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Diff for /imach/src/imach.c between versions 1.233 and 1.293

-version 1.233, 2016/08/23 07:40:50
+version 1.293, 2019/05/09 15:17:34
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.293  2019/05/09 15:17:34  brouard
+   *** empty log message ***
+   Revision 1.292  2019/05/09 14:17:20  brouard
+   Summary: Some updates
+   Revision 1.291  2019/05/09 13:44:18  brouard
+   Summary: Before ncovmax
+   Revision 1.290  2019/05/09 13:39:37  brouard
+   Summary: 0.99r18 unlimited number of individuals
+   The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
+   Revision 1.289  2018/12/13 09:16:26  brouard
+   Summary: Bug for young ages (<-30) will be in r17
+   Revision 1.288  2018/05/02 20:58:27  brouard
+   Summary: Some bugs fixed
+   Revision 1.287  2018/05/01 17:57:25  brouard
+   Summary: Bug fixed by providing frequencies only for non missing covariates
+   Revision 1.286  2018/04/27 14:27:04  brouard
+   Summary: some minor bugs
+   Revision 1.285  2018/04/21 21:02:16  brouard
+   Summary: Some bugs fixed, valgrind tested
+   Revision 1.284  2018/04/20 05:22:13  brouard
+   Summary: Computing mean and stdeviation of fixed quantitative variables
+   Revision 1.283  2018/04/19 14:49:16  brouard
+   Summary: Some minor bugs fixed
+   Revision 1.282  2018/02/27 22:50:02  brouard
+   *** empty log message ***
+   Revision 1.281  2018/02/27 19:25:23  brouard
+   Summary: Adding second argument for quitting
+   Revision 1.280  2018/02/21 07:58:13  brouard
+   Summary: 0.99r15
+   New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
+   Revision 1.279  2017/07/20 13:35:01  brouard
+   Summary: temporary working
+   Revision 1.278  2017/07/19 14:09:02  brouard
+   Summary: Bug for mobil_average=0 and prevforecast fixed(?)
+   Revision 1.277  2017/07/17 08:53:49  brouard
+   Summary: BOM files can be read now
+   Revision 1.276  2017/06/30 15:48:31  brouard
+   Summary: Graphs improvements
+   Revision 1.275  2017/06/30 13:39:33  brouard
+   Summary: Saito's color
+   Revision 1.274  2017/06/29 09:47:08  brouard
+   Summary: Version 0.99r14
+   Revision 1.273  2017/06/27 11:06:02  brouard
+   Summary: More documentation on projections
+   Revision 1.272  2017/06/27 10:22:40  brouard
+   Summary: Color of backprojection changed from 6 to 5(yellow)
+   Revision 1.271  2017/06/27 10:17:50  brouard
+   Summary: Some bug with rint
+   Revision 1.270  2017/05/24 05:45:29  brouard
+   *** empty log message ***
+   Revision 1.269  2017/05/23 08:39:25  brouard
+   Summary: Code into subroutine, cleanings
+   Revision 1.268  2017/05/18 20:09:32  brouard
+   Summary: backprojection and confidence intervals of backprevalence
+   Revision 1.267  2017/05/13 10:25:05  brouard
+   Summary: temporary save for backprojection
+   Revision 1.266  2017/05/13 07:26:12  brouard
+   Summary: Version 0.99r13 (improvements and bugs fixed)
+   Revision 1.265  2017/04/26 16:22:11  brouard
+   Summary: imach 0.99r13 Some bugs fixed
+   Revision 1.264  2017/04/26 06:01:29  brouard
+   Summary: Labels in graphs
+   Revision 1.263  2017/04/24 15:23:15  brouard
+   Summary: to save
+   Revision 1.262  2017/04/18 16:48:12  brouard
+   *** empty log message ***
+   Revision 1.261  2017/04/05 10:14:09  brouard
+   Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
+   Revision 1.260  2017/04/04 17:46:59  brouard
+   Summary: Gnuplot indexations fixed (humm)
+   Revision 1.259  2017/04/04 13:01:16  brouard
+   Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
+   Revision 1.258  2017/04/03 10:17:47  brouard
+   Summary: Version 0.99r12
+   Some cleanings, conformed with updated documentation.
+   Revision 1.257  2017/03/29 16:53:30  brouard
+   Summary: Temp
+   Revision 1.256  2017/03/27 05:50:23  brouard
+   Summary: Temporary
+   Revision 1.255  2017/03/08 16:02:28  brouard
+   Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
+   Revision 1.254  2017/03/08 07:13:00  brouard
+   Summary: Fixing data parameter line
+   Revision 1.253  2016/12/15 11:59:41  brouard
+   Summary: 0.99 in progress
+   Revision 1.252  2016/09/15 21:15:37  brouard
+   *** empty log message ***
+   Revision 1.251  2016/09/15 15:01:13  brouard
+   Summary: not working
+   Revision 1.250  2016/09/08 16:07:27  brouard
+   Summary: continue
+   Revision 1.249  2016/09/07 17:14:18  brouard
+   Summary: Starting values from frequencies
+   Revision 1.248  2016/09/07 14:10:18  brouard
+   *** empty log message ***
+   Revision 1.247  2016/09/02 11:11:21  brouard
+   *** empty log message ***
+   Revision 1.246  2016/09/02 08:49:22  brouard
+   *** empty log message ***
+   Revision 1.245  2016/09/02 07:25:01  brouard
+   *** empty log message ***
+   Revision 1.244  2016/09/02 07:17:34  brouard
+   *** empty log message ***
+   Revision 1.243  2016/09/02 06:45:35  brouard
+   *** empty log message ***
+   Revision 1.242  2016/08/30 15:01:20  brouard
+   Summary: Fixing a lots
+   Revision 1.241  2016/08/29 17:17:25  brouard
+   Summary: gnuplot problem in Back projection to fix
+   Revision 1.240  2016/08/29 07:53:18  brouard
+   Summary: Better
+   Revision 1.239  2016/08/26 15:51:03  brouard
+   Summary: Improvement in Powell output in order to copy and paste
+   Author:
+   Revision 1.238  2016/08/26 14:23:35  brouard
+   Summary: Starting tests of 0.99
+   Revision 1.237  2016/08/26 09:20:19  brouard
+   Summary: to valgrind
+   Revision 1.236  2016/08/25 10:50:18  brouard
+   *** empty log message ***
+   Revision 1.235  2016/08/25 06:59:23  brouard
+   *** empty log message ***
+   Revision 1.234  2016/08/23 16:51:20  brouard
+   *** empty log message ***
    Revision 1.233  2016/08/23 07:40:50  brouard
    Summary: not working
- Line 72
+ Line 260
    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 717  Back prevalence and projections:
+ Line 903  Back prevalence and projections:
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                          oldm=oldms;savm=savms;
-    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
       Computes the transition matrix starting at age 'age' over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
- Line 862  typedef struct {
+ Line 1048  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 877  typedef struct {
+ Line 1063  typedef struct {
  #define NINTERVMAX 8
  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
- #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
+ #define NCOVMAX 20  /**< Maximum number of covariates, including generated covariates V1*V2 */
  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
  #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
- #define MAXN 20000
+ /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
  #define YEARM 12. /**< Number of months per year */
  /* #define AGESUP 130 */
- #define AGESUP 150
+ /* #define AGESUP 150 */
+ #define AGESUP 200
+ #define AGEINF 0
  #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
  #define AGEBASE 40
  #define AGEOVERFLOW 1.e20
- Line 903  typedef struct {
+ Line 1091  typedef struct {
  /* $State$ */
  #include "version.h"
  char version[]=__IMACH_VERSION__;
- char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
+ char copyright[]="April 2018,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 920  int cptcoveff=0; /* Total number of cova
+ Line 1108  int cptcoveff=0; /* Total number of cova
  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 nobs=10;  /* Number of observations in the data lastobs-firstobs */
  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
  int npar=NPARMAX;
  int nlstate=2; /* Number of live states */
- Line 975  FILE *ficrescveij;
+ Line 1165  FILE *ficrescveij;
  char filerescve[FILENAMELENGTH];
  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
- FILE  *ficresvpl;
- char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
+ char model[MAXLINE]; /**< The model line */
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- Line 1015  double dval;
+ Line 1205  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 1072  double *agedc;
+ Line 1263  double *agedc;
  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                    * covar=matrix(0,NCOVMAX,1,n);
                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
- double **coqvar; /* Fixed quantitative covariate iqv */
+ double **coqvar; /* Fixed quantitative covariate nqv */
- double ***cotvar; /* Time varying covariate itv */
+ double ***cotvar; /* Time varying covariate ntv */
  double ***cotqvar; /* Time varying quantitative covariate itqv */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ /*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 */
- Line 1097  double *Tvalsel; /**< Selected modality
+ Line 1323  double *Tvalsel; /**< Selected modality
  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
  int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
  int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
+ int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
  int *Tage;
  int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
  int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
- Line 1106  int *Ndum; /** Freq of modality (tricode
+ Line 1334  int *Ndum; /** Freq of modality (tricode
  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
  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 */
- /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
-    if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
-    Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
- */
  int cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
- Line 1336  int nbocc(char *s, char occ)
+ Line 1563  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 2009  void powell(double p[], double **xi, int
+ Line 2236  void powell(double p[], double **xi, int
   void linmin(double p[], double xi[], int n, double *fret,
                double (*func)(double []));
  #else
   void linmin(double p[], double xi[], int n, double *fret,
-                                                  double (*func)(double []),int *flat);
+              double (*func)(double []),int *flat);
  #endif
-   int i,ibig,j;
+  int i,ibig,j,jk,k;
    double del,t,*pt,*ptt,*xit;
    double directest;
    double fp,fptt;
- Line 2044  void powell(double p[], double **xi, int
+ Line 2271  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;
        itmp = strlen(strcurr);
        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
-                                 strcurr[itmp-1]='\0';
+         strcurr[itmp-1]='\0';
        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
        for(niterf=10;niterf<=30;niterf+=10){
-                                 rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
+         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
-                                 forecast_time = *localtime(&rforecast_time);
+         forecast_time = *localtime(&rforecast_time);
-                                 strcpy(strfor,asctime(&forecast_time));
+         strcpy(strfor,asctime(&forecast_time));
-                                 itmp = strlen(strfor);
+         itmp = strlen(strfor);
-                                 if(strfor[itmp-1]=='\n')
+         if(strfor[itmp-1]=='\n')
-                                         strfor[itmp-1]='\0';
+           strfor[itmp-1]='\0';
-                                 printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
+         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
-                                 fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
+         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
        }
      }
      for (i=1;i<=n;i++) { /* For each direction i */
- Line 2122  void powell(double p[], double **xi, int
+ Line 2382  void powell(double p[], double **xi, int
                                  /* 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*(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 2168  void powell(double p[], double **xi, int
+ Line 2429  void powell(double p[], double **xi, int
        free_vector(pt,1,n);
        return;
      } /* enough precision */
-     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+     if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
        ptt[j]=2.0*p[j]-pt[j];
        xit[j]=p[j]-pt[j];
- Line 2227  void powell(double p[], double **xi, int
+ Line 2488  void powell(double p[], double **xi, int
        if (directest < 0.0) { /* Then we use it for new direction */
  #endif
  #ifdef DEBUGLINMIN
-                                 printf("Before linmin in direction P%d-P0\n",n);
+         printf("Before linmin in direction P%d-P0\n",n);
-                                 for (j=1;j<=n;j++) {
+         for (j=1;j<=n;j++) {
-                                         printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[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]);
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-                                         if(j % ncovmodel == 0){
+           if(j % ncovmodel == 0){
-                                                 printf("\n");
+             printf("\n");
-                                                 fprintf(ficlog,"\n");
+             fprintf(ficlog,"\n");
-                                         }
+           }
-                                 }
+         }
  #endif
  #ifdef LINMINORIGINAL
-                                 linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+         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.*/
+         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 */
+         flatdir[i]=flat; /* Function is vanishing in that direction i */
  #endif
  #ifdef DEBUGLINMIN
-                                 for (j=1;j<=n;j++) {
+         for (j=1;j<=n;j++) {
-                                         printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-                                         fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-                                         if(j % ncovmodel == 0){
+           if(j % ncovmodel == 0){
-                                                 printf("\n");
+             printf("\n");
-                                                 fprintf(ficlog,"\n");
+             fprintf(ficlog,"\n");
-                                         }
+           }
-                                 }
+         }
  #endif
-                                 for (j=1;j<=n;j++) {
+         for (j=1;j<=n;j++) {
-                                         xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
+           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 */
+           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++) {
+         for (j=1, flatd=0;j<=n;j++) {
-                                         if(flatdir[j]>0)
+           if(flatdir[j]>0)
-                                                 flatd++;
+             flatd++;
-                                 }
+         }
-                                 if(flatd >0){
+         if(flatd >0){
-                                         printf("%d flat directions\n",flatd);
+           printf("%d flat directions: ",flatd);
-                                         fprintf(ficlog,"%d flat directions\n",flatd);
+           fprintf(ficlog,"%d flat directions :",flatd);
-                                         for (j=1;j<=n;j++) {
+           for (j=1;j<=n;j++) {
-                                                 if(flatdir[j]>0){
+             if(flatdir[j]>0){
-                                                         printf("%d ",j);
+               printf("%d ",j);
-                                                         fprintf(ficlog,"%d ",j);
+               fprintf(ficlog,"%d ",j);
-                                                 }
+             }
-                                         }
+           }
-                                         printf("\n");
+           printf("\n");
-                                         fprintf(ficlog,"\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);
+         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);
+         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);
+         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);
+         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++){
+         for(j=1;j<=n;j++){
-                                         printf(" %lf",xit[j]);
+           printf(" %lf",xit[j]);
-                                         fprintf(ficlog," %lf",xit[j]);
+           fprintf(ficlog," %lf",xit[j]);
-                                 }
+         }
-                                 printf("\n");
+         printf("\n");
-                                 fprintf(ficlog,"\n");
+         fprintf(ficlog,"\n");
  #endif
        } /* end of t or directest negative */
  #ifdef POWELLNOF3INFF1TEST
  #else
-     } /* end if (fptt < fp)  */
+       } /* end if (fptt < fp)  */
  #endif
  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
-                 } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
+     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
  #else
  #endif
-   } /* loop iteration */
+                 } /* 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 and for covariate ij by left multiplying the unit
+     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
-      matrix by transitions matrix until convergence is reached with precision ftolpl */
+      *   (and selected quantitative values in nres)
-   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
+      *  by left multiplying the unit
-   /* Wx is row vector: population in state 1, population in state 2, population dead */
+      *  matrix by transitions matrix until convergence is reached with precision ftolpl
-   /* or prevalence in state 1, prevalence in state 2, 0 */
+      * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
-   /* newm is the matrix after multiplications, its rows are identical at a factor */
+      * Wx is row vector: population in state 1, population in state 2, population dead
-   /* Initial matrix pimij */
+      * or prevalence in state 1, prevalence in state 2, 0
+      * newm is the matrix after multiplications, its rows are identical at a factor.
