    fflush(fichtm);
-  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-  m=pow(2,cptcoveff);
+    m=pow(2,cptcoveff);
-  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-  jj1=0;
+    jj1=0;
-  for(k1=1; k1<=m;k1++){
-    /* for(i1=1; i1<=ncodemax[k1];i1++){ */
+    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,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-        for (cpt=1; cpt<=cptcoveff;cpt++)
+        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," 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," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
+          continue;
+        }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"<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 <br>\
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
- <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,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) \
  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<br>\
+  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
- <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
+ <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
-    /* } /\* end i1 *\/ */
+      /* } /\* end i1 *\/ */
-  }/* End k1 */
+    }/* End k1 */
-  fprintf(fichtm,"</ul>");
+   }/* End nres */
-  fflush(fichtm);
+    fprintf(fichtm,"</ul>");
+    fflush(fichtm);
  }
  /******************* Gnuplot file **************/
-     void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
    char dirfileres[132],optfileres[132];
-   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   char gplotcondition[132];
+   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 nres=0; /* Index of resultline */
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
- Line 5150  true period expectancies (those weighted
+ Line 6630  true period expectancies (those weighted
    /*#ifdef windows */
    fprintf(ficgp,"cd \"%s\" \n",pathc);
-     /*#endif */
+   /*#endif */
    m=pow(2,cptcoveff);
    /* 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");
+   fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
-     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
+   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
-     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
+   /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
-     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
+   fprintf(ficgp,"\nset ter pngcairo size 640, 480");
  /* nice for mle=4 plot by number of matrix products.
     replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
  /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
-     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
+   /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
-     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
+   fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
-     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
+   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
-     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
+   fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
-     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
+   fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
-     for (i=1; i<= nlstate ; i ++) {
+   for (i=1; i<= nlstate ; i ++) {
-       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
+     fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
-       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
+     fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
-       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
+     fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
-       for (j=2; j<= nlstate+ndeath ; j ++) {
+     for (j=2; j<= nlstate+ndeath ; j ++) {
-         fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
+       fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
-       }
+     }
-       fprintf(ficgp,";\nset out; unset ylabel;\n");
+     fprintf(ficgp,";\nset out; unset ylabel;\n");
-     }
+   }
-     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
+   /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
-     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
+   /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
-     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
+   /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
-     fprintf(ficgp,"\nset out;unset log\n");
+   fprintf(ficgp,"\nset out;unset log\n");
-     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
+   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
-  /* 1eme*/
+   /* 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 ; k1 ++) { /* For each 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 and each value */
+         if(m != 1 && TKresult[nres]!= k1)
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number 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: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
-         vlv= nbcode[Tvaraff[lv]][lv];
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         fprintf(ficgp," V%d=%d ",k,vlv);
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
-       }
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       fprintf(ficgp,"\n#\n");
+           /* 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 */
-      fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-      fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
+           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-      fprintf(ficgp,"set xlabel \"Age\" \n\
+           /* printf(" V%d=%d ",Tvaraff[k],vlv); */
- set ylabel \"Probability\" \n\
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
- set ter svg size 640, 480\n\
+         }
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
-      for (i=1; i<= nlstate ; i ++) {
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         }
-        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 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);
-      }
+         /* 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 ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
-      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
+       /* k1-1 error should be nres-1*/
-      fprintf(ficgp,"\nset out \n");
+         for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else        fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         fprintf(ficgp,"\" t\"Period (stable) 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));
+         if(backcast==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 */
+               /* 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];
+               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]][lv]);
+                 kl++;
+               }
+             } /* end covariate */
+           } /* end if no covariate */
+         } /* end if backcast */
+         fprintf(ficgp,"\nset out \n");
+       } /* nres */
      } /* k1 */
    } /* cpt */
    /*2 eme*/
-   for (k1=1; k1<= m ; k1 ++) {
+   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 ");
        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[lv]][lv];
+         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",k,vlv);
+         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        }
-       fprintf(ficgp,"\n#\n");
+       /* for(k=1; k <= ncovds; k++){ */
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       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+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-       } /* state */
-     } /* vpopbased */
-     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-   } /* k1 */
-   /*3eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[lv]][lv];
-         fprintf(ficgp," V%d=%d ",k,vlv);
        }
        fprintf(ficgp,"\n#\n");
+       if(invalidvarcomb[k1]){
-       /*       k=2+nlstate*(2*cpt-2); */
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       k=2+(nlstate+1)*(cpt-1);
+         continue;
-       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
+       }
-       fprintf(ficgp,"set ter svg size 640, 480\n\
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+         if(vpopbased==0)
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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 ++) {
+           k=2*i;
+           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);
+           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; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
+     } /* end nres */
+   } /* k1 end 2 eme*/
-       */
-       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(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-       }
+   /*3eme*/
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
+   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 ++) {
+         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%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);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         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 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 ++) {
+           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.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
+       }
+     } /* 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 (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
+       if(m != 1 && TKresult[nres]!= k1)
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         continue;
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         vlv= nbcode[Tvaraff[lv]][lv];
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         fprintf(ficgp," V%d=%d ",k,vlv);
+           /* 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 */
-       fprintf(ficgp,"\n#\n");
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+         }
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
- set ter svg size 640, 480\n\
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
- unset log y\n\
+         }
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         fprintf(ficgp,"\n#\n");
-       k=3;
+         if(invalidvarcomb[k1]){
-       for (i=1; i<= nlstate ; i ++){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         if(i==1)
+           continue;
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         }
-         else
-           fprintf(ficgp,", '' ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
-         l=(nlstate+ndeath)*(i-1)+1;
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
-         for (j=2; j<= nlstate+ndeath ; j ++)
+         k=3;
-           fprintf(ficgp,"+$%d",k+l+j-1);
+         for (i=1; i<= nlstate ; i ++){
-         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+           if(i==1){
-       } /* nlstate */
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-       fprintf(ficgp,"\nset out\n");
+           }else{
-     } /* end cpt state*/
+             fprintf(ficgp,", '' ");
-   } /* end covariate */
+           }
+           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\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 */
-       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);
+       if(m != 1 && TKresult[nres]!= k1)
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+         continue;
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         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);
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         vlv= nbcode[Tvaraff[lv]][lv];
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         fprintf(ficgp," V%d=%d ",k,vlv);
+           /* 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 */
-       fprintf(ficgp,"\n#\n");
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+         }
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
- set ter svg size 640, 480\n\
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
- unset log y\n\
+         }
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         fprintf(ficgp,"\n#\n");
-       k=3;
+         if(invalidvarcomb[k1]){
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         if(j==1)
+           continue;
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+         }
-         else
-           fprintf(ficgp,", '' ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
-         l=(nlstate+ndeath)*(cpt-1) +j;
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
-         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
-         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+         k=3;
-         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+           if(j==1)
-       } /* nlstate */
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-       fprintf(ficgp,", '' ");
+           else
-       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+             fprintf(ficgp,", '' ");
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           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);
-         if(j < nlstate)
+           /* for (i=2; i<= nlstate+ndeath ; i ++) */
-           fprintf(ficgp,"$%d +",k+l);
+           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-         else
+           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         } /* nlstate */
-       }
+         fprintf(ficgp,", '' ");
-       fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-     } /* end cpt state*/
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-   } /* end covariate */
+           l=(nlstate+ndeath)*(cpt-1) +j;
+           if(j < nlstate)
+             fprintf(ficgp,"$%d +",k+l);
+           else
+             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         }
+         fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* 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)
+       continue;
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): '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 */
          /* 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[lv]][lv];
+         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",k,vlv);
+         fprintf(ficgp," 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][k4]);
+       }
        fprintf(ficgp,"\n#\n");
+       if(invalidvarcomb[k1]){
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
+         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         continue;
+       }
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
        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);
- Line 5420  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7002  plot [%.f:%.f]  ", ageminpar, agemaxpar)
        fprintf(ficgp,"\nset out\n");
      } /* end cpt state*/
    } /* end covariate */
+ /* 7eme */
+   if(backcast == 1){
+     /* CV back preval stable (period) 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 ending state */
+         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): '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 */
+           /* 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);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         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-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3; /* Offset */
+         for (i=1; i<= nlstate ; i ++){ /* State of origin */
+           if(i==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+           else
+             fprintf(ficgp,", '' ");
+           /* l=(nlstate+ndeath)*(i-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+(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);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if backcast */
+   /* 8eme */
    if(prevfcast==1){
-   /* Projection from cross-sectional to stable (period) for each covariate */
+     /* Projection from cross-sectional to 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(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);
          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
- Line 5432  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7069  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            /* 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[lv]][lv];
+           vlv= nbcode[Tvaraff[k]][lv];
-           fprintf(ficgp," V%d=%d ",k,vlv);
+           fprintf(ficgp," 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][k4]);
+         }
          fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