+      * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
+      * Output is prlim.
+      * Initial matrix pimij
+      */
    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
    /*  0,                   0                  , 1} */
- Line 2325  double **prevalim(double **prlim, int nl
+ Line 2591  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 */
- Line 2333  double **prevalim(double **prlim, int nl
+ Line 2599  double **prevalim(double **prlim, int nl
    double **newm;
    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
    int ncvloop=0;
+   int first=0;
    min=vector(1,nlstate);
    max=vector(1,nlstate);
- Line 2355  double **prevalim(double **prlim, int nl
+ Line 2622  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 */
-                         /* Here comes the value of the covariate 'ij' */
+       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
-       /* 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 */
-     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
-     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
+       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
-     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
+       /* 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<=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])]; */
+     for (k=1; k<=cptcovage;k++){  /* For product with age */
-       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,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("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]];
+         }
+       }
+     }
      /*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]);*/
- Line 2408  double **prevalim(double **prlim, int nl
+ Line 2696  double **prevalim(double **prlim, int nl
        free_vector(meandiff,1,nlstate);
        return prlim;
      }
-   } /* age loop */
+   } /* agefin loop */
      /* After some age loop it doesn't converge */
-   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+   if(!first){
- Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+     first=1;
+     printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
+   }
+   fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
    free_vector(min,1,nlstate);
    free_vector(max,1,nlstate);
- Line 2425  Earliest age to start was %d-%d=%d, ncvl
+ Line 2717  Earliest age to start was %d-%d=%d, ncvl
   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
-  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
+   double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
  {
-   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
+   /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
       matrix by transitions matrix until convergence is reached with precision ftolpl */
    /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
    /* Wx is row vector: population in state 1, population in state 2, population dead */
- Line 2448  Earliest age to start was %d-%d=%d, ncvl
+ Line 2740  Earliest age to start was %d-%d=%d, ncvl
    /* If we start from prlim again, prlim tends to a constant matrix */
    int i, ii,j,k;
+   int first=0;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
    double **out, cov[NCOVMAX+1], **bmij();
- Line 2462  Earliest age to start was %d-%d=%d, ncvl
+ Line 2755  Earliest age to start was %d-%d=%d, ncvl
    max=vector(1,nlstate);
    meandiff=vector(1,nlstate);
-         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
+   dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
-         oldm=oldms; savm=savms;
+   oldm=oldms; savm=savms;
-         /* Starting with matrix unity */
+   /* Starting with matrix unity */
-         for (ii=1;ii<=nlstate+ndeath;ii++)
+   for (ii=1;ii<=nlstate+ndeath;ii++)
-                 for (j=1;j<=nlstate+ndeath;j++){
+     for (j=1;j<=nlstate+ndeath;j++){
        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      }
- Line 2476  Earliest age to start was %d-%d=%d, ncvl
+ Line 2769  Earliest age to start was %d-%d=%d, ncvl
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
    /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
-   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
+   /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
+   for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
      ncvloop++;
      newm=savm; /* oldm should be kept from previous iteration or unity at start */
                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
- Line 2484  Earliest age to start was %d-%d=%d, ncvl
+ Line 2778  Earliest age to start was %d-%d=%d, ncvl
      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("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
      }
-     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+     /* for (k=1; k<=cptcovn;k++) { */
-     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
+     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
-     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
+     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
-     for (k=1; k<=cptcovprod;k++) /* Useless */
+     /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
-       /* cov[2+nagesqr+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<=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 */
+       /* 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]];
+         }
+       }
+     }
      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- Line 2509  Earliest age to start was %d-%d=%d, ncvl
+ Line 2835  Earliest age to start was %d-%d=%d, ncvl
      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
+     /* if((int)age == 86 || (int)age == 87){ */
+     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
+     /*   for(i=1; i<=nlstate+ndeath; i++) { */
+     /*  printf("%d newm= ",i); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",newm[i][j]); */
+     /*  } */
+     /*  printf("oldm * "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",oldm[i][j]); */
+     /*  } */
+     /*  printf(" bmmij "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",pmmij[i][j]); */
+     /*  } */
+     /*  printf("\n"); */
+     /*   } */
+     /* } */
      savm=oldm;
      oldm=newm;
      for(j=1; j<=nlstate; j++){
        max[j]=0.;
        min[j]=1.;
      }
      for(j=1; j<=nlstate; j++){
        for(i=1;i<=nlstate;i++){
-                                 /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
+         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
-                                 bprlim[i][j]= newm[i][j];
+         bprlim[i][j]= newm[i][j];
-                                 max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
+         max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
-                                 min[i]=FMIN(min[i],bprlim[i][j]);
+         min[i]=FMIN(min[i],bprlim[i][j]);
        }
      }
- Line 2529  Earliest age to start was %d-%d=%d, ncvl
+ Line 2874  Earliest age to start was %d-%d=%d, ncvl
        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 */
+     } /* i loop */
      *ncvyear= -( (int)age- (int)agefin);
-     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
+     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
      if(maxmax < ftolpl){
        /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
        free_vector(min,1,nlstate);
- Line 2539  Earliest age to start was %d-%d=%d, ncvl
+ Line 2884  Earliest age to start was %d-%d=%d, ncvl
        free_vector(meandiff,1,nlstate);
        return bprlim;
      }
-   } /* age loop */
+   } /* agefin loop */
      /* After some age loop it doesn't converge */
-   printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+   if(!first){
+     first=1;
+     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
+ Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+   }
+   fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
    free_vector(min,1,nlstate);
- Line 2556  Oldest age to start was %d-%d=%d, ncvloo
+ Line 2906  Oldest age to start was %d-%d=%d, ncvloo
  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
  {
    /* According to parameters values stored in x and the covariate's values stored in cov,
-      computes the probability to be observed in state j being in state i by appying the
+      computes the probability to be observed in state j (after stepm years) being in state i by appying the
       model to the ncovmodel covariates (including constant and age).
       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
- Line 2565  double **pmij(double **ps, double *cov,
+ Line 2915  double **pmij(double **ps, double *cov,
       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
-      Outputs ps[i][j] the probability to be observed in j being in j according to
+      Outputs ps[i][j] or probability to be observed in j being in i according to
       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+      Sum on j ps[i][j] should equal to 1.
    */
    double s1, lnpijopii;
    /*double t34;*/
- Line 2618  double **pmij(double **ps, double *cov,
+ Line 2969  double **pmij(double **ps, double *cov,
        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]); */
- Line 2630  double **pmij(double **ps, double *cov,
+ Line 2997  double **pmij(double **ps, double *cov,
    /*
      for(i=1; i<= npar; i++) printf("%f ",x[i]);
                  goto end;*/
-   return ps;
+   return ps; /* Pointer is unchanged since its call */
  }
  /*************** backward transition probabilities ***************/
- Line 2639  double **pmij(double **ps, double *cov,
+ Line 3006  double **pmij(double **ps, double *cov,
  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
  {
-   /* Computes the backward probability at age agefin and covariate ij
+   /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
-    * and returns in **ps as well as **bmij.
+    * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
     */
    int i, ii, j,k;
    double **out, **pmij();
    double sumnew=0.;
    double agefin;
+   double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
    double **dnewm, **dsavm, **doldm;
    double **bbmij;
- Line 2656  double **pmij(double **ps, double *cov,
+ Line 3023  double **pmij(double **ps, double *cov,
    dsavm=ddsavms;
    agefin=cov[2];
+   /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
    /* bmij *//* age is cov[2], ij is included in cov, but we need for
-      the observed prevalence (with this covariate ij) */
+      the observed prevalence (with this covariate ij) at beginning of transition */
-   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
+   /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-   /* We do have the matrix Px in savm  and we need pij */
+   /* P_x */
+   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
+   /* outputs pmmij which is a stochastic matrix in row */
+   /* Diag(w_x) */
+   /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
+   sumnew=0.;
+   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
+   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
+     /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]);  */
+     sumnew+=prevacurrent[(int)agefin][ii][ij];
+   }
+   if(sumnew >0.01){  /* At least some value in the prevalence */
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       for (j=1;j<=nlstate+ndeath;j++)
+         doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
+     }
+   }else{
+     for (ii=1;ii<=nlstate+ndeath;ii++){
+       for (j=1;j<=nlstate+ndeath;j++)
+       doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
+     }
+     /* if(sumnew <0.9){ */
+     /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
+     /* } */
+   }
+   k3=0.0;  /* We put the last diagonal to 0 */
+   for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
+       doldm[ii][ii]= k3;
+   }
+   /* End doldm, At the end doldm is diag[(w_i)] */
+   /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
+   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
+   /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
+   /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
    for (j=1;j<=nlstate+ndeath;j++){
-     sumnew=0.; /* w1 p11 + w2 p21 only on live states */
+     sumnew=0.;
      for (ii=1;ii<=nlstate;ii++){
-       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
+       /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
+       sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
      } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
      for (ii=1;ii<=nlstate+ndeath;ii++){
-       if(sumnew >= 1.e-10){
          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
-         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
          /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
-         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
+         /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
          /* }else */
-         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
+       dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
-       }else{
-         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
-       }
      } /*End ii */
-   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
+   } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
-   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
-   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
+   ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
-   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
+   /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
-   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
-   /* left Product of this matrix by diag matrix of prevalences (savm) */
-   for (j=1;j<=nlstate+ndeath;j++){
-     for (ii=1;ii<=nlstate+ndeath;ii++){
-       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
-     }
-   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
-   ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
-   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
    /* end bmij */
-   return ps;
+   return ps; /*pointer is unchanged */
  }
  /*************** transition probabilities ***************/
- Line 2715  double **bpmij(double **ps, double *cov,
+ Line 3107  double **bpmij(double **ps, double *cov,
    /*double t34;*/
    int i,j, nc, ii, jj;
-         for(i=1; i<= nlstate; i++){
+   for(i=1; i<= nlstate; i++){
-                 for(j=1; j<i;j++){
+     for(j=1; j<i;j++){
-                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
-                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*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); */
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-                         }
+       }
-                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-                 }
+     }
-                 for(j=i+1; j<=nlstate+ndeath;j++){
+     for(j=i+1; j<=nlstate+ndeath;j++){
-                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+       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[(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];
+         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); */
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-                         }
+       }
-                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-                 }
+     }
-         }
+   }
-         for(i=1; i<= nlstate; i++){
+   for(i=1; i<= nlstate; i++){
-                 s1=0;
+     s1=0;
-                 for(j=1; j<i; j++){
+     for(j=1; j<i; j++){
-                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-                 }
+     }
-                 for(j=i+1; j<=nlstate+ndeath; j++){
+     for(j=i+1; j<=nlstate+ndeath; j++){
-                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-                 }
+     }
-                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-                 ps[i][i]=1./(s1+1.);
+     ps[i][i]=1./(s1+1.);
-                 /* Computing other pijs */
+     /* Computing other pijs */
-                 for(j=1; j<i; j++)
+     for(j=1; j<i; j++)
-                         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-                 for(j=i+1; j<=nlstate+ndeath; j++)
+     for(j=i+1; j<=nlstate+ndeath; j++)
-                         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-         } /* end i */
+   } /* end i */
-         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-                 for(jj=1; jj<= nlstate+ndeath; jj++){
+     for(jj=1; jj<= nlstate+ndeath; jj++){
-                         ps[ii][jj]=0;
+       ps[ii][jj]=0;
-                         ps[ii][ii]=1;
+       ps[ii][ii]=1;
-                 }
+     }
-         }
+   }
-         /* Added for backcast */ /* Transposed matrix too */
+   /* Added for backcast */ /* Transposed matrix too */
-         for(jj=1; jj<= nlstate+ndeath; jj++){
+   for(jj=1; jj<= nlstate+ndeath; jj++){
-                 s1=0.;
+     s1=0.;
-                 for(ii=1; ii<= nlstate+ndeath; ii++){
+     for(ii=1; ii<= nlstate+ndeath; ii++){
-                         s1+=ps[ii][jj];
+       s1+=ps[ii][jj];
-                 }
+     }
-                 for(ii=1; ii<= nlstate; ii++){
+     for(ii=1; ii<= nlstate; ii++){
-                         ps[ii][jj]=ps[ii][jj]/s1;
+       ps[ii][jj]=ps[ii][jj]/s1;
-                 }
+     }
-         }
+   }
-         /* Transposition */
+   /* Transposition */
-         for(jj=1; jj<= nlstate+ndeath; jj++){
+   for(jj=1; jj<= nlstate+ndeath; jj++){
-                 for(ii=jj; ii<= nlstate+ndeath; ii++){
+     for(ii=jj; ii<= nlstate+ndeath; ii++){
-                         s1=ps[ii][jj];
+       s1=ps[ii][jj];
-                         ps[ii][jj]=ps[jj][ii];
+       ps[ii][jj]=ps[jj][ii];
-                         ps[jj][ii]=s1;
+       ps[jj][ii]=s1;
-                 }
+     }
-         }
+   }
-         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-         /*   } */
+   /*   } */
-         /*   printf("\n "); */
+   /*   printf("\n "); */
-         /* } */
+   /* } */
-         /* printf("\n ");printf("%lf ",cov[2]);*/
+   /* printf("\n ");printf("%lf ",cov[2]);*/
-         /*
+   /*
-                 for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
-                 goto end;*/
+     goto end;*/
-         return ps;
+   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;
    for(i=nrl; i<= nrh; i++)
      for(k=ncolol; k<=ncoloh; k++){
        out[i][k]=0.;
        for(j=ncl; j<=nch; j++)
          out[i][k] +=in[i][j]*b[j][k];
      }
    return out;
  }
- /************* 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 )
+ /************* 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, int nres )
  {
    /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
       'nhstepm*hstepm*stepm' months (i.e. until
- Line 2851  double ***hpxij(double ***po, int nhstep
+ Line 3243  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 */
-         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,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,Tvar[k])]; */
+         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
+         /* 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)); */
-         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+       }
-         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
-       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
-       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
-         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,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]); */
-       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       }
+       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);*/
- Line 2887  double ***hpxij(double ***po, int nhstep
+ Line 3297  double ***hpxij(double ***po, int nhstep
      }
      for(i=1; i<=nlstate+ndeath; i++)
        for(j=1;j<=nlstate+ndeath;j++) {
-                                 po[i][j][h]=newm[i][j];
+         po[i][j][h]=newm[i][j];
-                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
        }
      /*printf("h=%d ",h);*/
    } /* end h */
-         /*     printf("\n H=%d \n",h); */
+   /*     printf("\n H=%d \n",h); */
    return po;
  }
  /************* Higher Back Matrix Product ***************/
  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
- double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
+ double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
  {
-   /* Computes the transition matrix starting at age 'age' over
+   /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
       nhstepm*hstepm matrices.