          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 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 */
            /*#  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 */
- Line 5454  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7096  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              fprintf(ficgp,",\\\n '' ");
            }
            if(cptcoveff ==0){ /* No covariate */
-             fprintf(ficgp," u 2:("); /* Age is in 2 */
+             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)) t 'p.%d' with line ", \
+               fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
-+(cpt-1)*(nlstate+1)+1+(i-1),  2+1+(i-1)+(nlstate+1)*nlstate,cpt );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
              else
-               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
-+(cpt-1)*(nlstate+1)+1+(i-1),  2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-           }else{
+           }else{ /* more than 2 covariates */
-             fprintf(ficgp,"u 6:(("); /* Age is in 6 */
+             if(cptcoveff ==1){
-             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+               ioffset=4; /* Age is in 4 */
-             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             }else{
+               ioffset=6; /* Age is in 6 */
+               /*#  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 */
+             }
+             fprintf(ficgp," u %d:(",ioffset);
              kl=0;
-             for (k=1; k<=cptcoveff; k++){    /* For each covariate  */
+             strcpy(gplotcondition,"(");
-               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+             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 */
                /* 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[lv]][lv];
+               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of 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 *\/ */
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
-               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+               kl++;
-               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+               if(k <cptcoveff && cptcoveff>1)
-               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
-               if(k==cptcoveff)
+             }
-                 if(i==nlstate+1)
+             strcpy(gplotcondition+strlen(gplotcondition),")");
-                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
+             /* 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 *\/ */
-+(cpt-1)*(nlstate+1)+1+(i-1),  6+1+(i-1)+(nlstate+1)*nlstate,cpt );
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
-                 else
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
-                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
+             /* ''  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*/
-+(cpt-1)*(nlstate+1)+1+(i-1),  6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+             if(i==nlstate+1){
-               else{
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
-                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-                 kl++;
+             }else{
-               }
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
-             } /* end covariate */
+                       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");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if prevfcast */
-   /* proba elementaires */
+   /* 9eme writing MLE parameters */
-   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
+   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 5513  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7165  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          fprintf(ficgp,"\n");
        }
      }
-    }
+   }
    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 5531  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7184  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
    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*/
+   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,"#   jk=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(jk=1; jk <=m; jk++)  /* For each combination of covariate */
-        fprintf(ficgp,"\nset ter svg size 640, 480 ");
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-        if (ng==1){
+       if(m != 1 && TKresult[nres]!= jk)
-          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
+         continue;
-          fprintf(ficgp,"\nunset log y");
+       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
-        }else if (ng==2){
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-          fprintf(ficgp,"\nset log y");
+       }
-        }else if (ng==3){
+       fprintf(ficgp,"\n#\n");
-          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);
-          fprintf(ficgp,"\nset log y");
+       fprintf(ficgp,"\nset ter svg size 640, 480 ");
-        }else
+       if (ng==1){
-          fprintf(ficgp,"\nunset title ");
+         fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
-        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
+         fprintf(ficgp,"\nunset log y");
-        i=1;
+       }else if (ng==2){
-        for(k2=1; k2<=nlstate; k2++) {
+         fprintf(ficgp,"\nset ylabel \"Probability\"\n");
-          k3=i;
+         fprintf(ficgp,"\nset log y");
-          for(k=1; k<=(nlstate+ndeath); k++) {
+       }else if (ng==3){
-            if (k != k2){
+         fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
-              switch( ng) {
+         fprintf(ficgp,"\nset log y");
-              case 1:
+       }else
-                if(nagesqr==0)
+         fprintf(ficgp,"\nunset title ");
-                  fprintf(ficgp," p%d+p%d*x",i,i+1);
+       fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
-                else /* nagesqr =1 */
+       i=1;
-                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+       for(k2=1; k2<=nlstate; k2++) {
-                break;
+         k3=i;
-              case 2: /* ng=2 */
+         for(k=1; k<=(nlstate+ndeath); k++) {
-                if(nagesqr==0)
+           if (k != k2){
-                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+             switch( ng) {
-                else /* nagesqr =1 */
+             case 1:
-                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
+               if(nagesqr==0)
-                break;
+                 fprintf(ficgp," p%d+p%d*x",i,i+1);
-              case 3:
+               else /* nagesqr =1 */
-                if(nagesqr==0)
+                 fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+               break;
-                else /* nagesqr =1 */
+             case 2: /* ng=2 */
-                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
+               if(nagesqr==0)
-                break;
+                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-              }
+               else /* nagesqr =1 */
-              ij=1;/* To be checked else nbcode[0][0] wrong */
+                 fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
-              for(j=3; j <=ncovmodel-nagesqr; j++) {
+               break;
-                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
+             case 3:
-                if(ij <=cptcovage) { /* Bug valgrind */
+               if(nagesqr==0)
-                  if((j-2)==Tage[ij]) { /* Bug valgrind */
+                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
-                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+               else /* nagesqr =1 */
-                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                 fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
-                    ij++;
+               break;
-                  }
+             }
-                }
+             ij=1;/* To be checked else nbcode[0][0] wrong */
-                else
+             ijp=1; /* product no age */
-                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
-              }
+             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
-              if(ng != 1){
+               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
-                fprintf(ficgp,")/(1");
+               if(j==Tage[ij]) { /* Product by age */
+                 if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                for(k1=1; k1 <=nlstate; k1++){
+                   if(DummyV[j]==0){
-                  if(nagesqr==0)
+                     fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
-                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                   }else{ /* quantitative */
-                  else /* nagesqr =1 */
+                     fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
-                    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,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                   }
-                  ij=1;
+                   ij++;
-                  for(j=3; j <=ncovmodel-nagesqr; j++){
+                 }
-                    if(ij <=cptcovage) { /* Bug valgrind */
+               }else if(j==Tprod[ijp]) { /* */
-                      if((j-2)==Tage[ij]) { /* Bug valgrind */
+                 /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
-                        fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                 if(ijp <=cptcovprod) { /* Product */
-                        /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                   if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
-                        ij++;
+                     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(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
-                    }
+                       fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
-                    else
+                     }else{ /* Vn is dummy and Vm is quanti */
-                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                       /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,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]]);
-                  fprintf(ficgp,")");
+                     }
-                }
+                   }else{ /* Vn*Vm Vn is quanti */
-                fprintf(ficgp,")");
+                     if(DummyV[Tvard[ijp][2]]==0){
-                if(ng ==2)
+                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
-                  fprintf(ficgp," t \"p%d%d\" ", k2,k);
+                     }else{ /* Both quanti */
-                else /* ng= 3 */
+                       fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
-                  fprintf(ficgp," t \"i%d%d\" ", k2,k);
+                     }
-              }else{ /* end ng <> 1 */
+                   }
-                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+                   ijp++;
-              }
+                 }
-              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+               } else{  /* simple covariate */
-              i=i+ncovmodel;
+                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */
-            }
+                 if(Dummy[j]==0){
-          } /* end k */
+                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
-        } /* end k2 */
+                 }else{ /* quantitative */
-        fprintf(ficgp,"\n set out\n");
+                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
-      } /* end jk */
+                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
-    } /* end ng */
+                 }
-  /* avoid: */
+               } /* end simple */
-    fflush(ficgp);
+             } /* end j */
+           }else{
+             i=i-ncovmodel;
+             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
+               fprintf(ficgp," (1.");
+           }
+           if(ng != 1){
+             fprintf(ficgp,")/(1");
+             for(k1=1; k1 <=nlstate; k1++){
+               if(nagesqr==0)
+                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*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);
+               ij=1;
+               for(j=3; j <=ncovmodel-nagesqr; j++){
+                 if((j-2)==Tage[ij]) { /* Bug valgrind */
+                   if(ij <=cptcovage) { /* Bug valgrind */
+                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                     /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                     ij++;
+                   }
+                 }
+                 else
+                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
+               }
+               fprintf(ficgp,")");
+             }
+             fprintf(ficgp,")");
+             if(ng ==2)
+               fprintf(ficgp," t \"p%d%d\" ", k2,k);
+             else /* ng= 3 */
+               fprintf(ficgp," t \"i%d%d\" ", k2,k);
+           }else{ /* end ng <> 1 */
+             if( k !=k2) /* logit p11 is hard to draw */
+               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+           }
+           if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
+             fprintf(ficgp,",");
+           if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
+             fprintf(ficgp,",");
+           i=i+ncovmodel;
+         } /* end k */
+       } /* end k2 */
+       fprintf(ficgp,"\n set out\n");
+     } /* end jk */
+   } /* end ng */
+   /* avoid: */
+   fflush(ficgp);
  }  /* end gnuplot */
  /*************** Moving average **************/
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
+ /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
+  int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
-   int i, cpt, cptcod;
-   int modcovmax =1;
+    int i, cpt, cptcod;
-   int mobilavrange, mob;
+    int modcovmax =1;
-   double age;
+    int mobilavrange, mob;
+    int iage=0;
-   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
-                            a covariate has 2 modalities */
+    double sum=0.;
-   if (cptcovn<1) modcovmax=1; /* At least 1 pass */
+    double age;
+    double *sumnewp, *sumnewm;
-   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+    double *agemingood, *agemaxgood; /* Currently identical for all covariates */
-     if(mobilav==1) mobilavrange=5; /* default */
-     else mobilavrange=mobilav;
-     for (age=bage; age<=fage; age++)
+    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
-       for (i=1; i<=nlstate;i++)
+    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
-         for (cptcod=1;cptcod<=modcovmax;cptcod++)
-           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+    sumnewp = vector(1,ncovcombmax);
-     /* We keep the original values on the extreme ages bage, fage and for
+    sumnewm = vector(1,ncovcombmax);
-        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+    agemingood = vector(1,ncovcombmax);
-        we use a 5 terms etc. until the borders are no more concerned.
+    agemaxgood = vector(1,ncovcombmax);
-     */
-     for (mob=3;mob <=mobilavrange;mob=mob+2){
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
+      sumnewm[cptcod]=0.;
-         for (i=1; i<=nlstate;i++){
+      sumnewp[cptcod]=0.;
-           for (cptcod=1;cptcod<=modcovmax;cptcod++){
+      agemingood[cptcod]=0;
-             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
+      agemaxgood[cptcod]=0;
-               for (cpt=1;cpt<=(mob-1)/2;cpt++){
+    }
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
+    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
-                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
-               }
+    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
+      if(mobilav==1) mobilavrange=5; /* default */
-           }
+      else mobilavrange=mobilav;
-         }
+      for (age=bage; age<=fage; age++)
-       }/* end age */
+        for (i=1; i<=nlstate;i++)
-     }/* end mob */
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
-   }else return -1;
+            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
-   return 0;
+      /* We keep the original values on the extreme ages bage, fage and for
- }/* End movingaverage */
+         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
+         we use a 5 terms etc. until the borders are no more concerned.