- Line 2908  double ***hbxij(double ***po, int nhstep
+ Line 3318  double ***hbxij(double ***po, int nhstep
       (typically every 2 years instead of every month which is too big
       for the memory).
       Model is determined by parameters x and covariates have to be
-      included manually here.
+      included manually here. Then we use a call to bmij(x and cov)
+      The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
    */
    int i, j, d, h, k;
-   double **out, cov[NCOVMAX+1];
+   double **out, cov[NCOVMAX+1], **bmij();
-   double **newm;
+   double **newm, ***newmm;
    double agexact;
    double agebegin, ageend;
    double **oldm, **savm;
-   oldm=oldms;savm=savms;
+   newmm=po; /* To be saved */
+   oldm=oldms;savm=savms; /* Global pointers */
    /* Hstepm could be zero and should return the unit matrix */
    for (i=1;i<=nlstate+ndeath;i++)
      for (j=1;j<=nlstate+ndeath;j++){
- Line 2932  double ***hbxij(double ***po, int nhstep
+ Line 3343  double ***hbxij(double ***po, int nhstep
        newm=savm;
        /* Covariates have to be included here again */
        cov[1]=1.;
-       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
+       agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
        cov[2]=agexact;
        if(nagesqr==1)
          cov[3]= agexact*agexact;
-       for (k=1; k<=cptcovn;k++)
+       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,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+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+         /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
-         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]; */
+       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
-       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
+         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
+       }
+       for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
+         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("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
+       }
+       for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,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])]; */
+       }
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
        /* Careful transposed matrix */
-       /* age is in cov[2] */
+       /* age is in cov[2], prevacurrent at beginning of transition. */
        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
- Line 2977  double ***hbxij(double ***po, int nhstep
+ Line 3399  double ***hbxij(double ***po, int nhstep
      for(i=1; i<=nlstate+ndeath; i++)
        for(j=1;j<=nlstate+ndeath;j++) {
          po[i][j][h]=newm[i][j];
-         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
+         /* if(h==nhstepm) */
+         /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
        }
-     /*printf("h=%d ",h);*/
+     /* printf("h=%d %.1f ",h, agexact); */
    } /* end h */
-   /*     printf("\n H=%d \n",h); */
+   /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
    return po;
  }
- Line 3039  double func( double *x)
+ Line 3462  double func( double *x)
           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
           to be observed in j being in i according to the model.
        */
-       ioffset=2+nagesqr+cptcovage;
+       ioffset=2+nagesqr ;
     /* Fixed */
-                         for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
+       for (k=1; k<=ncovf;k++){ /* 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[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 */
- Line 3057  double func( double *x)
+ Line 3480  double func( double *x)
           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
        */
        for(mi=1; mi<= wav[i]-1; mi++){
-                                 for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
+         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
-                                         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
+           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
-                                 }
+           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
-                                 for (ii=1;ii<=nlstate+ndeath;ii++)
+         }
-                                         for (j=1;j<=nlstate+ndeath;j++){
+         for (ii=1;ii<=nlstate+ndeath;ii++)
-                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           for (j=1;j<=nlstate+ndeath;j++){
-                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);
+             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-                                         }
+             savm[ii][j]=(ii==j ? 1.0 : 0.0);
-                                 for(d=0; d<dh[mi][i]; d++){
+           }
-                                         newm=savm;
+         for(d=0; d<dh[mi][i]; d++){
-                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+           newm=savm;
-                                         cov[2]=agexact;
+           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
-                                         if(nagesqr==1)
+           cov[2]=agexact;
-                                                 cov[3]= agexact*agexact;  /* Should be changed here */
+           if(nagesqr==1)
-                                         for (kk=1; kk<=cptcovage;kk++) {
+             cov[3]= agexact*agexact;  /* Should be changed here */
-                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
+           for (kk=1; kk<=cptcovage;kk++) {
-                                         }
+           if(!FixedV[Tvar[Tage[kk]]])
-                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+           else
-                                         savm=oldm;
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
-                                         oldm=newm;
+           }
-                                 } /* end mult */
+           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-                                 /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
+           savm=oldm;
-                                 /* But now since version 0.9 we anticipate for bias at large stepm.
+           oldm=newm;
-                                  * If stepm is larger than one month (smallest stepm) and if the exact delay
+         } /* end mult */
-                                  * (in months) between two waves is not a multiple of stepm, we rounded to
-                                  * the nearest (and in case of equal distance, to the lowest) interval but now
+         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
-                                  * we keep into memory the bias bh[mi][i] and also the previous matrix product
+         /* But now since version 0.9 we anticipate for bias at large stepm.
-                                  * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
+          * If stepm is larger than one month (smallest stepm) and if the exact delay
-                                  * probability in order to take into account the bias as a fraction of the way
+          * (in months) between two waves is not a multiple of stepm, we rounded to
+          * the nearest (and in case of equal distance, to the lowest) interval but now
+          * 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
                                   * -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 less biased than in previous versions.
                                   */
-                                 s1=s[mw[mi][i]][i];
+         s1=s[mw[mi][i]][i];
-                                 s2=s[mw[mi+1][i]][i];
+         s2=s[mw[mi+1][i]][i];
-                                 bbh=(double)bh[mi][i]/(double)stepm;
+         bbh=(double)bh[mi][i]/(double)stepm;
-                                 /* bias bh is positive if real duration
+         /* bias bh is positive if real duration
-                                  * is higher than the multiple of stepm and negative otherwise.
+          * is higher than the multiple of stepm and negative otherwise.
-                                  */
+          */
-                                 /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
+         /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
-                                 if( s2 > nlstate){
+         if( s2 > nlstate){
-                                         /* i.e. if s2 is a death state and if the date of death is known
+           /* i.e. if s2 is a death state and if the date of death is known
-                                                  then the contribution to the likelihood is the probability to
+              then the contribution to the likelihood is the probability to
-                                                  die between last step unit time and current  step unit time,
+              die between last step unit time and current  step unit time,
-                                                  which is also equal to probability to die before dh
+              which is also equal to probability to die before dh
-                                                  minus probability to die before dh-stepm .
+              minus probability to die before dh-stepm .
-                                                  In version up to 0.92 likelihood was computed
+              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
+           /* If, at the beginning of the maximization mostly, the
-                                                  cumulative probability or probability to be dead is
+              cumulative probability or probability to be dead is
-                                                  constant (ie = 1) over time d, the difference is equal to
+              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
+              s1 at precedent wave, to be dead a month before current
-                                                  wave is equal to probability, being at state s1 at
+              wave is equal to probability, being at state s1 at
-                                                  precedent wave, to be dead at mont of the current
+              precedent wave, to be dead at mont of the current
-                                                  wave. Then the observed probability (that this person died)
+              wave. Then the observed probability (that this person died)
-                                                  is null according to current estimated parameter. In fact,
+              is null according to current estimated parameter. In fact,
-                                                  it should be very low but not zero otherwise the log go to
+              it should be very low but not zero otherwise the log go to
-                                                  infinity.
+              infinity.
-                                         */
+           */
  /* #ifdef INFINITYORIGINAL */
  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
  /* #else */
- Line 3354  double funcone( double *x)
+ Line 3781  double funcone( double *x)
    for(k=1; k<=nlstate; k++) ll[k]=0.;
    ioffset=0;
    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
-     ioffset=2+nagesqr+cptcovage;
+     /* ioffset=2+nagesqr+cptcovage; */
+     ioffset=2+nagesqr;
      /* Fixed */
      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
      /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
- Line 3381  double funcone( double *x)
+ Line 3809  double funcone( double *x)
      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
      /* Wave varying (but not age varying) */
        for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
-                                 cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
+         /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
-                         }
+         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
+       }
        /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
-                                 /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-                                 /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
-                                 /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
+       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
-                                 /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
+       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
-                                 /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
+       /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
        /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
-                         /*      iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
-                         /*      /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
+       /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
-                         /*      cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
+       /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
        /* } */
        for (ii=1;ii<=nlstate+ndeath;ii++)
-                                 for (j=1;j<=nlstate+ndeath;j++){
+         for (j=1;j<=nlstate+ndeath;j++){
-                                         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+           oldm[ii][j]=(ii==j ? 1.0 : 0.0);
-                                         savm[ii][j]=(ii==j ? 1.0 : 0.0);
+           savm[ii][j]=(ii==j ? 1.0 : 0.0);
-                                 }
+         }
        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
-                                 /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
+       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
-                                         and mw[mi+1][i]. dh depends on stepm.*/
+         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
-                                 newm=savm;
+           and mw[mi+1][i]. dh depends on stepm.*/
-                                 agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         newm=savm;
-                                 cov[2]=agexact;
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
-                                 if(nagesqr==1)
+         cov[2]=agexact;
-                                         cov[3]= agexact*agexact;
+         if(nagesqr==1)
-                                 for (kk=1; kk<=cptcovage;kk++) {
+           cov[3]= agexact*agexact;
-                                         cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+         for (kk=1; kk<=cptcovage;kk++) {
-                                 }
+           if(!FixedV[Tvar[Tage[kk]]])
-                                 /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
-                                 /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+           else
-                                 out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
-,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         }
-                                 /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
-                                 /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
-                                 savm=oldm;
+         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-                                 oldm=newm;
+,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+         /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
+         /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
+         savm=oldm;
+         oldm=newm;
        } /* end mult */
        s1=s[mw[mi][i]][i];
        s2=s[mw[mi+1][i]][i];
        /* if(s2==-1){ */
-       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
+       /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
        /*        /\* exit(1); *\/ */
        /* } */
        bbh=(double)bh[mi][i]/(double)stepm;
- Line 3434  double funcone( double *x)
+ Line 3867  double funcone( double *x)
         * is higher than the multiple of stepm and negative otherwise.