+      */
+      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++){
+              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;
+            }
+          }
+        }/* end age */
+      }/* end mob */
+    }else
+      return -1;
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+      /* 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; age--){/* From oldest to youngest, finding the youngest wrong */
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        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 */
+      }/* 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.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+          agemaxgood[cptcod]=age;
+        }else{ /* bad */
+          for (i=1; i<=nlstate;i++){
+            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+          } /* i */
+        } /* end bad */
+      }/* age */
+      sum=0.;
+      for (i=1; i<=nlstate;i++){
+        sum+=mobaverage[(int)agemaxgood[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 ascending age!\n",cptcod);
+        /* for (i=1; i<=nlstate;i++){ */
+        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        /* } /\* i *\/ */
+      } /* end bad */
+      for (age=bage; age<=fage; age++){
+        /* printf("%d %d ", cptcod, (int)age); */
+        sumnewp[cptcod]=0.;
+        sumnewm[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewp[cptcod]+=probs[(int)age][i][cptcod];
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
+        }
+        /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
+      }
+      /* printf("\n"); */
+      /* } */
+      /* brutal averaging */
+      for (i=1; i<=nlstate;i++){
+        for (age=1; age<=bage; age++){
+          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]); */
+        }
+        for (age=fage; age<=AGESUP; age++){
+          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]); */
+        }
+      } /* end i status */
+      for (i=nlstate+1; i<=nlstate+ndeath;i++){
+        for (age=1; age<=AGESUP; age++){
+          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
+          mobaverage[(int)age][i][cptcod]=0.;
+        }
+      }
+    }/* end cptcod */
+    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
+    free_vector(agemaxgood,1, ncovcombmax);
+    free_vector(agemingood,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 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){
    /* proj1, year, month, day of starting projection
       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;
+    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 *popeffectif,*popcount;
    double ***p3mat;
-   double ***mobaverage;
+   /* double ***mobaverage; */
    char fileresf[FILENAMELENGTH];
    agelim=AGESUP;
- Line 5696  void prevforecast(char fileres[], double
+ Line 7512  void prevforecast(char fileres[], double
    */
    /* 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(fileresf,"F_");
    strcat(fileresf,fileresu);
- Line 5704  void prevforecast(char fileres[], double
+ Line 7519  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' \n", fileresf);
+   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
    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;
- Line 5735  void prevforecast(char fileres[], double
+ Line 7543  void prevforecast(char fileres[], double
    if(jprojmean==0) jprojmean=1;
    if(mprojmean==0) jprojmean=1;
-   i1=cptcoveff;
+   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,"#****** Routine prevforecast **\n");
  /*            if (h==(int)(YEARM*yearp)){ */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   for(k=1; k<=i1;k++){
-       k=k+1;
+     if(i1 != 1 && TKresult[nres]!= k)
-       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+       continue;
-       for(j=1;j<=cptcoveff;j++) {
+     if(invalidvarcomb[k]){
-         fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
-       }
+       continue;
-       fprintf(ficresf," yearproj age");
+     }
-       for(j=1; j<=nlstate+ndeath;j++){
+     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
-         for(i=1; i<=nlstate;i++)
+     for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficresf," p%d%d",i,j);
+       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficresf," p.%d",j);
+     }
-       }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         fprintf(ficresf,"\n");
+     }
-         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+     fprintf(ficresf," yearproj age");
+     for(j=1; j<=nlstate+ndeath;j++){
-         for (agec=fage; agec>=(ageminpar-1); agec--){
+       for(i=1; i<=nlstate;i++)
-           nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+         fprintf(ficresf," p%d%d",i,j);
-           nhstepm = nhstepm/hstepm;
+       fprintf(ficresf," wp.%d",j);
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+     }
-           oldm=oldms;savm=savms;
+     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
-           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+       fprintf(ficresf,"\n");
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+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;
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
+         for (h=0; h<=nhstepm; h++){
+           if (h*hstepm/YEARM*stepm ==yearp) {
+             fprintf(ficresf,"\n");
+             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);
+           }
+           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][k];
+               else {
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+               }
+               if (h*hstepm/YEARM*stepm== yearp) {
+                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
+               }
+             } /* end i */
+             if (h*hstepm/YEARM*stepm==yearp) {
+               fprintf(ficresf," %.3f", ppij);
+             }
+           }/* end j */
+         } /* end h */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+     } /* 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 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);  */
+ /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
+ /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
+ /*   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 *\/ */
-           for (h=0; h<=nhstepm; h++){
+ /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
-             if (h*hstepm/YEARM*stepm ==yearp) {
-               fprintf(ficresf,"\n");
+ /*   fclose(ficresfb); */
-               for(j=1;j<=cptcoveff;j++)
+ /*   printf("End of Computing Back forecasting \n"); */
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
-               fprintf(ficresf,"%.f %.f ",anproj1+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(ficresf," %.3f", p3mat[i][j][h]);
-                 }
-               } /* end i */
-               if (h*hstepm/YEARM*stepm==yearp) {
-                 fprintf(ficresf," %.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(ficresf);
- }
  /************** Forecasting *****not tested NB*************/
- void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+ /* 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){ */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
-   int *popage;
-   double calagedatem, agelim, kk1, kk2;
-   double *popeffectif,*popcount;
-   double ***p3mat,***tabpop,***tabpopprev;
-   double ***mobaverage;
-   char filerespop[FILENAMELENGTH];
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   agelim=AGESUP;
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
-   strcpy(filerespop,"POP_");
+ /*   int *popage; */
-   strcat(filerespop,fileresu);
+ /*   double calagedatem, agelim, kk1, kk2; */
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+ /*   double *popeffectif,*popcount; */
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+ /*   double ***p3mat,***tabpop,***tabpopprev; */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ /*   /\* double ***mobaverage; *\/ */
-   }
+ /*   char filerespop[FILENAMELENGTH]; */
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+ /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   agelim=AGESUP; */
+ /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
+ /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+ /*   strcpy(filerespop,"POP_");  */
+ /*   strcat(filerespop,fileresu); */
+ /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
+ /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
+ /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
+ /*   } */
+ /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
+ /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
-   if (mobilav!=0) {
+ /*   /\* if (mobilav!=0) { *\/ */
-     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
-     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
+ /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
-       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+ /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-       printf(" Error in movingaverage mobilav=%d\n",mobilav);
+ /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-     }
+ /*   /\*   } *\/ */
-   }
+ /*   /\* } *\/ */
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
-   if (stepm<=12) stepsize=1;
+ /*   if (stepm<=12) stepsize=1; */
-   agelim=AGESUP;
+ /*   agelim=AGESUP; */
-   hstepm=1;
-   hstepm=hstepm/stepm;
-   if (popforecast==1) {
+ /*   hstepm=1; */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ /*   hstepm=hstepm/stepm;  */
-       printf("Problem with population file : %s\n",popfile);exit(0);
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ /*   if (popforecast==1) { */
-     }
+ /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
-     popage=ivector(0,AGESUP);
+ /*       printf("Problem with population file : %s\n",popfile);exit(0); */
-     popeffectif=vector(0,AGESUP);
+ /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
-     popcount=vector(0,AGESUP);
+ /*     }  */
+ /*     popage=ivector(0,AGESUP); */
+ /*     popeffectif=vector(0,AGESUP); */
+ /*     popcount=vector(0,AGESUP); */
-     i=1;
+ /*     i=1;    */
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+ /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
-     imx=i;
+ /*     imx=i; */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
-   }
+ /*   } */
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+ /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
-       k=k+1;
+ /*       k=k+1; */
-       fprintf(ficrespop,"\n#******");
+ /*       fprintf(ficrespop,"\n#******"); */
-       for(j=1;j<=cptcoveff;j++) {
+ /*       for(j=1;j<=cptcoveff;j++) { */
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
-       }
+ /*       } */
-       fprintf(ficrespop,"******\n");
+ /*       fprintf(ficrespop,"******\n"); */
-       fprintf(ficrespop,"# Age");
+ /*       fprintf(ficrespop,"# Age"); */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+ /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+ /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
-       for (cpt=0; cpt<=0;cpt++) {
+ /*       for (cpt=0; cpt<=0;cpt++) {  */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
-           nhstepm = nhstepm/hstepm;
+ /*        nhstepm = nhstepm/hstepm;  */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-           oldm=oldms;savm=savms;
+ /*        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);   */
-           for (h=0; h<=nhstepm; h++){
-             if (h==(int) (calagedatem+YEARM*cpt)) {
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
-             }
-             for(j=1; j<=nlstate+ndeath;j++) {
-               kk1=0.;kk2=0;
-               for(i=1; i<=nlstate;i++) {
-                 if (mobilav==1)
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-                 else {
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-                 }
-               }
-               if (h==(int)(calagedatem+12*cpt)){
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
-                   /*fprintf(ficrespop," %.3f", kk1);
-                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
-               }
-             }
-             for(i=1; i<=nlstate;i++){
-               kk1=0.;
-                 for(j=1; j<=nlstate;j++){
-                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
-                 }
-                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
-             }
-             if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
-               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
-           }
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-         }
-       }
-   /******/
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
-           nhstepm = nhstepm/hstepm;
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        for (h=0; h<=nhstepm; h++){ */
-           oldm=oldms;savm=savms;
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
-           for (h=0; h<=nhstepm; h++){
+ /*          }  */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ /*            kk1=0.;kk2=0; */
-             }
+ /*            for(i=1; i<=nlstate;i++) {               */
-             for(j=1; j<=nlstate+ndeath;j++) {
+ /*              if (mobilav==1)  */
-               kk1=0.;kk2=0;
+ /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
-               for(i=1; i<=nlstate;i++) {
+ /*              else { */
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
-               }
+ /*              } */
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+ /*            } */
-             }
+ /*            if (h==(int)(calagedatem+12*cpt)){ */
-           }
+ /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*              /\*fprintf(ficrespop," %.3f", kk1); */
-         }
+ /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
-       }
+ /*            } */
-    }
+ /*          } */
-   }
+ /*          for(i=1; i<=nlstate;i++){ */
+ /*            kk1=0.; */
+ /*            for(j=1; j<=nlstate;j++){ */
+ /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
+ /*            } */
+ /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
+ /*          } */
+ /*          if (h==(int)(calagedatem+12*cpt)) */
+ /*            for(j=1; j<=nlstate;j++)  */
+ /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
+ /*        } */
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*      } */
+ /*       } */
+ /*       /\******\/ */
+ /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
+ /*        nhstepm = nhstepm/hstepm;  */
+ /*        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);   */
+ /*        for (h=0; h<=nhstepm; h++){ */
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
+ /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
+ /*          }  */
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
+ /*            kk1=0.;kk2=0; */
+ /*            for(i=1; i<=nlstate;i++) {               */
+ /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
+ /*            } */
+ /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
+ /*          } */
+ /*        } */
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+ /*      } */
+ /*       } */