         */
        if( s2 > nlstate && (mle <5) ){  /* Jackson */
-                                 lli=log(out[s1][s2] - savm[s1][s2]);
+         lli=log(out[s1][s2] - savm[s1][s2]);
        } else if  ( s2==-1 ) { /* alive */
-                                 for (j=1,survp=0. ; j<=nlstate; j++)
+         for (j=1,survp=0. ; j<=nlstate; j++)
-                                         survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
-                                 lli= log(survp);
+         lli= log(survp);
        }else if (mle==1){
-                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        } else if(mle==2){
-                                 lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
        } else if(mle==3){  /* exponential inter-extrapolation */
-                                 lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
+         lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
        } else if (mle==4){  /* mle=4 no inter-extrapolation */
-                                 lli=log(out[s1][s2]); /* Original formula */
+         lli=log(out[s1][s2]); /* Original formula */
        } else{  /* mle=0 back to 1 */
-                                 lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
-                                 /*lli=log(out[s1][s2]); */ /* Original formula */
+         /*lli=log(out[s1][s2]); */ /* Original formula */
        } /* End of if */
        ipmx +=1;
        sw += weight[i];
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
        if(globpr){
-                                 fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
+         fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
   %11.6f %11.6f %11.6f ", \
-                                                                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
+                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
-*weight[i]*lli,out[s1][s2],savm[s1][s2]);
+*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
-                                 for(k=1,llt=0.,l=0.; k<=nlstate; k++){
+         for(k=1,llt=0.,l=0.; k<=nlstate; k++){
-                                         llt +=ll[k]*gipmx/gsw;
+           llt +=ll[k]*gipmx/gsw;
-                                         fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
+           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
-                                 }
+         }
-                                 fprintf(ficresilk," %10.6f\n", -llt);
+         fprintf(ficresilk," %10.6f\n", -llt);
        }
          } /* end of wave */
  } /* end of individual */
- Line 3480  return -l;
+ Line 3913  return -l;
  /*************** function likelione ***********/
- void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
  {
    /* This routine should help understanding what is done with
       the selection of individuals/waves and
- Line 3504  void likelione(FILE *ficres,double p[],
+ Line 3937  void likelione(FILE *ficres,double p[],
      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
    }
-   *fretone=(*funcone)(p);
+   *fretone=(*func)(p);
    if(*globpri !=0){
      fclose(ficresilk);
      if (mle ==0)
- Line 3512  void likelione(FILE *ficres,double p[],
+ Line 3945  void likelione(FILE *ficres,double p[],
      else if(mle >=1)
        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
+     fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
      for (k=1; k<= nlstate ; k++) {
        fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
- Line 3814  double hessij( double x[], double **hess
+ Line 4247  double hessij( double x[], double **hess
        kmax=kmax+10;
      }
      if(kmax >=10 || firstime ==1){
-       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
+       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
-       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
+       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      }
- Line 3904  void ludcmp(double **a, int n, int *indx
+ Line 4337  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 3970  void pstamp(FILE *fichier)
+ Line 4412  void pstamp(FILE *fichier)
    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
  }
  /************ Frequencies ********************/
- void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
+ void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
- {  /* Some frequencies */
+ {  /* Some frequencies as well as proposing some starting values */
-   int i, m, jk, j1, bool, z1,j, k, iv;
+   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
    int iind=0, iage=0;
    int mi; /* Effective wave */
    int first;
    double ***freq; /* Frequencies */
-   double *meanq;
+   double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
+   int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
+   double *meanq, *stdq, *idq;
    double **meanqt;
    double *pp, **prop, *posprop, *pospropt;
    double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
- Line 3989  void  freqsummary(char fileres[], int ia
+ Line 4435  void  freqsummary(char fileres[], int ia
    double agebegin, ageend;
    pp=vector(1,nlstate);
-   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
    pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
    meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+   idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
    meanqt=matrix(1,lastpass,1,nqtveff);
    strcpy(fileresp,"P_");
    strcat(fileresp,fileresu);
- Line 4003  void  freqsummary(char fileres[], int ia
+ Line 4451  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 4013  void  freqsummary(char fileres[], int ia
+ Line 4461  void  freqsummary(char fileres[], int ia
    }
    else{
      fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
              fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies 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);
    }
-   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-AGEMARGE,iagemax+3+AGEMARGE);
+   y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+   x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
+   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    j1=0;
    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
    j=cptcoveff;  /* Only dummy covariates of the model */
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   first=1;
    /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
       reference=low_education V1=0,V2=0
       med_educ                V1=1 V2=0,
       high_educ               V1=0 V2=1
       Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
    */
+   dateintsum=0;
+   k2cpt=0;
-   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
+   if(cptcoveff == 0 )
-     posproptt=0.;
+     nl=1;  /* Constant and age model only */
-     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   else
-       scanf("%d", i);*/
+     nl=2;
-     for (i=-5; i<=nlstate+ndeath; i++)
-       for (jk=-5; jk<=nlstate+ndeath; jk++)
+   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
-                                 for(m=iagemin; m <= iagemax+3; m++)
+   /* Loop on nj=1 or 2 if dummy covariates j!=0
-                                         freq[i][jk][m]=0;
+    *   Loop on j1(1 to 2**cptcoveff) covariate combination
+    *     freq[s1][s2][iage] =0.
-     for (i=1; i<=nlstate; i++)  {
+    *     Loop on iind
-       for(m=iagemin; m <= iagemax+3; m++)
+    *       ++freq[s1][s2][iage] weighted
-                                 prop[i][m]=0;
+    *     end iind
-       posprop[i]=0;
+    *     if covariate and j!0
-       pospropt[i]=0;
+    *       headers Variable on one line
-     }
+    *     endif cov j!=0
-     /* for (z1=1; z1<= nqfveff; z1++) {   */
+    *     header of frequency table by age
-     /*   meanq[z1]+=0.; */
+    *     Loop on age
-     /*   for(m=1;m<=lastpass;m++){ */
+    *       pp[s1]+=freq[s1][s2][iage] weighted
-     /*  meanqt[m][z1]=0.; */
+    *       pos+=freq[s1][s2][iage] weighted
-     /*   } */
+    *       Loop on s1 initial state
-     /* } */
+    *         fprintf(ficresp
+    *       end s1
-     dateintsum=0;
+    *     end age
-     k2cpt=0;
+    *     if j!=0 computes starting values
-     /* For that combination of covariate j1, we count and print the frequencies in one pass */
+    *     end compute starting values
-     for (iind=1; iind<=imx; iind++) { /* For each individual iind */
+    *   end j1
-       bool=1;
+    * end nl
-       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
+    */
-                                 if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
-           /* for (z1=1; z1<= nqfveff; z1++) {   */
+     if(nj==1)
-           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
+       j=0;  /* First pass for the constant */
-           /* } */
+     else{
-                                         for (z1=1; z1<=cptcoveff; z1++) {
+       j=cptcoveff; /* Other passes for the covariate values */
-                                                 /* if(Tvaraff[z1] ==-20){ */
-                                                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-                                                 /* }else  if(Tvaraff[z1] ==-10){ */
-                                                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
-                                                 /* }else  */
-                                                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-                                                         /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
-                                                         bool=0;
-                                                         /* 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 */
-       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[iind];mi++){ /* For that wave */
-                                         m=mw[mi][iind];
-                                         if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-                                                 for (z1=1; z1<=cptcoveff; z1++) {
-                                                         if( Fixed[Tmodelind[z1]]==1){
-                                                                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-                                                                 if (cotvar[m][iv][iind]!= 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]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-                                                                         bool=0;
-                                                                 }
-                                                         }
-                                                 }
-                                         }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
-                                         /* bool =0 we keep that guy which corresponds to the combination of dummy values */
-                                         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 */
-                                                                 /* 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)) {
-                                                         dateintsum=dateintsum+k2;
-                                                         k2cpt++;
-                                                         /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
-                                                 }
-                                         } /* end bool 2 */
-                                 } /* end m */
-       } /* end bool */
-     } /* 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  (ncoveff>0) { */
-     if  (cptcoveff>0) {
-       fprintf(ficresp, "\n#********** Variable ");
-       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
-       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-       for (z1=1; z1<=cptcoveff; z1++){
-                                 fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                                 fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                                 fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       }
-       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(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-     }
-     fprintf(ficresp, "\n");
-     fprintf(ficresphtm, "\n");
-     /* Header of frequency table by age */
-     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-     fprintf(ficresphtmfr,"<th>Age</th> ");
-     for(jk=-1; jk <=nlstate+ndeath; jk++){
-       for(m=-1; m <=nlstate+ndeath; m++){
-                                 if(jk!=0 && m!=0)
-                                         fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
-       }
      }
-     fprintf(ficresphtmfr, "\n");
+     first=1;
+     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
-     /* For each age */
+       posproptt=0.;
-     for(iage=iagemin; iage <= iagemax+3; iage++){
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-       fprintf(ficresphtm,"<tr>");
+         scanf("%d", i);*/
-       if(iage==iagemax+1){
+       for (i=-5; i<=nlstate+ndeath; i++)
-                                 fprintf(ficlog,"1");
+         for (s2=-5; s2<=nlstate+ndeath; s2++)
-                                 fprintf(ficresphtmfr,"<tr><th>0</th> ");
+           for(m=iagemin; m <= iagemax+3; m++)
-       }else if(iage==iagemax+2){
+             freq[i][s2][m]=0;
-                                 fprintf(ficlog,"0");
-                                 fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+       for (i=1; i<=nlstate; i++)  {
-       }else if(iage==iagemax+3){
+         for(m=iagemin; m <= iagemax+3; m++)
-                                 fprintf(ficlog,"Total");
+           prop[i][m]=0;
-                                 fprintf(ficresphtmfr,"<tr><th>Total</th> ");
+         posprop[i]=0;
-       }else{
+         pospropt[i]=0;
-                                 if(first==1){
+       }
-                                         first=0;
+       for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
-                                         printf("See log file for details...\n");
+         idq[z1]=0.;
-                                 }
+         meanq[z1]=0.;
-                                 fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
+         stdq[z1]=0.;
-                                 fprintf(ficlog,"Age %d", iage);
+       }
+       /* for (z1=1; z1<= nqtveff; z1++) { */
+       /*   for(m=1;m<=lastpass;m++){ */
+       /*          meanqt[m][z1]=0.; */
+       /*        } */
+       /* }       */
+       /* dateintsum=0; */
+       /* k2cpt=0; */
+       /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
+       for (iind=1; iind<=imx; iind++) { /* For each individual iind */
+         bool=1;
+         if(j !=0){
+           if(anyvaryingduminmodel==0){ /* If All fixed covariates */
+             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
+                 /* if(Tvaraff[z1] ==-20){ */
+                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
+                 /* }else  if(Tvaraff[z1] ==-10){ */
+                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
+                 /* }else  */
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
+                   /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
+                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
+                   /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
+                      bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
+                      j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+                 } /* Onlyf fixed */
+               } /* end z1 */
+             } /* cptcovn > 0 */
+           } /* end any */
+         }/* end j==0 */
+         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
+           /* for(m=firstpass; m<=lastpass; m++){ */
+           for(mi=1; mi<wav[iind];mi++){ /* For each wave */
+             m=mw[mi][iind];
+             if(j!=0){
+               if(anyvaryingduminmodel==1){ /* Some are varying covariates */
+                 for (z1=1; z1<=cptcoveff; z1++) {
+                   if( Fixed[Tmodelind[z1]]==1){
+                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
+                                                                                       value is -1, we don't select. It differs from the
+                                                                                       constant and age model which counts them. */
+                       bool=0; /* not selected */
+                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
+                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
+                       bool=0;
+                     }
+                   }
+                 }
+               }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
+             } /* end j==0 */
+             /* bool =0 we keep that guy which corresponds to the combination of dummy values */
+             if(bool==1){ /*Selected */
+               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+                  and mw[mi+1][iind]. dh depends on stepm. */
+               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+               ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+               if(m >=firstpass && m <=lastpass){
+                 k2=anint[m][iind]+(mint[m][iind]/12.);
+                 /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+                 if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+                 if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+                 if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                   prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+                 if (m<lastpass) {
+                   /* if(s[m][iind]==4 && s[m+1][iind]==4) */
+                   /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
+                   if(s[m][iind]==-1)
+                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
+                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
+                     idq[z1]=idq[z1]+weight[iind];
+                     meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
+                     stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
+                   }
+                   /* if((int)agev[m][iind] == 55) */
+                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
+                   /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
+                   freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
+                 }
+               } /* end if between passes */
+               if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
+                 dateintsum=dateintsum+k2; /* on all covariates ?*/
+                 k2cpt++;
+                 /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
+               }
+             }else{
+               bool=1;
+             }/* end bool 2 */
+           } /* end m */
+           /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
+           /*   idq[z1]=idq[z1]+weight[iind]; */
+           /*   meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /\* Computes mean of quantitative with selected filter *\/ */
+           /*   stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/  /\* Computes mean of quantitative with selected filter *\/ */
+           /* } */
+         } /* end bool */
+       } /* end iind = 1 to imx */
+       /* prop[s][age] is 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);*/
+       if(cptcoveff==0 && nj==1) /* no covariate and first pass */
+         pstamp(ficresp);
+       if  (cptcoveff>0 && j!=0){
+         pstamp(ficresp);
+         printf( "\n#********** Variable ");
+         fprintf(ficresp, "\n#********** Variable ");
+         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+         fprintf(ficlog, "\n#********** Variable ");
+         for (z1=1; z1<=cptcoveff; z1++){
+           if(!FixedV[Tvaraff[z1]]){
+             printf( "V%d(fixed)=%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)]);
+           }
+         }
+         printf( "**********\n#");
+         fprintf(ficresp, "**********\n#");
+         fprintf(ficresphtm, "**********</h3>\n");
+         fprintf(ficresphtmfr, "**********</h3>\n");
+         fprintf(ficlog, "**********\n");
        }
-       for(jk=1; jk <=nlstate ; jk++){
+       /*
-                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+         Printing means of quantitative variables if any
-                                         pp[jk] += freq[jk][m][iage];
+       */
-       }
+       for (z1=1; z1<= nqfveff; z1++) {
-       for(jk=1; jk <=nlstate ; jk++){
+         fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
-                                 for(m=-1, pos=0; m <=0 ; m++)
+         fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
-                                         pos += freq[jk][m][iage];
+         if(weightopt==1){
-                                 if(pp[jk]>=1.e-10){
+           printf(" Weighted mean and standard deviation of");
-                                         if(first==1){
+           fprintf(ficlog," Weighted mean and standard deviation of");
-                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+           fprintf(ficresphtmfr," Weighted mean and standard deviation of");
-                                         }
+         }
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+         printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
-                                 }else{
+         fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
-                                         if(first==1)
+         fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
-                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       }
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+       /* for (z1=1; z1<= nqtveff; z1++) { */
-                                 }
+       /*        for(m=1;m<=lastpass;m++){ */
+       /*          fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
+       /*   } */
+       /* } */
+       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
+       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
+         fprintf(ficresp, " Age");
+       if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       for(i=1; i<=nlstate;i++) {
+         if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
+         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
+       }
+       if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
+       fprintf(ficresphtm, "\n");
+       /* Header of frequency table by age */
+       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
+       fprintf(ficresphtmfr,"<th>Age</th> ");
+       for(s2=-1; s2 <=nlstate+ndeath; s2++){
+         for(m=-1; m <=nlstate+ndeath; m++){
+           if(s2!=0 && m!=0)
+             fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
+         }
        }
+       fprintf(ficresphtmfr, "\n");
-       for(jk=1; jk <=nlstate ; jk++){
-                                 /* posprop[jk]=0; */
+       /* For each age */
-                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+       for(iage=iagemin; iage <= iagemax+3; iage++){
-                                         pp[jk] += freq[jk][m][iage];
+         fprintf(ficresphtm,"<tr>");
-       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
+         if(iage==iagemax+1){
+           fprintf(ficlog,"1");
-       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
+           fprintf(ficresphtmfr,"<tr><th>0</th> ");
-                                 pos += pp[jk]; /* pos is the total number of transitions until this age */
+         }else if(iage==iagemax+2){