+ /*     }  */
+ /*   } */
+ /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+ /*   if (popforecast==1) { */
+ /*     free_ivector(popage,0,AGESUP); */
+ /*     free_vector(popeffectif,0,AGESUP); */
+ /*     free_vector(popcount,0,AGESUP); */
+ /*   } */
+ /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   fclose(ficrespop); */
+ /* } /\* End of popforecast *\/ */
-   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   if (popforecast==1) {
-     free_ivector(popage,0,AGESUP);
-     free_vector(popeffectif,0,AGESUP);
-     free_vector(popcount,0,AGESUP);
-   }
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-   fclose(ficrespop);
- } /* End of popforecast */
  int fileappend(FILE *fichier, char *optionfich)
  {
    if((fichier=fopen(optionfich,"a"))==NULL) {
- Line 6102  double gompertz(double x[])
+ Line 8048  double gompertz(double x[])
    double A,B,L=0.0,sump=0.,num=0.;
    int i,n=0; /* n is the size of the sample */
-   for (i=0;i<=imx-1 ; i++) {
+   for (i=1;i<=imx ; i++) {
      sump=sump+weight[i];
      /*    sump=sump+1;*/
      num=num+1;
- Line 6227  int readdata(char datafile[], int firsto
+ Line 8173  int readdata(char datafile[], int firsto
    /*-------- data file ----------*/
    FILE *fic;
    char dummy[]="                         ";
-   int i=0, j=0, n=0;
+   int i=0, j=0, n=0, iv=0, v;
+   int lstra;
    int linei, month, year,iout;
    char line[MAXLINE], linetmp[MAXLINE];
    char stra[MAXLINE], strb[MAXLINE];
    char *stratrunc;
-   int lstra;
+   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
+   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
+   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\n", datafile);fflush(stdout);
+     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
-     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
+     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
    }
    i=1;
- Line 6259  int readdata(char datafile[], int firsto
+ Line 8228  int readdata(char datafile[], int firsto
      }
      trimbb(linetmp,line); /* Trims multiple blanks in line */
      strcpy(line, linetmp);
+     /* 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, ' ');
+         if(strb[0]=='.') { /* Missing value */
+           lval=-1;
+           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
+           cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
+           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);
+             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;
+           }
+         }else{
+           errno=0;
+           /* what_kind_of_number(strb); */
+           dval=strtod(strb,&endptr);
+           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
+           /* if(strb != endptr && *endptr == '\0') */
+           /*    dval=dlval; */
+           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+           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);
+             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;
+           }
+           cotqvar[j][iv][i]=dval;
+           cotvar[j][ntv+iv][i]=dval;
+         }
+         strcpy(line,stra);
+       }/* end loop ntqv */
+       for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
+         cutv(stra, strb, line, ' ');
+         if(strb[0]=='.') { /* Missing value */
+           lval=-1;
+         }else{
+           errno=0;
+           lval=strtol(strb,&endptr,10);
+           /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+           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);
+             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;
+           }
+         }
+         if(lval <-1 || lval >1){
+           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 \
+  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                 \
+  build V1=0 V2=0 for the reference value (1),\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                                \
+  Exiting.\n",lval,linei, i,line,j);
+           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 \
+  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                 \
+  build V1=0 V2=0 for the reference value (1),\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                                \
+  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
+           return 1;
+         }
+         cotvar[j][iv][i]=(double)(lval);
+         strcpy(line,stra);
+       }/* end loop ntv */
+       /* Statuses  at wave */
        cutv(stra, strb, line, ' ');
-       if(strb[0]=='.') { /* Missing status */
+       if(strb[0]=='.') { /* Missing value */
          lval=-1;
        }else{
          errno=0;
          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')){
            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);
            return 1;
          }
        }
        s[j][i]=lval;
+       /* Date of Interview */
        strcpy(line,stra);
        cutv(stra, strb,line,' ');
        if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
- Line 6292  int readdata(char datafile[], int firsto
+ Line 8333  int readdata(char datafile[], int firsto
        anint[j][i]= (double) year;
        mint[j][i]= (double)month;
        strcpy(line,stra);
-     } /* ENd Waves */
+     } /* End loop on waves */
+     /* Date of death */
      cutv(stra, strb,line,' ');
      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
- Line 6302  int readdata(char datafile[], int firsto
+ Line 8344  int readdata(char datafile[], int firsto
        year=9999;
      }else{
        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
-         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
+       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-         return 1;
+       return 1;
      }
      andc[i]=(double) year;
      moisdc[i]=(double) month;
      strcpy(line,stra);
+     /* Date of birth */
      cutv(stra, strb,line,' ');
      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
      }
- Line 6318  int readdata(char datafile[], int firsto
+ Line 8361  int readdata(char datafile[], int firsto
      }else{
        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
-         return 1;
+       return 1;
      }
      if (year==9999) {
        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
-         return 1;
+       return 1;
      }
      annais[i]=(double)(year);
      moisnais[i]=(double)(month);
      strcpy(line,stra);
+     /* Sample weight */
      cutv(stra, strb,line,' ');
      errno=0;
      dval=strtod(strb,&endptr);
- Line 6342  int readdata(char datafile[], int firsto
+ Line 8386  int readdata(char datafile[], int firsto
      weight[i]=dval;
      strcpy(line,stra);
+     for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
+       cutv(stra, strb, line, ' ');
+       if(strb[0]=='.') { /* Missing value */
+         lval=-1;
+       }else{
+         errno=0;
+         /* what_kind_of_number(strb); */
+         dval=strtod(strb,&endptr);
+         /* if(strb != endptr && *endptr == '\0') */
+         /*   dval=dlval; */
+         /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+         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) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, 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) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
+           return 1;
+         }
+         coqvar[iv][i]=dval;
+         covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
+       }
+       strcpy(line,stra);
+     }/* end loop nqv */
+     /* Covariate values */
      for (j=ncovcol;j>=1;j--){
        cutv(stra, strb,line,' ');
-       if(strb[0]=='.') { /* Missing status */
+       if(strb[0]=='.') { /* Missing covariate value */
          lval=-1;
        }else{
          errno=0;
- Line 6359  int readdata(char datafile[], int firsto
+ Line 8426  int readdata(char datafile[], int firsto
          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 \
   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);
          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 \
   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);
          return 1;
        }
- Line 6380  int readdata(char datafile[], int firsto
+ Line 8447  int readdata(char datafile[], int firsto
        strcpy(line,stra);
      }
      lstra=strlen(stra);
      if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
        stratrunc = &(stra[lstra-9]);
        num[i]=atol(stratrunc);
- Line 6392  int readdata(char datafile[], int firsto
+ Line 8459  int readdata(char datafile[], int firsto
      i=i+1;
    } /* End loop reading  data */
    *imax=i-1; /* Number of individuals */
    fclose(fic);
    return (0);
    /* endread: */
-     printf("Exiting readdata: ");
+   printf("Exiting readdata: ");
-     fclose(fic);
+   fclose(fic);
-     return (1);
+   return (1);
+ }
+ void removefirstspace(char **stri){/*, char stro[]) {*/
+   char *p1 = *stri, *p2 = *stri;
+   while (*p2 == ' ')
+     p2++;
+   /* while ((*p1++ = *p2++) !=0) */
+   /*   ; */
+   /* do */
+   /*   while (*p2 == ' ') */
+   /*     p2++; */
+   /* while (*p1++ == *p2++); */
+   *stri=p2;
+ }
+ 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, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
+   char resultsav[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){
+     printf("Error. 'v' must be in upper case 'V' result: %s ",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);
+     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);
+   }
+   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 ' '
+                                       resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
+        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
+     }else
+       cutl(strc,strd,resultsav,'=');
+     Tvalsel[k]=atof(strc); /* 1 */
+     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
+     Tvarsel[k]=atoi(strc);
+     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
+     /* cptcovsel++;     */
+     if (nbocc(stra,'=') >0)
+       strcpy(resultsav,stra); /* and analyzes it */
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     if(Typevar[k1]==0){ /* Single covariate in model */
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           match=1;
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+       }
+     }
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+     match=0;
+     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       if(Typevar[k1]==0){ /* Single */
+         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
+           resultmodel[k1]=k2;  /* 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);
+     }else if(match > 1){
+       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+     }
+   }
+   /* 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 */
+   /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
+   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
+   /* 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 */
+   /*    5 0 0 1 */
+   /*    6 1 0 1 */ /* V4=1, V3=0, V1=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++){ /* model line */
+     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
+       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
+       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
+       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][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 */
+       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
+       k4++;;
+     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
+       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
+       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= 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 */
+       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+       k4q++;;
+     }
+   }
+   TKresult[nres]=++k; /* Combination for the nresult and the model */
+   return (0);
  }
- void removespace(char *str) {
-   char *p1 = str, *p2 = str;
+ int decodemodel( char model[], int lastobs)
-   do
+  /**< This routine decodes the model and returns:
-     while (*p2 == ' ')
+         * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
-       p2++;
+         * - nagesqr = 1 if age*age in the model, otherwise 0.
-   while (*p1++ == *p2++);
+         * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
- }
+         * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+         * - cptcovage number of covariates with age*products =2
- int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
+         * - cptcovs number of simple covariates
-    * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
+         * - 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
-    * - nagesqr = 1 if age*age in the model, otherwise 0.
+         *     which is a new column after the 9 (ncovcol) variables.
-    * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
+         * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
-    * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
+         * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
-    * - cptcovage number of covariates with age*products =2
+         *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
-    * - cptcovs number of simple covariates
+         * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
-    * - 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
-    * - 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 .
-  */
  {
-   int i, j, k, ks;
+   int i, j, k, ks, v;
-   int  j1, k1, k2;
+   int  j1, k1, k2, k3, k4;
    char modelsav[80];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
    char *strpt;
- Line 6451  int decodemodel ( char model[], int last
+ Line 8645  int decodemodel ( char model[], int last
      if ((strpt=strstr(model,"age*age")) !=0){
        printf(" strpt=%s, model=%s\n",strpt, model);
        if(strpt != model){
-       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
   corresponding column of parameters.\n",model);
-       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
+         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
   corresponding column of parameters.\n",model); fflush(ficlog);
-       return 1;
+         return 1;
-     }
+       }
        nagesqr=1;
        if (strstr(model,"+age*age") !=0)
          substrchaine(modelsav, model, "+age*age");
- Line 6472  int decodemodel ( char model[], int last
+ Line 8665  int decodemodel ( char model[], int last
      if (strlen(modelsav) >1){
        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
-       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2  */
+       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */
        cptcovt= j+1; /* Number of total covariates in the model, not including
-                    * cst, age and age*age
+                      * cst, age and age*age
-                    * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
+                      * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
-                   /* including age products which are counted in cptcovage.
+       /* including age products which are counted in cptcovage.