-                                 posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
+           fprintf(ficlog,"0");
-                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
+         }else if(iage==iagemax+3){
-                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+           fprintf(ficlog,"Total");
-       }
+           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
-       for(jk=1; jk <=nlstate ; jk++){
+         }else{
-                                 if(pos>=1.e-5){
+           if(first==1){
-                                         if(first==1)
+             first=0;
-                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+             printf("See log file for details...\n");
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+           }
-                                 }else{
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
-                                         if(first==1)
+           fprintf(ficlog,"Age %d", iage);
-                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+         }
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+         for(s1=1; s1 <=nlstate ; s1++){
-                                 }
+           for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
-                                 if( iage <= iagemax){
+             pp[s1] += freq[s1][m][iage];
-                                         if(pos>=1.e-5){
+         }
-                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+         for(s1=1; s1 <=nlstate ; s1++){
-                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+           for(m=-1, pos=0; m <=0 ; m++)
-                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
+             pos += freq[s1][m][iage];
-                                                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
+           if(pp[s1]>=1.e-10){
-                                         }
+             if(first==1){
-                                         else{
+               printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
-                                                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
+             }
-                                                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
-                                         }
+           }else{
-                                 }
+             if(first==1)
-                                 pospropt[jk] +=posprop[jk];
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
-       } /* end loop jk */
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
-       /* pospropt=0.; */
+           }
-       for(jk=-1; jk <=nlstate+ndeath; jk++){
+         }
-                                 for(m=-1; m <=nlstate+ndeath; m++){
-                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+         for(s1=1; s1 <=nlstate ; s1++){
-                                                 if(first==1){
+           /* posprop[s1]=0; */
-                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
+           for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-                                                 }
+             pp[s1] += freq[s1][m][iage];
-                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
+         }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
-                                         }
-                                         if(jk!=0 && m!=0)
+         for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
-                                                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
+           pos += pp[s1]; /* pos is the total number of transitions until this age */
-                                 }
+           posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
-       } /* end loop jk */
+                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-       posproptt=0.;
+           pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
-       for(jk=1; jk <=nlstate; jk++){
+                                           from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-                                 posproptt += pospropt[jk];
+         }
-       }
-       fprintf(ficresphtmfr,"</tr>\n ");
+         /* Writing ficresp */
-       if(iage <= iagemax){
+         if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
-                                 fprintf(ficresp,"\n");
+           if( iage <= iagemax){
-                                 fprintf(ficresphtm,"</tr>\n");
+             fprintf(ficresp," %d",iage);
+           }
+         }else if( nj==2){
+           if( iage <= iagemax){
+             fprintf(ficresp," %d",iage);
+             for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           }
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           if(pos>=1.e-5){
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
+             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
+           }
+           if( iage <= iagemax){
+             if(pos>=1.e-5){
+               if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
+                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               }else if( nj==2){
+                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               }
+               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
+               /*probs[iage][s1][j1]= pp[s1]/pos;*/
+               /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
+             } else{
+               if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
+               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
+             }
+           }
+           pospropt[s1] +=posprop[s1];
+         } /* end loop s1 */
+         /* pospropt=0.; */
+         for(s1=-1; s1 <=nlstate+ndeath; s1++){
+           for(m=-1; m <=nlstate+ndeath; m++){
+             if(freq[s1][m][iage] !=0 ) { /* minimizing output */
+               if(first==1){
+                 printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
+               }
+               /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
+               fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
+             }
+             if(s1!=0 && m!=0)
+               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
+           }
+         } /* end loop s1 */
+         posproptt=0.;
+         for(s1=1; s1 <=nlstate; s1++){
+           posproptt += pospropt[s1];
+         }
+         fprintf(ficresphtmfr,"</tr>\n ");
+         fprintf(ficresphtm,"</tr>\n");
+         if((cptcoveff==0 && nj==1)|| nj==2 ) {
+           if(iage <= iagemax)
+             fprintf(ficresp,"\n");
+         }
+         if(first==1)
+           printf("Others in log...\n");
+         fprintf(ficlog,"\n");
+       } /* end loop age iage */
+       fprintf(ficresphtm,"<tr><th>Tot</th>");
+       for(s1=1; s1 <=nlstate ; s1++){
+         if(posproptt < 1.e-5){
+           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
+         }else{
+           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
+         }
        }
-       if(first==1)
+       fprintf(ficresphtm,"</tr>\n");
-                                 printf("Others in log...\n");
+       fprintf(ficresphtm,"</table>\n");
-       fprintf(ficlog,"\n");
+       fprintf(ficresphtmfr,"</table>\n");
-     } /* 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);
+         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,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+         invalidvarcomb[j1]=0;
        }
-     }
+       fprintf(ficresphtmfr,"</table>\n");
-     fprintf(ficresphtm,"</tr>\n");
+       fprintf(ficlog,"\n");
-     fprintf(ficresphtm,"</table>\n");
+       if(j!=0){
-     fprintf(ficresphtmfr,"</table>\n");
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
-     if(posproptt < 1.e-5){
+         for(i=1,s1=1; i <=nlstate; i++){
-       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+           for(k=1; k <=(nlstate+ndeath); k++){
-       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+             if (k != i) {
-       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
-       invalidvarcomb[j1]=1;
+                 if(jj==1){  /* Constant case (in fact cste + age) */
-     }else{
+                   if(j1==1){ /* All dummy covariates to zero */
-       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
-       invalidvarcomb[j1]=0;
+                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
-     }
+                     printf("%d%d ",i,k);
-     fprintf(ficresphtmfr,"</table>\n");
+                     fprintf(ficlog,"%d%d ",i,k);
-   } /* end selected combination of covariate j1 */
+                     printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
-   dateintmean=dateintsum/k2cpt;
+                     fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                     pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
-   fclose(ficresp);
+                   }
-   fclose(ficresphtm);
+                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
-   fclose(ficresphtmfr);
+                   for(iage=iagemin; iage <= iagemax+3; iage++){
-   free_vector(meanq,1,nqfveff);
+                     x[iage]= (double)iage;
-   free_matrix(meanqt,1,lastpass,1,nqtveff);
+                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+                     /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
-   free_vector(pospropt,1,nlstate);
+                   }
-   free_vector(posprop,1,nlstate);
+                   /* Some are not finite, but linreg will ignore these ages */
-   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+                   no=0;
-   free_vector(pp,1,nlstate);
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
-   /* End of freqsummary */
+                   pstart[s1]=b;
- }
+                   pstart[s1-1]=a;
+                 }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */
- /************ Prevalence ********************/
+                   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]);
- void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+                   printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
- {
+                   pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
-   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+                   printf("%d%d ",i,k);
+                   fprintf(ficlog,"%d%d ",i,k);
+                   printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
+                 }else{ /* Other cases, like quantitative fixed or varying covariates */
+                   ;
+                 }
+                 /* printf("%12.7f )", param[i][jj][k]); */
+                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+                 s1++;
+               } /* end jj */
+             } /* end k!= i */
+           } /* end k */
+         } /* end i, s1 */
+       } /* end j !=0 */
+     } /* end selected combination of covariate j1 */
+     if(j==0){ /* We can estimate starting values from the occurences in each case */
+       printf("#Freqsummary: Starting values for the constants:\n");
+       fprintf(ficlog,"\n");
+       for(i=1,s1=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(jj=1; jj <=ncovmodel; jj++){
+               pstart[s1]=p[s1]; /* Setting pstart to p values by default */
+               if(jj==1){ /* Age has to be done */
+                 pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
+                 printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                 fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+               }
+               /* printf("%12.7f )", param[i][jj][k]); */
+               /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+               s1++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       } /* end of state i */
+       printf("#Freqsummary\n");
+       fprintf(ficlog,"\n");
+       for(s1=-1; s1 <=nlstate+ndeath; s1++){
+         for(s2=-1; s2 <=nlstate+ndeath; s2++){
+           /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
+           printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
+           /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /* } */
+         }
+       } /* end loop s1 */
+       printf("\n");
+       fprintf(ficlog,"\n");
+     } /* end j=0 */
+   } /* end j */
+   if(mle == -2){  /* We want to use these values as starting values */
+     for(i=1, jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j!=i){
+           /*ca[0]= k+'a'-1;ca[1]='\0';*/
+           printf("%1d%1d",i,j);
+           fprintf(ficparo,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             /*    printf(" %lf",param[i][j][k]); */
+             /*    fprintf(ficparo," %lf",param[i][j][k]); */
+             p[jk]=pstart[jk];
+             printf(" %f ",pstart[jk]);
+             fprintf(ficparo," %f ",pstart[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficparo,"\n");
+         }
+       }
+     }
+   } /* end mle=-2 */
+   dateintmean=dateintsum/k2cpt;
+   fclose(ficresp);
+   fclose(ficresphtm);
+   fclose(ficresphtmfr);
+   free_vector(idq,1,nqfveff);
+   free_vector(meanq,1,nqfveff);
+   free_vector(stdq,1,nqfveff);
+   free_matrix(meanqt,1,lastpass,1,nqtveff);
+   free_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);
+   /* End of freqsummary */
+ }
+ /* Simple linear regression */
+ int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
+   /* y=a+bx regression */
+   double   sumx = 0.0;                        /* sum of x                      */
+   double   sumx2 = 0.0;                       /* sum of x**2                   */
+   double   sumxy = 0.0;                       /* sum of x * y                  */
+   double   sumy = 0.0;                        /* sum of y                      */
+   double   sumy2 = 0.0;                       /* sum of y**2                   */
+   double   sume2 = 0.0;                       /* sum of square or residuals */
+   double yhat;
+   double denom=0;
+   int i;
+   int ne=*no;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     sumx  += x[i];
+     sumx2 += x[i]*x[i];
+     sumxy += x[i] * y[i];
+     sumy  += y[i];
+     sumy2 += y[i]*y[i];
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   denom = (ne * sumx2 - sumx*sumx);
+   if (denom == 0) {
+     // vertical, slope m is infinity
+     *b = INFINITY;
+     *a = 0;
+     if (r) *r = 0;
+     return 1;
+   }
+   *b = (ne * sumxy  -  sumx * sumy) / denom;
+   *a = (sumy * sumx2  -  sumx * sumxy) / denom;
+   if (r!=NULL) {
+     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
+       sqrt((sumx2 - sumx*sumx/ne) *
+            (sumy2 - sumy*sumy/ne));
+   }
+   *no=ne;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     yhat = y[i] - *a -*b* x[i];
+     sume2  += yhat * yhat ;
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
+   *sa= *sb * sqrt(sumx2/ne);
+   return 0;
+ }
+ /************ Prevalence ********************/
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+ {
+   /* 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.
    */
- Line 4351  void prevalence(double ***probs, double
+ Line 5092  void prevalence(double ***probs, double
    iagemin= (int) agemin;
    iagemax= (int) agemax;
    /*pp=vector(1,nlstate);*/
-   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    j1=0;
    /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}
-   first=1;
+   first=0;
    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
      for (i=1; i<=nlstate; i++)
-       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
          prop[i][iage]=0.0;
      printf("Prevalence combination of varying and fixed dummies %d\n",j1);
      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
- Line 4392  void prevalence(double ***probs, double
+ Line 5133  void prevalence(double ***probs, double
              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                if(agev[m][i]==1) agev[m][i]=iagemax+2;
-               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
                  printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
                  exit(1);
                }
- Line 4416  void prevalence(double ***probs, double
+ Line 5157  void prevalence(double ***probs, double
            if(posprop>=1.e-5){
              probs[i][jk][j1]= prop[jk][i]/posprop;
            } else{
-             if(first==1){
+             if(!first){
-               first=0;
+               first=1;
-               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
+               printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
+             }else{
+               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
              }
            }
          }
- Line 4429  void prevalence(double ***probs, double
+ Line 5172  void prevalence(double ***probs, double
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*free_vector(pp,1,nlstate);*/
-   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
  }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- Line 4478  void  concatwav(int wav[], int **dh, int
+ Line 5221  void  concatwav(int wav[], int **dh, int
  #else
          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 pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
              firsthree=1;
            }
-           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+           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;
          }
- Line 4508  void  concatwav(int wav[], int **dh, int
+ Line 5251  void  concatwav(int wav[], int **dh, int
        /* if(mi==0)  never been interviewed correctly before death */
        /* Only death is a correct wave */
        mw[mi][i]=m;
-     }
+     } /* else not in a death state */
  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
+     else if ((int) andc[i] != 9999) {  /* Date of death is known */
-       /* m++; */
-       /* mi++; */
-       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
-       /* mw[mi][i]=m; */
        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
            nbwarn++;
- Line 4527  void  concatwav(int wav[], int **dh, int
+ Line 5266  void  concatwav(int wav[], int **dh, int
          }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.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. 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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. 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{ /* end date of interview is known */
+       }else{ /* if date of interview is unknown */
          /* death is known but not confirmed by death status at any wave */
          if(firstfour==0){
            printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
- Line 4563  void  concatwav(int wav[], int **dh, int
+ Line 5302  void  concatwav(int wav[], int **dh, int
        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 4650  void  concatwav(int wav[], int **dh, int
+ Line 5389  void  concatwav(int wav[], int **dh, int
  /*********** Tricode ****************************/
   void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
- {
+  {
-   /**< Uses cptcovn+2*cptcovprod as the number of covariates */
+    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
-   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
+    /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
-    * Boring subroutine which should only output nbcode[Tvar[j]][k]
+     * Boring subroutine which should only output nbcode[Tvar[j]][k]
-    * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
+     * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
-    * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
+     * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
-   */
+     */
-   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
+    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
-   int modmaxcovj=0; /* Modality max of covariates j */
+    int modmaxcovj=0; /* Modality max of covariates j */
-   int cptcode=0; /* Modality max of covariates j */
+    int cptcode=0; /* Modality max of covariates j */
-   int modmincovj=0; /* Modality min of covariates j */
+    int modmincovj=0; /* Modality min of covariates j */
-   /* cptcoveff=0;  */
+    /* cptcoveff=0;  */
-         /* *cptcov=0; */
+    /* *cptcov=0; */
-   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
+    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
+    for (k=1; k <= maxncov; k++)
-   /* Loop on covariates without age and products and no quantitative variable */
+      for(j=1; j<=2; j++)
-   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
+        nbcode[k][j]=0; /* Valgrind */
-   for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-     for (j=-1; (j < maxncov); j++) Ndum[j]=0;
+    /* Loop on covariates without age and products and no quantitative variable */
-     if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
+    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-       switch(Fixed[k]) {
+      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-       case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
+      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-                                 for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
+        switch(Fixed[k]) {
-                                         ij=(int)(covar[Tvar[k]][i]);
+        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-                                         /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+          for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
-                                          * If product of Vn*Vm, still boolean *:
+            ij=(int)(covar[Tvar[k]][i]);
-                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+             * If product of Vn*Vm, still boolean *:
-                                         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+             * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-                                                  modality of the nth covariate of individual i. */
+             * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-                                         if (ij > modmaxcovj)
+            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-                                                 modmaxcovj=ij;
+               modality of the nth covariate of individual i. */
-                                         else if (ij < modmincovj)
+            if (ij > modmaxcovj)
-                                                 modmincovj=ij;
+              modmaxcovj=ij;
-                                         if ((ij < -1) && (ij > NCOVMAX)){
+            else if (ij < modmincovj)
-                                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+              modmincovj=ij;
-                                                 exit(1);
+            if (ij <0 || ij >1 ){
-                                         }else
+              printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
-                                                 Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+              fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
-                                         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+            }
-                                         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+            if ((ij < -1) || (ij > NCOVMAX)){
-                                         /* getting the maximum value of the modality of the covariate
+              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-                                                  (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+              exit(1);
-                                                  female ies 1, then modmaxcovj=1.