-                   * but the covariates which are products must be treated
+        * but the covariates which are products must be treated
-                   * separately: ncovn=4- 2=2 (V1+V3). */
+        * separately: ncovn=4- 2=2 (V1+V3). */
        cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
        /*   Design
         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
         *  <          ncovcol=8                >
- Line 6490  int decodemodel ( char model[], int last
+ Line 8683  int decodemodel ( char model[], int last
         *   k=  1    2      3       4     5       6      7        8
         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
         *  covar[k,i], value of kth covariate if not including age for individual i:
-        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
-        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
+        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
         *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
         *  Tage[++cptcovage]=k
         *       if products, new covar are created after ncovcol with k1
- Line 6516  int decodemodel ( char model[], int last
+ Line 8709  int decodemodel ( char model[], int last
         *       {2,   1,     4,      8,    5,      6,     3,       7}
         * Struct []
         */
        /* This loop fills the array Tvar from the string 'model'.*/
        /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
        /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
- Line 6531  int decodemodel ( char model[], int last
+ Line 8724  int decodemodel ( char model[], int last
        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
        /*
         * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
-         Tvar[k]=0;
+         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
+       }
        cptcovage=0;
        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
          cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
- Line 6547  int decodemodel ( char model[], int last
+ Line 8741  int decodemodel ( char model[], int last
              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 */
+             Typevar[k]=1;  /* 1 for age product */
              cptcovage++; /* Sums 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 */
              /*printf("stre=%s ", stre);*/
- Line 6554  int decodemodel ( char model[], int last
+ Line 8749  int decodemodel ( char model[], int last
              cptcovprod--;
              cutl(stre,strb,strc,'V');
              Tvar[k]=atoi(stre);
+             Typevar[k]=1;  /* 1 for age product */
              cptcovage++;
              Tage[cptcovage]=k;
            } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
- Line 6561  int decodemodel ( char model[], int last
+ Line 8757  int decodemodel ( char model[], int last
              cptcovn++;
              cptcovprodnoage++;k1++;
              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+             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
+                                                 because this model-covariate is a construction we invent a new column
-                                    ncovcol + k1
+                                                 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 */
+                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, 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 */
              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-             k2=k2+2;
+             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]=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) */
+             /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
+             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
+             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
              for (i=1; i<=lastobs;i++){
                /* Computes the new covariate which is a product of
                   covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
- Line 6584  int decodemodel ( char model[], int last
+ Line 8784  int decodemodel ( char model[], int last
            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
            /*  scanf("%d",i);*/
            cutl(strd,strc,strb,'V');
-           ks++; /**< Number of simple covariates */
+           ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
-           cptcovn++;
+           cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
            Tvar[k]=atoi(strd);
+           Typevar[k]=0;  /* 0 for simple covariates */
          }
          strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
-         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+                                 /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
-           scanf("%d",i);*/
+                                   scanf("%d",i);*/
        } /* end of loop + on total covariates */
      } /* end if strlen(modelsave == 0) age*age might exist */
    } /* end if strlen(model == 0) */
    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
-   printf("cptcovprod=%d ", cptcovprod);
+      printf("cptcovprod=%d ", cptcovprod);
-   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+      fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+      scanf("%d ",i);*/
-   scanf("%d ",i);*/
+ /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
+    of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
+ /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
+    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
+    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;
+ */
+ /* Dispatching between quantitative and time varying covariates */
+   /* 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\
+ 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\
+ 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;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       nsd++;
+       modell[k].maintype= FTYPE;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       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 */
+       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 &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       modell[k].maintype= FTYPE;
+       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 */
+       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 */
+       Fixed[k]= 0;
+       Dummy[k]= 1;
+       nqfveff++;
+       modell[k].maintype= FTYPE;
+       modell[k].subtype= FQ;
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
+       ncovf++;
+       TvarF[ncovf]=Tvar[k];
+       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 dummy variables */
+       Fixed[k]= 1;
+       Dummy[k]= 0;
+       ntveff++; /* Only simple time varying dummy variable */
+       modell[k].maintype= VTYPE;
+       modell[k].subtype= VD;
+       nsd++;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       ncovv++; /* Only simple time varying variables */
+       TvarV[ncovv]=Tvar[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);
+       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
+     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
+       Fixed[k]= 1;
+       Dummy[k]= 1;
+       nqtveff++;
+       modell[k].maintype= VTYPE;
+       modell[k].subtype= VQ;
+       ncovv++; /* Only simple time varying variables */
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
+       TvarV[ncovv]=Tvar[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 */
+       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
+       printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
+       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
+     }else if (Typevar[k] == 1) {  /* product with age */
+       ncova++;
+       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*/
+     }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]);
+     }
+     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
+     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+   }
+   /* 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] == 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]]);
+             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);
+             return(1);
+           }
+         }else if (Typevar[k1] ==2){
+           k3=Tposprod[k1];
+           k4=Tposprod[k2];
+           if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
+             printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             return(1);
+           }
+         }
+       }
+     }
+   }
+   printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
+   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
+   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
+   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
    return (0); /* with covar[new additional covariate if product] and Tage if age */
    /*endread:*/
-     printf("Exiting decodemodel: ");
+   printf("Exiting decodemodel: ");
-     return (1);
+   return (1);
  }
  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
- {
+ {/* Check ages at death */
    int i, m;
+   int firstone=0;
    for (i=1; i<=imx; i++) {
      for(m=2; (m<= maxwav); m++) {
        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;
-         s[m][i]=-1;
+         if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
+           s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
          *nberr = *nberr + 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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
+         if(firstone == 0){
-         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 are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
+           firstone=1;
-         s[m][i]=-1;
+         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,"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;  /* 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 6910  void syscompilerinfo(int logged)
+ Line 9411  void syscompilerinfo(int logged)
  #endif
-  }
+ }
-  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
+ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
    /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-   int i, j, k, i1 ;
+   int i, j, k, i1, k4=0, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
    double tot;
- Line 6925  void syscompilerinfo(int logged)
+ Line 9426  void syscompilerinfo(int logged)
      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
    }
-   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing 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,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
    fprintf(ficrespl,"\n");
-     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
-     agebase=ageminpar;
+   agebase=ageminpar;
-     agelim=agemaxpar;
+   agelim=agemaxpar;
-     i1=pow(2,cptcoveff);
+   /* i1=pow(2,ncoveff); */
-     if (cptcovn < 1){i1=1;}
+   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+   if (cptcovn < 1){i1=1;}
-     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
-     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
+       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-         k=k+1;
+       /* k=k+1; */
-         /* to clean */
+       /* to clean */
-         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-         fprintf(ficrespl,"#******");
+       fprintf(ficrespl,"#******");
-         printf("#******");
+       printf("#******");
-         fprintf(ficlog,"#******");
+       fprintf(ficlog,"#******");
-         for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         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)]);
+         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(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         }
+       }
-         fprintf(ficrespl,"******\n");
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         printf("******\n");
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         fprintf(ficlog,"******\n");
+         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         fprintf(ficrespl,"#Age ");
+       }
-         for(j=1;j<=cptcoveff;j++) {
+       fprintf(ficrespl,"******\n");
-           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       printf("******\n");
-         }
+       fprintf(ficlog,"******\n");
-         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       if(invalidvarcomb[k]){
-         fprintf(ficrespl,"Total Years_to_converge\n");
+         printf("\nCombination (%d) ignored because no case \n",k);
+         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
-         for (age=agebase; age<=agelim; age++){
+         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,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<=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,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 */
-         return 0;
+   } /* 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) --------------*/
+         /* Computes the back prevalence limit  for any combination      of covariate values
+    * at any age between ageminpar and agemaxpar
+          */
+   int i, j, k, i1, nres=0 ;
+   /* double ftolpl = 1.e-10; */
+   double age, agebase, agelim;
+   double tot;
+   /* double ***mobaverage; */
+   /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
+   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;
+     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+   }
+   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   pstamp(ficresplb);
+   fprintf(ficresplb,"# Period (stable) back 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");
+   /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
+   agebase=ageminpar;
+   agelim=agemaxpar;
+   i1=pow(2,cptcoveff);
+   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;
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       fprintf(ficresplb,"#******");
+       printf("#******");
+       fprintf(ficlog,"#******");
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         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)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       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 ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
+       fprintf(ficresplb,"Total Years_to_converge\n");
+       for (age=agebase; age<=agelim; age++){
+         /* for (age=agebase; age<=agebase; age++){ */
+         if(mobilavproj > 0){
+           /* 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, ftolpl, ncvyearp, k, nres);
+         }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);
+           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);
+         }else{
+           /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
+         }
+         fprintf(ficresplb,"%.0f ",age );
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         tot=0.;
+         for(i=1; i<=nlstate;i++){
+           tot +=  bprlim[i][i];
+           fprintf(ficresplb," %.5f", bprlim[i][i]);
+         }
+         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+       } /* 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); */
+   return 0;
+ }
  int hPijx(double *p, int bage, int fage){
      /*------------- h Pij x at various ages ------------*/
- Line 6991  int hPijx(double *p, int bage, int fage)
+ Line 9617  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 7010  int hPijx(double *p, int bage, int fage)
+ Line 9636  int hPijx(double *p, int bage, int fage)
      agelim=AGESUP;
      hstepm=stepsize*YEARM; /* Every year of age */
      hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
      /* hstepm=1;   aff par mois*/
      pstamp(ficrespij);
      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
      i1= pow(2,cptcoveff);
-    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+                 /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
+                 /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
-    /*   k=k+1;  */
+                 /*      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)]);
+       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 7032  int hPijx(double *p, int bage, int fage)
+ Line 9665  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 7051  int hPijx(double *p, int bage, int fage)
+ Line 9684  int hPijx(double *p, int bage, int fage)
        }
        /*}*/
      }
-         return 0;
+     return 0;
  }
+  int hBijx(double *p, int bage, int fage, double ***prevacurrent){
+     /*------------- h Bij x at various ages ------------*/
+   int stepsize;
+   /* int agelim; */
+         int ageminl;
+   int hstepm;
+   int nhstepm;
+   int h, i, i1, j, k, nres;
+   double agedeb;
+   double ***p3mat;
+   strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
+   if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
+     printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+     fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
+   }
+   printf("Computing pij back: result on file '%s' \n", filerespijb);
+   fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   /*if (stepm<=24) stepsize=2;*/
+   /* agelim=AGESUP; */
+   ageminl=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 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(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(ficrespijb,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++)
+         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficrespijb,"******\n");
+       if(invalidvarcomb[k]){
+         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+         continue;
+       }
+       /* 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) */
+         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
+         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,prevacurrent,nlstate,stepm, k);
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+         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," %1d-%1d",i,j);
+         fprintf(ficrespijb,"\n");
+         for (h=0; h<=nhstepm; h++){
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+           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]);
+           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 7077  int main(int argc, char *argv[])
+ Line 9797  int main(int argc, char *argv[])
    int itimes;
    int NDIM=2;
    int vpopbased=0;
+   int nres=0;
+   int endishere=0;
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
- Line 7085  int main(int argc, char *argv[])
+ Line 9807  int main(int argc, char *argv[])
    double agedeb=0.;
    double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
+   double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
    double fret;
    double dum=0.; /* Dummy variable */
    double ***p3mat;
-   double ***mobaverage;
+   /* double ***mobaverage; */
    char line[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
-   char model[MAXLINE], modeltemp[MAXLINE];
+   char  modeltemp[MAXLINE];
+   char resultline[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
    char *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
- Line 7105  int main(int argc, char *argv[])
+ Line 9830  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;
    int mobilav=0,popforecast=0;
    int hstepm=0, nhstepm=0;
    int agemortsup;
- Line 7115  int main(int argc, char *argv[])
+ Line 9841  int main(int argc, char *argv[])
    double bage=0, fage=110., age, agelim=0., agebase=0.;
    double ftolpl=FTOL;
    double **prlim;
+   double **bprlim;
    double ***param; /* Matrix of parameters */
-   double  *p;
+   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 */
- Line 7126  int main(int argc, char *argv[])
+ Line 9854  int main(int argc, char *argv[])
    double *epj, vepp;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
    double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
    int *dcwave;
- Line 7327  int main(int argc, char *argv[])
+ Line 10057  int main(int argc, char *argv[])
      }else
        break;
    }
-   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
+   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
-                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
+                         &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
-     if (num_filled != 8) {
+     if (num_filled != 11) {
-       printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+       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);
      }
-     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, 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);
    }
    /* 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 7371  int main(int argc, char *argv[])
+ Line 10101  int main(int argc, char *argv[])
    /* 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 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(ficlog,"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(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]=='#'){
- Line 7401  int main(int argc, char *argv[])
+ Line 10131  int main(int argc, char *argv[])
    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
+   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
+   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
    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 7422  int main(int argc, char *argv[])
+ Line 10155  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 7430  int main(int argc, char *argv[])
+ Line 10169  int main(int argc, char *argv[])
      fclose (ficlog);
      goto end;
      exit(0);
-   }
+   }  else if(mle==-5) { /* Main Wizard */
-   else if(mle==-3) { /* Main Wizard */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
      fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      matcov=matrix(1,npar,1,npar);
      hess=matrix(1,npar,1,npar);
-   }
+   }  else{ /* Begin of mle != -1 or -5 */
-   else{
      /* Read guessed parameters */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
- Line 7453  int main(int argc, char *argv[])
+ Line 10190  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++){
- Line 7488  run imach with mle=-1 to get a correct t
+ Line 10226  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 7527  run imach with mle=-1 to get a correct t
+ Line 10266  run imach with mle=-1 to get a correct t
        }
      }
      fflush(ficlog);
      /* Reads covariance matrix */
      delti=delti3[1][1];
      /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
- Line 7544  run imach with mle=-1 to get a correct t
+ Line 10283  run imach with mle=-1 to get a correct t
        fputs(line,ficlog);
      }
      ungetc(c,ficpar);
      matcov=matrix(1,npar,1,npar);
      hess=matrix(1,npar,1,npar);
      for(i=1; i <=npar; i++)
        for(j=1; j <=npar; j++) matcov[i][j]=0.;
      /* Scans npar lines */
      for(i=1; i <=npar; i++){
-       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
+       count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
        if(count != 3){
          printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
- Line 7561  Please run with mle=-1 to get a correct
+ Line 10300  Please run with mle=-1 to get a correct
  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
          exit(1);
-       }else
+       }else{
-       if(mle==1)
+         if(mle==1)
-         printf("%1d%1d%1d",i1,j1,jk);
+           printf("%1d%1d%d",i1,j1,jk);
-       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
+       }
-       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
+       fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
+       fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
        for(j=1; j <=i; j++){
          fscanf(ficpar," %le",&matcov[i][j]);
          if(mle==1){
- Line 7577  Please run with mle=-1 to get a correct
+ Line 10317  Please run with mle=-1 to get a correct
        fscanf(ficpar,"\n");
        numlinepar++;
        if(mle==1)
-         printf("\n");
+                                 printf("\n");
        fprintf(ficlog,"\n");
        fprintf(ficparo,"\n");
      }
- Line 7603  Please run with mle=-1 to get a correct
+ Line 10343  Please run with mle=-1 to get a correct
      }
      fprintf(ficres,"#%s\n",version);
    }    /* End of mle != -3 */
    /*  Main data
     */
    n= lastobs;
- Line 7612  Please run with mle=-1 to get a correct
+ Line 10352  Please run with mle=-1 to get a correct
    annais=vector(1,n);
    moisdc=vector(1,n);
    andc=vector(1,n);
+   weight=vector(1,n);
    agedc=vector(1,n);
    cod=ivector(1,n);
-   weight=vector(1,n);
+   for(i=1;i<=n;i++){
-   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+     num[i]=0;
+     moisnais[i]=0;
+     annais[i]=0;
+     moisdc[i]=0;
+     andc[i]=0;
+     agedc[i]=0;
+     cod[i]=0;
+     weight[i]=1.0; /* Equal weights, 1 by default */
+   }
    mint=matrix(1,maxwav,1,n);
    anint=matrix(1,maxwav,1,n);
    s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
- Line 7628  Please run with mle=-1 to get a correct
+ Line 10377  Please run with mle=-1 to get a correct
      goto end;
    /* Calculation of the number of parameters from char model */
-     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+   /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
          k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
          k=3 V4 Tvar[k=3]= 4 (from V4)
          k=2 V1 Tvar[k=2]= 1 (from V1)
          k=1 Tvar[1]=2 (from V2)
-     */
+   */
    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   TvarsDind=ivector(1,NCOVMAX); /*  */
+   TvarsD=ivector(1,NCOVMAX); /*  */
+   TvarsQind=ivector(1,NCOVMAX); /*  */
+   TvarsQ=ivector(1,NCOVMAX); /*  */
+   TvarF=ivector(1,NCOVMAX); /*  */
+   TvarFind=ivector(1,NCOVMAX); /*  */
+   TvarV=ivector(1,NCOVMAX); /*  */
+   TvarVind=ivector(1,NCOVMAX); /*  */
+   TvarA=ivector(1,NCOVMAX); /*  */
+   TvarAind=ivector(1,NCOVMAX); /*  */
+   TvarFD=ivector(1,NCOVMAX); /*  */
+   TvarFDind=ivector(1,NCOVMAX); /*  */
+   TvarFQ=ivector(1,NCOVMAX); /*  */
+   TvarFQind=ivector(1,NCOVMAX); /*  */
+   TvarVD=ivector(1,NCOVMAX); /*  */
+   TvarVDind=ivector(1,NCOVMAX); /*  */
+   TvarVQ=ivector(1,NCOVMAX); /*  */
+   TvarVQind=ivector(1,NCOVMAX); /*  */
+   Tvalsel=vector(1,NCOVMAX); /*  */
+   Tvarsel=ivector(1,NCOVMAX); /*  */
+   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
+   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
+   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
    /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
        For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
- Line 7644  Please run with mle=-1 to get a correct
+ Line 10418  Please run with mle=-1 to get a correct
      ncovcol + k1
      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
      Tvar[3=V1*V4]=4+1 etc */
-   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+   Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
+   Tposprod=ivector(1,NCOVMAX); /* 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)
+      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
    */
    Tvaraff=ivector(1,NCOVMAX); /* Unclear */
    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
- Line 7656  Please run with mle=-1 to get a correct
+ Line 10432  Please run with mle=-1 to get a correct
 covariates (3 plus signs)
                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                        */
+   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual dummy, fixed or varying:
+                                 * Tmodelind[Tvaraff[3]]=9,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 ,
+                                 * V1 df, V2 qf, V3 & V4 dv, V5 qv
+                                 * Tmodelind[1]@9={9,0,3,2,}*/
+   TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
+   TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual quantitative, fixed or varying:
+                                 * Tmodelqind[1]=1,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*/
  /* Main decodemodel */
-   if(decodemodel(model, lastobs) == 1)
+   if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
      goto end;
    if((double)(lastobs-imx)/(double)imx > 1.10){
- Line 7685  Please run with mle=-1 to get a correct
+ Line 10473  Please run with mle=-1 to get a correct
    free_vector(annais,1,n);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
-   free_vector(moisdc,1,n);
+   /* free_vector(moisdc,1,n); */
-   free_vector(andc,1,n);
+   /* free_vector(andc,1,n); */
    /* */
    wav=ivector(1,imx);
- Line 7706  Please run with mle=-1 to get a correct
+ Line 10494  Please run with mle=-1 to get a correct
    */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-   /* */
+   /* Concatenates waves */
-   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
+   free_vector(moisdc,1,n);
+   free_vector(andc,1,n);
+   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;
    Ndum =ivector(-1,NCOVMAX);
-   if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
+   cptcoveff=0;
-     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
+     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
+   }
+   ncovcombmax=pow(2,cptcoveff);
+   invalidvarcomb=ivector(1, ncovcombmax);
+   for(i=1;i<ncovcombmax;i++)
+     invalidvarcomb[i]=0;
    /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
    /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
    /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
    /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
- Line 7730  Please run with mle=-1 to get a correct
+ Line 10528  Please run with mle=-1 to get a correct
     */
    h=0;
    /*if (cptcovn > 0) */
    m=pow(2,cptcoveff);
            /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
- Line 7775  Please run with mle=-1 to get a correct
+ Line 10569  Please run with mle=-1 to get a correct
       *              bbbbbbbb
       *              76543210
       *   h-1        00000101 (6-1=5)
-      *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
+      *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
       *           &
       *     1        00000001 (1)
-      *              00000001        = 1 & ((h-1) >> (k-1))
+      *              00000000        = 1 & ((h-1) >> (k-1))
-      *          +1= 00000010 =2
+      *          +1= 00000001 =1
       *
       * h=14, k=3 => h'=h-1=13, k'=k-1=2
       *          h'      1101 =2^3+2^2+0x2^1+2^0
- Line 7801  Please run with mle=-1 to get a correct
+ Line 10595  Please run with mle=-1 to get a correct
       *                  2211
       *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
       *                  V3=2
+                  * codtabm and decodtabm are identical
       */
-   /* /\* for(h=1; h <=100 ;h++){  *\/ */
-   /*   /\* printf("h=%2d ", h); *\/ */
-   /*    /\* for(k=1; k <=10; k++){ *\/ */
-   /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
-   /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */
-   /*    /\* } *\/ */
-   /*    /\* printf("\n"); *\/ */
-   /* } */
-   /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
-   /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
-   /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
-   /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */
-   /*      h++; */
-   /*      if (h>m)  */
-   /*        h=1; */
-   /*      codtab[h][k]=j; */
-   /*      /\* codtab[12][3]=1; *\/ */
-   /*      /\*codtab[h][Tvar[k]]=j;*\/ */
-   /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
-   /*    }  */
-   /*     } */
-   /*   } */
-   /* }  */
-   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
-      codtab[1][2]=1;codtab[2][2]=2; */
-   /* for(i=1; i <=m ;i++){  */
-   /*    for(k=1; k <=cptcovn; k++){ */
-   /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
-   /*    } */
-   /*    printf("\n"); */
-   /* } */
-   /*   scanf("%d",i);*/
   free_ivector(Ndum,-1,NCOVMAX);
- Line 7909  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 10672  Title=%s <br>Datafile=%s Firstpass=%d La
  #endif
    /* 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,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");
- Line 7920  Youngest age at first (selected) pass %.