+            }else
-                                         */
+              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-                                 } /* end for loop on individuals i */
+            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-                                 printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-                                 fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+            /* getting the maximum value of the modality of the covariate
-                                 cptcode=modmaxcovj;
+               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                                 /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+               female ies 1, then modmaxcovj=1.
-                                 /*for (i=0; i<=cptcode; i++) {*/
+            */
-                                 for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
+          } /* end for loop on individuals i */
-                                         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
+          printf(" 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", k, Tvar[k], j, Ndum[j]);
+          fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-                                         if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
+          cptcode=modmaxcovj;
-                                                 if( j != -1){
+          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-                                                         ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
+          /*for (i=0; i<=cptcode; i++) {*/
-                                                                                                                                  covariate for which somebody answered excluding
+          for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
-                                                                                                                                  undefined. Usually 2: 0 and 1. */
+            printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-                                                 }
+            fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-                                                 ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
+            if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-                                                                                                                                                 covariate for which somebody answered including
+              if( j != -1){
-                                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */
+                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
-                                         }       /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
+                                   covariate for which somebody answered excluding
-                                                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+                                   undefined. Usually 2: 0 and 1. */
-                                 } /* Ndum[-1] number of undefined modalities */
+              }
+              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
+                                      covariate for which somebody answered including
+                                      undefined. Usually 3: -1, 0 and 1. */
+            }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
+                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+          } /* Ndum[-1] number of undefined modalities */
-                                 /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-                                 /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
+          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
-                                 /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
+          /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
-                                 /* modmincovj=3; modmaxcovj = 7; */
+          /* modmincovj=3; modmaxcovj = 7; */
-                                 /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
+          /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
-                                 /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
+          /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
-                           /*             defining two dummy variables: variables V1_1 and V1_2.*/
+          /*              defining two dummy variables: variables V1_1 and V1_2.*/
-               /* nbcode[Tvar[j]][ij]=k; */
+          /* nbcode[Tvar[j]][ij]=k; */
-               /* nbcode[Tvar[j]][1]=0; */
+          /* nbcode[Tvar[j]][1]=0; */
-               /* nbcode[Tvar[j]][2]=1; */
+          /* nbcode[Tvar[j]][2]=1; */
-               /* nbcode[Tvar[j]][3]=2; */
+          /* nbcode[Tvar[j]][3]=2; */
-               /* To be continued (not working yet). */
+          /* To be continued (not working yet). */
-               ij=0; /* ij is similar to i but can jump over null modalities */
+          ij=0; /* ij is similar to i but can jump over null modalities */
-                                 for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+          /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-                   break;
+          /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
-                 }
+          /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
-                                         ij++;
+           * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
-                                         nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
+          /*, could be restored in the future */
-                                         cptcode = ij; /* New max modality for covar j */
+          for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-                                 } /* end of loop on modality i=-1 to 1 or more */
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-                                 break;
+              break;
-       case 1: /* Testing on varying covariate, could be simple and
+            }
-                * should look at waves or product of fixed *
+            ij++;
-                * varying. No time to test -1, assuming 0 and 1 only */
+            nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
-                                 ij=0;
+            cptcode = ij; /* New max modality for covar j */
-                                 for(i=0; i<=1;i++){
+          } /* end of loop on modality i=-1 to 1 or more */
-                                         nbcode[Tvar[k]][++ij]=i;
+          break;
-                                 }
+        case 1: /* Testing on varying covariate, could be simple and
-                                 break;
+                 * should look at waves or product of fixed *
-       default:
+                 * varying. No time to test -1, assuming 0 and 1 only */
-                                 break;
+          ij=0;
-       } /* end switch */
+          for(i=0; i<=1;i++){
-     } /* end dummy test */
+            nbcode[Tvar[k]][++ij]=i;
+          }
-     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+          break;
-     /*  /\*recode from 0 *\/ */
+        default:
-     /*                               k is a modality. If we have model=V1+V1*sex  */
+          break;
-     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+        } /* end switch */
-     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+      } /* end dummy test */
-     /*  } */
+    } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
-     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
-     /*  if (ij > ncodemax[j]) { */
+    for (k=-1; k< maxncov; k++) Ndum[k]=0;
-     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+    /* Look at fixed dummy (single or product) covariates to check empty modalities */
-     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-     /*    break; */
+      /* 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 */
-     /*   }  /\* end of loop on modality k *\/ */
+      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 */
-   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+      /* 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} */
-   for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   /* Look at fixed dummy (single or product) covariates to check empty modalities */
+    ij=0;
-   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
+    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
-     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-     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 */
+      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     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 */
+      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-     /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
+      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+        /* If product not in single variable we don't print results */
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-   ij=0;
+        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
-   /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
+        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*/
-   for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
-     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+        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((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
+        if(Fixed[k]!=0)
-     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
+          anyvaryingduminmodel=1;
-       /* If product not in single variable we don't print results */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
-       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
-       ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
-       Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
+        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
-       Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
-       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 */
+        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
-       if(Fixed[k]!=0)
+      }
-         anyvaryingduminmodel=1;
+    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
+    /* ij--; */
-                         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
+    /* cptcoveff=ij; /\*Number of total covariates*\/ */
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
+    *cptcov=ij; /*Number of total real effective covariates: effective
-                         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+                 * because they can be excluded from the model and real
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
+                 * if in the model but excluded because missing values, but how to get k from ij?*/
-                         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+    for(j=ij+1; j<= cptcovt; j++){
-     }
+      Tvaraff[j]=0;
-   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+      Tmodelind[j]=0;
-   /* ij--; */
+    }
-   /* cptcoveff=ij; /\*Number of total covariates*\/ */
+    for(j=ntveff+1; j<= cptcovt; j++){
-   *cptcov=ij; /*Number of total real effective covariates: effective
+      TmodelInvind[j]=0;
-                                                          * 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?*/
+    /* To be sorted */
-   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 */
-   ;
- }
  /*********** 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 4831  void evsij(double ***eij, double x[], in
+ Line 5568  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 4862  void evsij(double ***eij, double x[], in
+ Line 5599  void evsij(double ***eij, double x[], in
    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
       nhstepm is the number of hstepm from age to agelim
       nstepm is the number of stepm from age to agelin.
-      Look at hpijx to understand the reason of that which relies in memory size
+      Look at hpijx to understand the reason which relies in memory size consideration
       and note for a fixed period like estepm months */
    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       survival function given by stepm (the optimization length). Unfortunately it
- Line 4894  void evsij(double ***eij, double x[], in
+ Line 5631  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 4929  void evsij(double ***eij, double x[], in
+ Line 5666  void evsij(double ***eij, double x[], in
  }
- void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
  {
    /* Covariances of health expectancies eij and of total life expectancies according
- Line 5042  void cvevsij(double ***eij, double x[],
+ Line 5779  void cvevsij(double ***eij, double x[],
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
- Line 5084  void cvevsij(double ***eij, double x[],
+ Line 5821  void cvevsij(double ***eij, double x[],
      }
      /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- Line 5093  void cvevsij(double ***eij, double x[],
+ Line 5830  void cvevsij(double ***eij, double x[],
            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          }
+     /* Standard deviation of expectancies ij */
      fprintf(ficresstdeij,"%3.0f",age );
      for(i=1; i<=nlstate;i++){
        eip=0.;
- Line 5108  void cvevsij(double ***eij, double x[],
+ Line 5846  void cvevsij(double ***eij, double x[],
      }
      fprintf(ficresstdeij,"\n");
+     /* Variance of expectancies ij */
      fprintf(ficrescveij,"%3.0f",age );
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
- Line 5139  void cvevsij(double ***eij, double x[],
+ Line 5878  void cvevsij(double ***eij, double x[],
  }
  /************ Variance ******************/
-  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
   {
-    /* Variance of health expectancies */
+    /** Variance of health expectancies
-    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+     *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
-    /* double **newm;*/
+     * double **newm;
-    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
+     * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
+     */
     /* int movingaverage(); */
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
+    int first=0;
     int k;
     double *xp;
-    double **gp, **gm;  /* for var eij */
+    double **gp, **gm;  /**< for var eij */
-    double ***gradg, ***trgradg; /*for var eij */
+    double ***gradg, ***trgradg; /**< for var eij */
-    double **gradgp, **trgradgp; /* for var p point j */
+    double **gradgp, **trgradgp; /**< for var p point j */
-    double *gpp, *gmp; /* for var p point j */
+    double *gpp, *gmp; /**< for var p point j */
-    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+    double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     /* double ***mobaverage; */
- Line 5196  void cvevsij(double ***eij, double x[],
+ Line 5937  void cvevsij(double ***eij, double x[],
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
+    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][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);
- Line 5209  void cvevsij(double ***eij, double x[],
+ Line 5958  void cvevsij(double ***eij, double x[],
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
-    /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
- Line 5264  void cvevsij(double ***eij, double x[],
+ Line 6013  void cvevsij(double ***eij, double x[],
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
+        /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
-        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+         * returns into prlim .
+         */
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
+        /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
- Line 5276  void cvevsij(double ***eij, double x[],
+ Line 6028  void cvevsij(double ***eij, double x[],
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
+        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
-        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
+         */
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
+        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
+         * at horizon h in state j including mortality.
+         */
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
-        /* Next for computing probability of death (h=1 means
+        /* Next for computing shifted+ probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months)
-           as a weighted average of prlim.
+           as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }
-        /* end probability of death */
+        /* Again with minus shift */
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
-        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
         if (popbased==1) {
           if(mobilav ==0){
- Line 5309  void cvevsij(double ***eij, double x[],
+ Line 6066  void cvevsij(double ***eij, double x[],
           }
         }
-        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
- Line 5325  void cvevsij(double ***eij, double x[],
+ Line 6082  void cvevsij(double ***eij, double x[],
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }
-        /* end probability of death */
+        /* end shifting computations */
+        /**< Computing gradient matrix at horizon h
+         */
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
+        /**< Gradient of overall mortality p.3 (or p.j)
-        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+         */
+        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
       } /* End theta */
+      /* We got the gradient matrix for each theta and state j */
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(h=0; h<=nhstepm; h++) /* veij */
- Line 5348  void cvevsij(double ***eij, double x[],
+ Line 6109  void cvevsij(double ***eij, double x[],
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
+      /**< as well as its transposed matrix
+       */
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
+      /* Computing trgradg by matcov by gradg at age and summing over h
+       * and k (nhstepm) formula 15 of article
+       * Lievre-Brouard-Heathcote
+       */
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
- Line 5365  void cvevsij(double ***eij, double x[],
+ Line 6132  void cvevsij(double ***eij, double x[],
         }
       }
-      /* pptj */
+      /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
+       * p.j overall mortality formula 49 but computed directly because
+       * we compute the grad (wix pijx) instead of grad (pijx),even if
+       * wix is independent of theta.
+       */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
- Line 5374  void cvevsij(double ***eij, double x[],
+ Line 6145  void cvevsij(double ***eij, double x[],
       /* end ppptj */
       /*  x centered again */
-      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
       if (popbased==1) {
         if(mobilav ==0){
- Line 5390  void cvevsij(double ***eij, double x[],
+ Line 6161  void cvevsij(double ***eij, double x[],
          computed over hstepm (estepm) matrices product = hstepm*stepm months)
          as a weighted average of prlim.
       */
-      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++)
           gmp[j] += prlim[i][i]*p3mat[i][j][1];
- Line 5453  void cvevsij(double ***eij, double x[],
+ Line 6224  void cvevsij(double ***eij, double x[],
   }  /* end varevsij */
  /************ Variance of prevlim ******************/
-  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
+  void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
  {
    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
-   double **dnewm,**doldm;
+   double **dnewmpar,**doldm;
    int i, j, nhstepm, hstepm;
    double *xp;
    double *gp, *gm;
- Line 5468  void cvevsij(double ***eij, double x[],
+ Line 6239  void cvevsij(double ***eij, double x[],
    int theta;
    pstamp(ficresvpl);
-   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
+   fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+   fprintf(ficresvpl,"# Age ");
+   if(nresult >=1)
+     fprintf(ficresvpl," Result# ");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
    fprintf(ficresvpl,"\n");
    xp=vector(1,npar);
-   dnewm=matrix(1,nlstate,1,npar);
+   dnewmpar=matrix(1,nlstate,1,npar);
    doldm=matrix(1,nlstate,1,nlstate);
    hstepm=1*YEARM; /* Every year of age */
- Line 5495  void cvevsij(double ***eij, double x[],
+ Line 6268  void cvevsij(double ***eij, double x[],
        for(i=1; i<=npar; i++){ /* Computes gradient */
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
-       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
-       else
+       /* else */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gp[i] = prlim[i][i];
          mgp[theta][i] = prlim[i][i];
        }
        for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
-       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
+       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
-       else
+       /* else */
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gm[i] = prlim[i][i];
          mgm[theta][i] = prlim[i][i];
- Line 5545  void cvevsij(double ***eij, double x[],
+ Line 6318  void cvevsij(double ***eij, double x[],
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] =0.;
      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
      }else{
-     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
-     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
      }
      for(i=1;i<=nlstate;i++)
        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      fprintf(ficresvpl,"%.0f ",age );
-     for(i=1; i<=nlstate;i++)
+     if(nresult >=1)
+       fprintf(ficresvpl,"%d ",nres );
+     for(i=1; i<=nlstate;i++){
        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+       /* for(j=1;j<=nlstate;j++) */
+       /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
+     }
      fprintf(ficresvpl,"\n");
      free_vector(gp,1,nlstate);
      free_vector(gm,1,nlstate);
- Line 5568  void cvevsij(double ***eij, double x[],
+ Line 6346  void cvevsij(double ***eij, double x[],
    free_vector(xp,1,npar);
    free_matrix(doldm,1,nlstate,1,npar);
-   free_matrix(dnewm,1,nlstate,1,nlstate);
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
+ }
+ /************ Variance of backprevalence limit ******************/
+  void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
+ {
+   /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
+   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+   double **dnewmpar,**doldm;
+   int i, j, nhstepm, hstepm;
+   double *xp;
+   double *gp, *gm;
+   double **gradg, **trgradg;
+   double **mgm, **mgp;
+   double age,agelim;
+   int theta;
+   pstamp(ficresvbl);
+   fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
+   fprintf(ficresvbl,"# Age ");
+   if(nresult >=1)
+     fprintf(ficresvbl," Result# ");
+   for(i=1; i<=nlstate;i++)
+       fprintf(ficresvbl," %1d-%1d",i,i);
+   fprintf(ficresvbl,"\n");
+   xp=vector(1,npar);
+   dnewmpar=matrix(1,nlstate,1,npar);
+   doldm=matrix(1,nlstate,1,nlstate);
+   hstepm=1*YEARM; /* Every year of age */
+   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+   agelim = AGEINF;
+   for (age=fage; age>=bage; age --){ /* If stepm=6 months */
+     nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+     if (stepm >= YEARM) hstepm=1;
+     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+     gradg=matrix(1,npar,1,nlstate);
+     mgp=matrix(1,npar,1,nlstate);
+     mgm=matrix(1,npar,1,nlstate);
+     gp=vector(1,nlstate);
+     gm=vector(1,nlstate);
+     for(theta=1; theta <=npar; theta++){
+       for(i=1; i<=npar; i++){ /* Computes gradient */
+         xp[i] = x[i] + (i==theta ?delti[theta]:0);
+       }
+       if(mobilavproj > 0 )
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+       else
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+       for(i=1;i<=nlstate;i++){
+         gp[i] = bprlim[i][i];
+         mgp[theta][i] = bprlim[i][i];
+       }
+      for(i=1; i<=npar; i++) /* Computes gradient */
+         xp[i] = x[i] - (i==theta ?delti[theta]:0);
+        if(mobilavproj > 0 )
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+        else
+         bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+       for(i=1;i<=nlstate;i++){
+         gm[i] = bprlim[i][i];
+         mgm[theta][i] = bprlim[i][i];
+       }
+       for(i=1;i<=nlstate;i++)
+         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+       /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
+     } /* End theta */
+     trgradg =matrix(1,nlstate,1,npar);
+     for(j=1; j<=nlstate;j++)
+       for(theta=1; theta <=npar; theta++)
+         trgradg[j][theta]=gradg[theta][j];
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\nmgm mgp %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf(" %d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+     /*   printf("\n gradg %d ",(int)age); */
+     /*   for(j=1; j<=nlstate;j++){ */
+     /*  printf("%d ",j); */
+     /*  for(theta=1; theta <=npar; theta++) */
+     /*    printf("%d %lf ",theta,gradg[theta][j]); */
+     /*  printf("\n "); */
+     /*   } */
+     /* } */
+     for(i=1;i<=nlstate;i++)
+       varbpl[i][(int)age] =0.;
+     if((int)age==79 ||(int)age== 80  ||(int)age== 81){
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+     }else{
+     matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+     matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+     }
+     for(i=1;i<=nlstate;i++)
+       varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+     fprintf(ficresvbl,"%.0f ",age );
+     if(nresult >=1)
+       fprintf(ficresvbl,"%d ",nres );
+     for(i=1; i<=nlstate;i++)
+       fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
+     fprintf(ficresvbl,"\n");
+     free_vector(gp,1,nlstate);
+     free_vector(gm,1,nlstate);
+     free_matrix(mgm,1,npar,1,nlstate);
+     free_matrix(mgp,1,npar,1,nlstate);
+     free_matrix(gradg,1,npar,1,nlstate);
+     free_matrix(trgradg,1,nlstate,1,npar);
+   } /* End age */
+   free_vector(xp,1,npar);
+   free_matrix(doldm,1,nlstate,1,npar);
+   free_matrix(dnewmpar,1,nlstate,1,nlstate);
  }
- Line 5648  void varprob(char optionfilefiname[], do
+ Line 6551  void varprob(char optionfilefiname[], do
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
-    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
+    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
  and drawn. It helps understanding how is the covariance between two incidences.\
- Line 5845  To be simple, these graphs help to under
+ Line 6748  To be simple, these graphs help to under
                   }
                   /* Eigen vectors */
-                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+                  if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
+                    printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+                    fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+                    v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
+                  }else
+                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   /*v21=sqrt(1.-v11*v11); *//* error */
                   v21=(lc1-v1)/cv12*v11;
                   v12=-v21;
- Line 5865  To be simple, these graphs help to under
+ Line 6773  To be simple, these graphs help to under
                     fprintf(ficgp,"\nset parametric;unset label");
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                     fprintf(ficgp,"\nset ter svg size 640, 480");
-                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+                    fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
- Line 5876  To be simple, these graphs help to under
+ Line 6784  To be simple, these graphs help to under
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
-                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
+                            mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
-                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                            mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
                   }else{
                     first=0;
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
-                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
+                            mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
-                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                            mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
                   }/* if first */
                 } /* age mod 5 */
               } /* end loop age */
- Line 5913  To be simple, these graphs help to under
+ Line 6821  To be simple, these graphs help to under
  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int prevfcast, int backcast, int estepm , \
+                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
-                   double jprev1, double mprev1,double anprev1, double dateprev1, \
+                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
-                   double jprev2, double mprev2,double anprev2, double dateprev2){
+                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
-   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 5934  void printinghtml(char fileresu[], char
+ Line 6844  void printinghtml(char fileresu[], char
   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
             stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
     fprintf(fichtm,"\
-  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+  - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
     fprintf(fichtm,"\
-  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
+  - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
     fprintf(fichtm,"\
   - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
- Line 5949  void printinghtml(char fileresu[], char
+ Line 6859  void printinghtml(char fileresu[], char
     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
     }
-    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     m=pow(2,cptcoveff);
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     jj1=0;
-    for(k1=1; k1<=m;k1++){
+    fprintf(fichtm," \n<ul>");
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
+      jj1++;
+      if (cptcovn > 0) {
+        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        fprintf(fichtm,"\">");
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
+        fprintf(fichtm,"************ Results for covariates");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        if(invalidvarcomb[k1]){
+          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
+          continue;
+        }
+        fprintf(fichtm,"</a></li>");
+      } /* cptcovn >0 */
+    }
+      fprintf(fichtm," \n</ul>");
+    jj1=0;
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
+        fprintf(fichtm,"\n<p><a name=\"rescov");
+        for (cpt=1; cpt<=cptcoveff;cpt++){
+          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
+        }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
+        }
+        fprintf(fichtm,"\"</a>");
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         for (cpt=1; cpt<=cptcoveff;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
-          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
+          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+          /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
         }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
+       }
         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         if(invalidvarcomb[k1]){
- Line 5974  void printinghtml(char fileresu[], char
+ Line 6940  void printinghtml(char fileresu[], char
         }
       }
       /* aij, bij */
-      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
+      fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
- <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Pij */
-      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
+      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
- <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Quasi-incidences */
       fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
- divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
+ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
- <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
+ <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Survival functions (period) in state j */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+        fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <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.\
+        fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
-  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
+  And probability to be observed in various states (up to %d) being in state %d at different ages.       \
-  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
+  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <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 */
+      /* Period (forward stable) prevalence in each health state */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <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, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
       }
       if(backcast==1){
-        /* Period (stable) back prevalence in each health state */
+        /* Backward prevalence in each health state */
         for(cpt=1; cpt<=nlstate;cpt++){
-          fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
         }
       }
       if(prevfcast==1){
-        /* Projection of prevalence up to period (stable) prevalence in each health state */
+        /* Projection of prevalence up to period (forward stable) prevalence in each health state */
+        for(cpt=1; cpt<=nlstate;cpt++){
+          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+ <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+        }
+      }
+      if(backcast==1){
+       /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
         for(cpt=1; cpt<=nlstate;cpt++){
-          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
+          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
- <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
+  from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
+  account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
+ with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
         }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <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 k1 */
- Line 6054  See page 'Matrix of variance-covariance
+ Line 7030  See page 'Matrix of variance-covariance
     <a href=\"%s\">%s</a> <br>\n</li>",
             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
     fprintf(fichtm,"\
-  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
     fprintf(fichtm,"\
   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
     fprintf(fichtm,"\
-  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
+  - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
  /*  if(popforecast==1) fprintf(fichtm,"\n */
- Line 6076  See page 'Matrix of variance-covariance
+ Line 7052  See page 'Matrix of variance-covariance
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     jj1=0;
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k1=1; k1<=m;k1++){
+      if(m != 1 && TKresult[nres]!= k1)
+        continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         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]){
- Line 6091  See page 'Matrix of variance-covariance
+ Line 7076  See page 'Matrix of variance-covariance
         }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
- prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
+ prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\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</a>\n<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 k1 */
+   }/* End nres */
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
  }
  /******************* Gnuplot file **************/
- void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
+ void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
    char dirfileres[132],optfileres[132];
-   char gplotcondition[132];
+   char gplotcondition[132], gplotlabel[132];
-   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
    int lv=0, vlv=0, kl=0;
    int ng=0;
    int vpopbased;
    int ioffset; /* variable offset for columns */
+   int iyearc=1; /* variable column for year of projection  */
+   int iagec=1; /* variable column for age of projection  */
+   int nres=0; /* Index of resultline */
+   int istart=1; /* For starting graphs in projections */
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
- Line 6128  void printinggnuplot(char fileresu[], ch
+ Line 7118  void printinggnuplot(char fileresu[], ch
    /*#endif */
    m=pow(2,cptcoveff);
+   /* diagram of the model */
+   fprintf(ficgp,"\n#Diagram of the model \n");
+   fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
+   fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
+   fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\n#show arrow\nunset label\n");
+   fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+   fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
+   fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
+   fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
+   fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
    /* Contribution to likelihood */
    /* Plot the probability implied in the likelihood */
    fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
- Line 6160  void printinggnuplot(char fileresu[], ch
+ Line 7164  void printinggnuplot(char fileresu[], ch
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
    /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
+   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
-     for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
+     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
-       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
+         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+         if(m != 1 && TKresult[nres]!= k1)
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
+           continue;
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* We are interested in selected combination by the resultline */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
-         vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
+         strcpy(gplotlabel,"(");
-         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
-       }
+           /* 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 */
-       if(invalidvarcomb[k1]){
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-         continue;
+           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-       }
+           /* printf(" V%d=%d ",Tvaraff[k],vlv); */
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
-       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
+         }
-       fprintf(ficgp,"set xlabel \"Age\" \n\
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
- set ylabel \"Probability\" \n   \
+           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
- set ter svg size 640, 480\n     \
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
-       for (i=1; i<= nlstate ; i ++) {
+         strcpy(gplotlabel+strlen(gplotlabel),")");
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         /* printf("\n#\n"); */
-         else        fprintf(ficgp," %%*lf (%%*lf)");
+         fprintf(ficgp,"\n#\n");
-       }
+         if(invalidvarcomb[k1]){
-       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);
+           /*k1=k1-1;*/ /* To be checked */
-       for (i=1; i<= nlstate ; i ++) {
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           continue;
-         else fprintf(ficgp," %%*lf (%%*lf)");
+         }
-       }
-       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);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
-       for (i=1; i<= nlstate ; i ++) {
+         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
-         else fprintf(ficgp," %%*lf (%%*lf)");
+         fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
-       }
+         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 ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
-       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
+         /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
-       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+       /* k1-1 error should be nres-1*/
-         /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+         for (i=1; i<= nlstate ; i ++) {
-         fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         if(cptcoveff ==0){
+           else        fprintf(ficgp," %%*lf (%%*lf)");
-           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
+         }
+         fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+         for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
+         for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
+         }
+         /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
+         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
+         if(cptcoveff ==0){
+           fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
          }else{
            kl=0;
            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
- Line 6220  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7239  plot [%.f:%.f] \"%s\" every :::%d::%d u
              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
              if(k==cptcoveff){
-               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
-+(cpt-1),  cpt );  /* 4 or 6 ?*/
++cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
              }else{
                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                kl++;
              }
            } /* end covariate */
          } /* end if no covariate */
-       } /* end if backcast */
-       fprintf(ficgp,"\nset out \n");
+         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%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 */
+           if(backcast == 1){
+             fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             /* k1-1 error should be nres-1*/
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else        fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"\" w l lt 4");
+           } /* end if backprojcast */
+         } /* end if backcast */
+         /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+         fprintf(ficgp,"\nset out ;unset title;\n");
+       } /* nres */
      } /* k1 */
    } /* cpt */
-   /*2 eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-     for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+   /*2 eme*/
-       lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+   for (k1=1; k1<= m ; k1 ++){
-       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+       if(m != 1 && TKresult[nres]!= k1)
-       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         continue;
-       vlv= nbcode[Tvaraff[k]][lv];
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+       strcpy(gplotlabel,"(");
-     }
-     fprintf(ficgp,"\n#\n");
-     if(invalidvarcomb[k1]){
-       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       continue;
-     }
-     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       if(vpopbased==0)
-         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-       else
-         fprintf(ficgp,"\nreplot ");
-       for (i=1; i<= nlstate+1 ; i ++) {
-         k=2*i;
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         fprintf(ficgp,"\" t\"\" w l lt 0,");
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-       } /* state */