+ Line 10684  Youngest age at first (selected) pass %.
  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
            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] */
    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
- Line 7934  Interval (in months) between two waves:
+ Line 10697  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(j=1;j<=NDIM;j++)
+         ximort[i][j]=0.;
      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
      cens=ivector(1,n);
      ageexmed=vector(1,n);
      agecens=vector(1,n);
      dcwave=ivector(1,n);
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
        for (m=firstpass; m<=lastpass; m++)
- Line 7949  Interval (in months) between two waves:
+ Line 10715  Interval (in months) between two waves:
            break;
          }
      }
      for (i=1; i<=imx; i++) {
        if (wav[i]>0){
          ageexmed[i]=agev[mw[1][i]][i];
          j=wav[i];
          agecens[i]=1.;
          if (ageexmed[i]> 1 && wav[i] > 0){
            agecens[i]=agev[mw[j][i]][i];
            cens[i]= 1;
- Line 8082  Interval (in months) between two waves:
+ Line 10848  Interval (in months) between two waves:
      for(i=1; i <=NDIM; i++)
        for(j=i+1;j<=NDIM;j++)
-         matcov[i][j]=matcov[j][i];
+                                 matcov[i][j]=matcov[j][i];
      printf("\nCovariance matrix\n ");
      fprintf(ficlog,"\nCovariance matrix\n ");
      for(i=1; i <=NDIM; i++) {
        for(j=1;j<=NDIM;j++){
-         printf("%f ",matcov[i][j]);
+                                 printf("%f ",matcov[i][j]);
-         fprintf(ficlog,"%f ",matcov[i][j]);
+                                 fprintf(ficlog,"%f ",matcov[i][j]);
        }
        printf("\n ");  fprintf(ficlog,"\n ");
      }
- Line 8130  Interval (in months) between two waves:
+ Line 10896  Interval (in months) between two waves:
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
+                 ageminpar=50;
+                 agemaxpar=100;
      if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
          printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
- Line 8137  Please run with mle=-1 to get a correct
+ Line 10905  Please run with mle=-1 to get a correct
          fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
  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
+     }else{
+                         printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
+                         fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
        printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
+                 }
      printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                       stepm, weightopt,\
                       model,imx,p,matcov,agemortsup);
- Line 8146  Please run with mle=-1 to get a correct
+ Line 10917  Please run with mle=-1 to get a correct
      free_vector(lsurv,1,AGESUP);
      free_vector(lpop,1,AGESUP);
      free_vector(tpop,1,AGESUP);
- #ifdef GSL
+     free_matrix(ximort,1,NDIM,1,NDIM);
      free_ivector(cens,1,n);
      free_vector(agecens,1,n);
      free_ivector(dcwave,1,n);
-     free_matrix(ximort,1,NDIM,1,NDIM);
+ #ifdef GSL
  #endif
    } /* Endof if mle==-3 mortality only */
    /* Standard  */
- Line 8164  Please run with mle=-1 to get a correct
+ Line 10935  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 8179  Please run with mle=-1 to get a correct
+ Line 10954  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 nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, 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");
- Line 8225  Please run with mle=-1 to get a correct
+ Line 11000  Please run with mle=-1 to get a correct
          }
        }
      } /* end of hesscov and Wald tests */
      /*  */
      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
      printf("# Scales (for hessian or gradient estimation)\n");
- Line 8334  Please run with mle=-1 to get a correct
+ Line 11109  Please run with mle=-1 to get a correct
      fflush(ficlog);
      fflush(ficres);
-       while(fgets(line, MAXLINE, ficpar)) {
+     while(fgets(line, MAXLINE, ficpar)) {
-     /* If line starts with a # it is a comment */
+       /* If line starts with a # it is a comment */
-     if (line[0] == '#') {
+       if (line[0] == '#') {
-       numlinepar++;
+         numlinepar++;
-       fputs(line,stdout);
+         fputs(line,stdout);
-       fputs(line,ficparo);
+         fputs(line,ficparo);
-       fputs(line,ficlog);
+         fputs(line,ficlog);
-       continue;
+         continue;
-     }else
+       }else
-       break;
+         break;
-   }
+     }
      /* while((c=getc(ficpar))=='#' && c!= EOF){ */
      /*   ungetc(c,ficpar); */
      /*   fgets(line, MAXLINE, ficpar); */
- Line 8356  Please run with mle=-1 to get a correct
+ Line 11131  Please run with mle=-1 to get a correct
      estepm=0;
      if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
-     if (num_filled != 6) {
+       if (num_filled != 6) {
-       printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
+         printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
-       printf("but line=%s\n",line);
+         fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
-       goto end;
+         goto end;
+       }
+       printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
      }
-     printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
+     /* 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 */
-   /* 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 */
      /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
      if (estepm==0 || estepm < stepm) estepm=stepm;
      if (fage <= 2) {
- Line 8377  Please run with mle=-1 to get a correct
+ Line 11152  Please run with mle=-1 to get a correct
      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
      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);
+         fputs(line,ficlog);
+         continue;
+       }else
+         break;
      }
-     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,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-     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);
+       if (num_filled != 7) {
-     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);
+         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);
-     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,"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,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+         goto end;
+       }
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       printf("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(ficparo,"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(ficres,"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);
+       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,ficparo);
+     }
+     while(fgets(line, MAXLINE, ficpar)) {
+       /* If line starts with a # it is a comment */
+       if (line[0] == '#') {
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         continue;
+       }else
+         break;
      }
-     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);
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
-     fprintf(ficlog,"pop_based=%d\n",popbased);
+       if (num_filled != 1) {
-     fprintf(ficparo,"pop_based=%d\n",popbased);
+         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);
-     fprintf(ficres,"pop_based=%d\n",popbased);
+         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;
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       }
-       ungetc(c,ficpar);
+       printf("pop_based=%d\n",popbased);
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"pop_based=%d\n",popbased);
-       fputs(line,stdout);
+       fprintf(ficparo,"pop_based=%d\n",popbased);
-       fputs(line,ficparo);
+       fprintf(ficres,"pop_based=%d\n",popbased);
      }
-     ungetc(c,ficpar);
+     /* Results */
-     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);
+     nresult=0;
-     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);
+     do{
-     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);
+       if(!fgets(line, MAXLINE, ficpar)){
-     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);
+         endishere=1;
-     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);
+         parameterline=14;
-     /* day and month of proj2 are not used but only year anproj2.*/
+       }else if (line[0] == '#') {
+         /* If line starts with a # it is a comment */
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         continue;
+       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
+         parameterline=11;
+       else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
+         parameterline=12;
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp))
+         parameterline=13;
+       else{
+         parameterline=14;
+       }
+       switch (parameterline){
+       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){
+           if (num_filled != 8) {
+             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\n, your line=%s . Probably you are running 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 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             goto end;
+           }
+           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.*/
+         }
+         break;
+       case 12:
+         /*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);*/
+         if((num_filled=sscanf(line,"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)) !=EOF){
+           if (num_filled != 8) {
+             printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             goto end;
+           }
+           printf("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.*/
+         }
+         break;
+       case 13:
+         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+           if (num_filled == 0){
+             resultline[0]='\0';
+             printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             break;
+           } else if (num_filled != 1){
+             printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+             fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+           }
+           nresult++; /* Sum of resultlines */
+           printf("Result %d: result=%s\n",nresult, resultline);
+           if(nresult > MAXRESULTLINES){
+             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             goto end;
+           }
+           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);
+           break;
+         case 14:
+           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);
+             goto end;
+           }
+           break;
+         default:
+           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); */
+     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
-         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+       printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
  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);
-         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+       fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
  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
+     }else{
-       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
+     }
-     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
+     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
                   jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
-    /*------------ free_vector  -------------*/
+     /*------------ free_vector  -------------*/
-    /*  chdir(path); */
+     /*  chdir(path); */
-     free_ivector(wav,1,imx);
+     /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
-     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
+     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
-     free_imatrix(bh,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_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
      free_lvector(num,1,n);
      free_vector(agedc,1,n);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
      /*free_matrix(covar,1,NCOVMAX,1,n);*/
      fclose(ficparo);
      fclose(ficres);
      /* Other results (useful)*/
      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
      prlim=matrix(1,nlstate,1,nlstate);
      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
      fclose(ficrespl);
- #ifdef FREEEXIT2
- #include "freeexit2.h"
- #endif
      /*------------- h Pij x at various ages ------------*/
      /*#include "hpijx.h"*/
      hPijx(p, bage, fage);
      fclose(ficrespij);
-   /*-------------- Variance of one-step probabilities---*/
+     /* ncovcombmax=  pow(2,cptcoveff); */
+     /*-------------- Variance of one-step probabilities---*/
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
+     /* Prevalence for each covariates in probs[age][status][cov] */
-     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
      for(i=1;i<=AGESUP;i++)
-       for(j=1;j<=NCOVMAX;j++)
+       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
-         for(k=1;k<=NCOVMAX;k++)
+         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);
+     if (mobilav!=0 ||mobilavproj !=0 ) {
+       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+       for(i=1;i<=AGESUP;i++)
+         for(j=1;j<=nlstate;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);
+         }
+       }
+       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
+       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+       else if (mobilavproj !=0) {
+         printf("Movingaveraging projected observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
+         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);
+         }
+       }
+     }/* end if moving average */
      /*---------- Forecasting ------------------*/
      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
      if(prevfcast==1){
        /*    if(stepm ==1){*/
        prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
-       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
-       /*      }  */
-       /*      else{ */
-       /*        erreur=108; */
-       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
-       /*      } */
      }
+     if(backcast==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);
+       /*--------------- 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,
+          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+       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);
+     }
      /* ------ Other prevalence ratios------------ */
-     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
+     free_ivector(wav,1,imx);
+     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
-     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
-     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
+     free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
-         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
-     */
-     if (mobilav!=0) {
-       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
-         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-         printf(" Error in movingaverage mobilav=%d\n",mobilav);
-       }
-     }
      /*---------- Health expectancies, no variances ------------*/
      strcpy(filerese,"E_");
      strcat(filerese,fileresu);
      if((ficreseij=fopen(filerese,"w"))==NULL) {
- Line 8531  Please run with mle=-1 to get a correct
+ Line 11428  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);
-     /*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(ficreseij,"\n#****** ");
-         for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         }
-         fprintf(ficreseij,"******\n");
-         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+     pstamp(ficreseij);
-         oldm=oldms;savm=savms;
-         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+     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)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficreseij,"******\n");
+       printf("******\n");
-         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+       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, 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);
-     /*---------- Health expectancies and variances ------------*/
+     /*---------- State-specific expectancies and variances ------------*/
      strcpy(filerest,"T_");
      strcat(filerest,fileresu);
      if((ficrest=fopen(filerest,"w"))==NULL) {
- Line 8563  Please run with mle=-1 to get a correct
+ Line 11472  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) {
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
      }
-     printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
      strcpy(filerescve,"CVE_");
      strcat(filerescve,fileresu);
      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
      }
-     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
-     fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
      strcpy(fileresv,"V_");
      strcat(fileresv,fileresu);
- Line 8589  Please run with mle=-1 to get a correct
+ Line 11498  Please run with mle=-1 to get a correct
        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
      }
-     printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
+     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
-     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
+     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);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++){
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-       fprintf(ficrest,"\n#****** ");
+     if (cptcovn < 1){i1=1;}
-       for(j=1;j<=cptcoveff;j++)
+     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;
+       printf("\n#****** Result for:");
+       fprintf(ficrest,"\n#****** Result for:");
+       fprintf(ficlog,"\n#****** Result for:");
+       for(j=1;j<=cptcoveff;j++){
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficrest,"******\n");
+       fprintf(ficlog,"******\n");
+       printf("******\n");
        fprintf(ficresstdeij,"\n#****** ");
        fprintf(ficrescveij,"\n#****** ");
- Line 8607  Please run with mle=-1 to get a correct
+ Line 11534  Please run with mle=-1 to get a correct
          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[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)]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficresvij,"******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       printf(" cvevsij %d, ",k);
+       printf(" cvevsij ");
-       fprintf(ficlog, " cvevsij %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 8634  Please run with mle=-1 to get a correct
+ Line 11569  Please run with mle=-1 to get a correct
        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 %d \n",vpopbased);
+         printf("varevsij vpopbased=%d \n",vpopbased);
-         fprintf(ficlog, "varevsij %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);
- Line 8650  Please run with mle=-1 to get a correct
+ Line 11585  Please run with mle=-1 to get a correct
          printf("Computing age specific 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 8687  Please run with mle=-1 to get a correct
+ Line 11622  Please run with mle=-1 to get a correct
        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 \n");fflush(stdout);
+       printf("done selection\n");fflush(stdout);
-       fprintf(ficlog,"done\n");fflush(ficlog);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
        /*}*/
-     } /* End k */
+     } /* End k selection */
-     free_vector(weight,1,n);
-     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     printf("done State-specific expectancies\n");fflush(stdout);
-     free_imatrix(s,1,maxwav+1,1,n);
+     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
-     free_matrix(anint,1,maxwav,1,n);
-     free_matrix(mint,1,maxwav,1,n);
-     free_ivector(cod,1,n);
-     free_ivector(tab,1,NCOVMAX);
-     fclose(ficresstdeij);
-     fclose(ficrescveij);
-     fclose(ficresvij);
-     fclose(ficrest);
-     printf("done Health expectancies\n");fflush(stdout);
-     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
-     fclose(ficpar);
-     /*------- Variance of period (stable) prevalence------*/
+     /*------- Variance of period (stable) prevalence------*/
      strcpy(fileresvpl,"VPL_");
      strcat(fileresvpl,fileresu);
      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
- Line 8717  Please run with mle=-1 to get a correct
+ Line 11641  Please run with mle=-1 to get a correct
      }
      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++){
+     i1=pow(2,cptcoveff);
-         fprintf(ficresvpl,"\n#****** ");
+     if (cptcovn < 1){i1=1;}
-         for(j=1;j<=cptcoveff;j++)
-           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
-         fprintf(ficresvpl,"******\n");
+     for(k=1; k<=i1;k++){
+       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,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)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficresvpl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
-         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       varpl=matrix(1,nlstate,(int) bage, (int) fage);
-         oldm=oldms;savm=savms;
+       oldm=oldms;savm=savms;
-         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
+       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
-         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       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_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
      /*---------- End : free ----------------*/
-     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+     if (mobilav!=0 ||mobilavproj !=0)
-     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
-   }  /* mle==-3 arrives here for freeing */
+     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-  /* endfree:*/
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   }  /* mle==-3 arrives here for freeing */
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   /* endfree:*/
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(matcov,1,npar,1,npar);
+   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(hess,1,npar,1,npar);
+   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
-     /*free_vector(delti,1,npar);*/
+   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_matrix(coqvar,1,maxwav,1,n);
-     free_matrix(agev,1,maxwav,1,imx);
+   free_matrix(covar,0,NCOVMAX,1,n);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_matrix(matcov,1,npar,1,npar);
+   free_matrix(hess,1,npar,1,npar);
-     free_ivector(ncodemax,1,NCOVMAX);
+   /*free_vector(delti,1,npar);*/
-     free_ivector(ncodemaxwundef,1,NCOVMAX);
+   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_ivector(Tvar,1,NCOVMAX);
+   free_matrix(agev,1,maxwav,1,imx);
-     free_ivector(Tprod,1,NCOVMAX);
+   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_ivector(Tvaraff,1,NCOVMAX);
-     free_ivector(Tage,1,NCOVMAX);
+   free_ivector(ncodemax,1,NCOVMAX);
+   free_ivector(ncodemaxwundef,1,NCOVMAX);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   free_ivector(Dummy,-1,NCOVMAX);
-     /* free_imatrix(codtab,1,100,1,10); */
+   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(TvarsDind,1,NCOVMAX);
+   free_ivector(TvarFD,1,NCOVMAX);
+   free_ivector(TvarFDind,1,NCOVMAX);
+   free_ivector(TvarF,1,NCOVMAX);
+   free_ivector(TvarFind,1,NCOVMAX);
+   free_ivector(TvarV,1,NCOVMAX);
+   free_ivector(TvarVind,1,NCOVMAX);
+   free_ivector(TvarA,1,NCOVMAX);
+   free_ivector(TvarAind,1,NCOVMAX);
+   free_ivector(TvarFQ,1,NCOVMAX);
+   free_ivector(TvarFQind,1,NCOVMAX);
+   free_ivector(TvarVD,1,NCOVMAX);
+   free_ivector(TvarVDind,1,NCOVMAX);
+   free_ivector(TvarVQ,1,NCOVMAX);
+   free_ivector(TvarVQind,1,NCOVMAX);
+   free_ivector(Tvarsel,1,NCOVMAX);
+   free_vector(Tvalsel,1,NCOVMAX);
+   free_ivector(Tposprod,1,NCOVMAX);
+   free_ivector(Tprod,1,NCOVMAX);
+   free_ivector(Tvaraff,1,NCOVMAX);
+   free_ivector(invalidvarcomb,1,ncovcombmax);
+   free_ivector(Tage,1,NCOVMAX);
+   free_ivector(Tmodelind,1,NCOVMAX);
+   free_ivector(TmodelInvind,1,NCOVMAX);
+   free_ivector(TmodelInvQind,1,NCOVMAX);
+   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   /* free_imatrix(codtab,1,100,1,10); */
    fflush(fichtm);
    fflush(ficgp);
    if((nberr >0) || (nbwarn>0)){
-     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
+     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
-     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
    }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
- Line 8786  Please run with mle=-1 to get a correct
+ Line 11776  Please run with mle=-1 to get a correct
    printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
    fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
    printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
- Line 8799  Please run with mle=-1 to get a correct
+ Line 11789  Please run with mle=-1 to get a correct
    fclose(ficgp);
    fclose(ficlog);
    /*------ End -----------*/
-    printf("Before Current directory %s!\n",pathcd);
+   printf("Before Current directory %s!\n",pathcd);
  #ifdef WIN32
-    if (_chdir(pathcd) != 0)
+   if (_chdir(pathcd) != 0)
-            printf("Can't move to directory %s!\n",path);
+     printf("Can't move to directory %s!\n",path);
-    if(_getcwd(pathcd,MAXLINE) > 0)
+   if(_getcwd(pathcd,MAXLINE) > 0)
  #else
-    if(chdir(pathcd) != 0)
+     if(chdir(pathcd) != 0)
-            printf("Can't move to directory %s!\n", path);
+       printf("Can't move to directory %s!\n", path);
-    if (getcwd(pathcd, MAXLINE) > 0)
+   if (getcwd(pathcd, MAXLINE) > 0)
  #endif
      printf("Current directory %s!\n",pathcd);
    /*strcat(plotcmd,CHARSEPARATOR);*/
- Line 8835  Please run with mle=-1 to get a correct
+ Line 11825  Please run with mle=-1 to get a correct
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
    if((outcmd=system(plotcmd)) != 0){
      printf("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");
- Line 8863  Please run with mle=-1 to get a correct
+ Line 11853  Please run with mle=-1 to get a correct
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
-   end:
+ end:
    while (z[0] != 'q') {
      printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);

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