-     } /* vpopbased */
-     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-   } /* k1 */
-   /*3eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
        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 */
- Line 6296  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7316  plot [%.f:%.f] \"%s\" every :::%d::%d u
          /* 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);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
        }
+       /* for(k=1; k <= ncovds; k++){ */
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
        }
-       /*       k=2+nlstate*(2*cpt-2); */
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
-       k=2+(nlstate+1)*(cpt-1);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
+         fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
-       fprintf(ficgp,"set ter svg size 640, 480\n\
+         if(vpopbased==0){
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
+           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         }else
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\nreplot ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         for (i=1; i<= nlstate+1 ; i ++) {
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           k=2*i;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
+           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           fprintf(ficgp,"\" t\"\" w l lt 0,");
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+           else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+         } /* state */
+       } /* vpopbased */
+       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
+     } /* end nres */
+   } /* k1 end 2 eme*/
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<= nlstate ; cpt ++) {
+         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           /* 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);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         /*       k=2+nlstate*(2*cpt-2); */
+         k=2+(nlstate+1)*(cpt-1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+         fprintf(ficgp,"set ter svg size 640, 480\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
+         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-       */
+         */
-       for (i=1; i< nlstate ; i ++) {
+         for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
+           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+           /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-       }
+         }
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
-     }
+       }
-   }
+       fprintf(ficgp,"\nunset label;\n");
+     } /* end nres */
+   } /* end kl 3eme */
    /* 4eme */
    /* Survival functions (period) from state i in state j by initial state i */
-   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       if(m != 1 && TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
+         strcpy(gplotlabel,"(");
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
- set ter svg size 640, 480\n                                                                                                                                                                                     \
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
- unset log y\n                                                                                                                                                                                                                                           \
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       k=3;
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       for (i=1; i<= nlstate ; i ++){
+           vlv= nbcode[Tvaraff[k]][lv];
-         if(i==1){
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
-         }else{
-           fprintf(ficgp,", '' ");
          }
-         l=(nlstate+ndeath)*(i-1)+1;
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         for (j=2; j<= nlstate+ndeath ; j ++)
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-           fprintf(ficgp,"+$%d",k+l+j-1);
+         }
-         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         strcpy(gplotlabel+strlen(gplotlabel),")");
-       } /* nlstate */
+         fprintf(ficgp,"\n#\n");
-       fprintf(ficgp,"\nset out\n");
+         if(invalidvarcomb[k1]){
-     } /* end cpt state*/
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-   } /* end covariate */
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
+         for (i=1; i<= nlstate ; i ++){
+           if(i==1){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           }else{
+             fprintf(ficgp,", '' ");
+           }
+           l=(nlstate+ndeath)*(i-1)+1;
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+           for (j=2; j<= nlstate+ndeath ; j ++)
+             fprintf(ficgp,"+$%d",k+l+j-1);
+           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end nres */
+   } /* end covariate k1 */
  /* 5eme */
    /* Survival functions (period) from state i in state j by final state j */
-   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
+   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv= 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);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
- set ter svg size 640, 480\n                                             \
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
- unset log y\n                                                           \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
-       k=3;
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           if(j==1)
-         if(j==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           else
-         else
+             fprintf(ficgp,", '' ");
-           fprintf(ficgp,", '' ");
+           l=(nlstate+ndeath)*(cpt-1) +j;
-         l=(nlstate+ndeath)*(cpt-1) +j;
+           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+           /* for (i=2; i<= nlstate+ndeath ; i ++) */
-         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+         } /* nlstate */
-       } /* nlstate */
+         fprintf(ficgp,", '' ");
-       fprintf(ficgp,", '' ");
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           l=(nlstate+ndeath)*(cpt-1) +j;
-         l=(nlstate+ndeath)*(cpt-1) +j;
+           if(j < nlstate)
-         if(j < nlstate)
+             fprintf(ficgp,"$%d +",k+l);
-           fprintf(ficgp,"$%d +",k+l);
+           else
-         else
+             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         }
-       }
+         fprintf(ficgp,"\nset out; unset label;\n");
-       fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
-     } /* end cpt state*/
+     } /* end covariate */
-   } /* end covariate */
+   } /* end nres */
  /* 6eme */
    /* CV preval stable (period) for each covariate */
-   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     if(m != 1 && TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       continue;
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
+       strcpy(gplotlabel,"(");
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6430  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7547  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          /* 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);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
        }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
        }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+       fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
        k=3; /* Offset */
-       for (i=1; i<= nlstate ; i ++){
+       for (i=1; i<= nlstate ; i ++){ /* State of origin */
          if(i==1)
            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
          else
            fprintf(ficgp,", '' ");
-         l=(nlstate+ndeath)*(i-1)+1;
+         l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
          for (j=2; j<= nlstate ; j ++)
            fprintf(ficgp,"+$%d",k+l+j-1);
          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
        } /* nlstate */
-       fprintf(ficgp,"\nset out\n");
+       fprintf(ficgp,"\nset out; unset label;\n");
      } /* end cpt state*/
    } /* end covariate */
  /* 7eme */
    if(backcast == 1){
-     /* CV back preval stable (period) for each covariate */
+     /* CV backward prevalence  for each covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
-       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6472  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7598  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            /* 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);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
          }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
            continue;
          }
-         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
          k=3; /* Offset */
-         for (i=1; i<= nlstate ; i ++){
+         for (i=1; i<= nlstate ; i ++){ /* State of arrival */
            if(i==1)
              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
            else
              fprintf(ficgp,", '' ");
            /* l=(nlstate+ndeath)*(i-1)+1; */
-           l=(nlstate+ndeath)*(cpt-1)+1;
+           l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
-           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
            /* for (j=2; j<= nlstate ; j ++) */
            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
-           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
          } /* nlstate */
-         fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if backcast */
    /* 8eme */
    if(prevfcast==1){
-     /* Projection from cross-sectional to stable (period) for each covariate */
+     /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
-         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6519  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7654  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            /* 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);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
          }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
- Line 6527  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7668  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          }
          fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
-         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
-         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+         istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+         /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+         for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
            /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
            /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
            /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-           if(i==1){
+           if(i==istart){
              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
            }else{
              fprintf(ficgp,",\\\n '' ");
- Line 6549  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7693  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
              /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
              fprintf(ficgp," u %d:(", ioffset);
-             if(i==nlstate+1)
+             if(i==nlstate+1){
-               fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
+               fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-             else
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",ioffset);
+               fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
+                      offyear,                           \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
+             }else
                fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
            }else{ /* more than 2 covariates */
-             if(cptcoveff ==1){
+             ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
-               ioffset=4; /* Age is in 4 */
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-             }else{
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-               ioffset=6; /* Age is in 6 */
+             iyearc=ioffset-1;
-               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+             iagec=ioffset;
-               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-             }
              fprintf(ficgp," u %d:(",ioffset);
              kl=0;
              strcpy(gplotcondition,"(");
- Line 6584  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7731  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
              if(i==nlstate+1){
-               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
-                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",iagec);
+               fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
+                       iyearc, iagec, offyear,                           \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
+ /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
              }else{
                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
              }
            } /* end if covariate */
          } /* nlstate */
-         fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if prevfcast */
+   if(backcast==1){
+     /* Back projection from cross-sectional to stable (mixed) for each covariate */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           /* 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);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
+         istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+         /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+         for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           if(i==istart){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
+           }else{
+             fprintf(ficgp,",\\\n '' ");
+           }
+           if(cptcoveff ==0){ /* No covariate */
+             ioffset=2; /* Age is in 2 */
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             fprintf(ficgp," u %d:(", ioffset);
+             if(i==nlstate+1){
+               fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",ioffset);
+               fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
+                      offbyear,                          \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
+             }else
+               fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
+           }else{ /* more than 2 covariates */
+             ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
+             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             iyearc=ioffset-1;
+             iagec=ioffset;
+             fprintf(ficgp," u %d:(",ioffset);
+             kl=0;
+             strcpy(gplotcondition,"(");
+             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
+               kl++;
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+               kl++;
+               if(k <cptcoveff && cptcoveff>1)
+                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+             }
+             strcpy(gplotcondition+strlen(gplotcondition),")");
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             if(i==nlstate+1){
+               fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",iagec);
+               /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
+               fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
+                       iyearc,iagec,offbyear,                            \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
+ /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
+             }else{
+               /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
+               fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
+             }
+           } /* end if covariate */
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if backcast */
-   /* 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 6616  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7884  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"##############\n#\n");
    /*goto avoid;*/
-   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
+   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
+   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
- Line 6631  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7900  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
    fprintf(ficgp,"#\n");
    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-     fprintf(ficgp,"# ng=%d\n",ng);
+     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
-     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
+     fprintf(ficgp,"#model=%s \n",model);
-     for(jk=1; jk <=m; jk++) {
+     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
-       fprintf(ficgp,"#    jk=%d\n",jk);
+     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
+     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
+       strcpy(gplotlabel,"(");
+       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
+       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
+         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+         /* 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);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+       }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
+       fprintf(ficgp,"\n#\n");
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
+       fprintf(ficgp,"\nset key outside ");
+       /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
+       fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
        fprintf(ficgp,"\nset ter svg size 640, 480 ");
        if (ng==1){
          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
- Line 6675  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7969  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                break;
              }
              ij=1;/* To be checked else nbcode[0][0] wrong */
-             for(j=3; j <=ncovmodel-nagesqr; j++) {
+             ijp=1; /* product no age */
+             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
+             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
-               if(ij <=cptcovage) { /* Bug valgrind */
+               if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                 if((j-2)==Tage[ij]) { /* Bug valgrind */
+                 if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
-                   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                   if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                     if(DummyV[j]==0){
-                   ij++;
+                       fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+                     }else{ /* quantitative */
+                       fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                       /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+                     }
+                     ij++;
+                   }
+                 }
+               }else if(cptcovprod >0){
+                 if(j==Tprod[ijp]) { /* */
+                   /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+                   if(ijp <=cptcovprod) { /* Product */
+                     if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
+                       if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                         /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
+                         fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                       }else{ /* Vn is dummy and Vm is quanti */
+                         /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                       }
+                     }else{ /* Vn*Vm Vn is quanti */
+                       if(DummyV[Tvard[ijp][2]]==0){
+                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+                       }else{ /* Both quanti */
+                         fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                       }
+                     }
+                     ijp++;
+                   }
+                 } /* end Tprod */
+               } else{  /* simple covariate */
+                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
+                 if(Dummy[j]==0){
+                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
+                 }else{ /* quantitative */
+                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
+                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                  }
-               }
+               } /* end simple */
-               else
+             } /* end j */
-                 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
-             }
            }else{
              i=i-ncovmodel;
              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
- Line 6696  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8026  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            if(ng != 1){
              fprintf(ficgp,")/(1");
-             for(k1=1; k1 <=nlstate; k1++){
+             for(cpt=1; cpt <=nlstate; cpt++){
                if(nagesqr==0)
-                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
                else /* nagesqr =1 */
-                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
+                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                ij=1;
                for(j=3; j <=ncovmodel-nagesqr; j++){
-                 if(ij <=cptcovage) { /* Bug valgrind */
+                  if(cptcovage >0){
-                   if((j-2)==Tage[ij]) { /* Bug valgrind */
+                    if((j-2)==Tage[ij]) { /* Bug valgrind */
-                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                      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,Tvar[j-2])]); */
+                        fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
-                     ij++;
+                        /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,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 */
+                  }else
+                    fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
                }
                fprintf(ficgp,")");
              }
              fprintf(ficgp,")");
              if(ng ==2)
-               fprintf(ficgp," t \"p%d%d\" ", k2,k);
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
              else /* ng= 3 */
-               fprintf(ficgp," t \"i%d%d\" ", k2,k);
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
            }else{ /* end ng <> 1 */
              if( k !=k2) /* logit p11 is hard to draw */
-               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
            }
            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
              fprintf(ficgp,",");
- Line 6732  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8063  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            i=i+ncovmodel;
          } /* end k */
        } /* end k2 */
-       fprintf(ficgp,"\n set out\n");
+       /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
-     } /* end jk */
+       fprintf(ficgp,"\n set out; unset title;set key default;\n");
+     } /* end k1 */
    } /* end ng */
    /* avoid: */
    fflush(ficgp);
- Line 6748  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8080  plot [%.f:%.f]  ", ageminpar, agemaxpar)
     int modcovmax =1;
     int mobilavrange, mob;
     int iage=0;
+    int firstA1=0, firstA2=0;
-    double sum=0.;
+    double sum=0., sumr=0.;
     double age;
-    double *sumnewp, *sumnewm;
+    double *sumnewp, *sumnewm, *sumnewmr;
-    double *agemingood, *agemaxgood; /* Currently identical for all covariates */
+    double *agemingood, *agemaxgood;
+    double *agemingoodr, *agemaxgoodr;
-    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
+    /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
-    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
+    /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
     sumnewp = vector(1,ncovcombmax);
     sumnewm = vector(1,ncovcombmax);
+    sumnewmr = vector(1,ncovcombmax);
     agemingood = vector(1,ncovcombmax);
+    agemingoodr = vector(1,ncovcombmax);
     agemaxgood = vector(1,ncovcombmax);
+    agemaxgoodr = vector(1,ncovcombmax);
     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-      sumnewm[cptcod]=0.;
+      sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
       sumnewp[cptcod]=0.;
-      agemingood[cptcod]=0;
+      agemingood[cptcod]=0, agemingoodr[cptcod]=0;
-      agemaxgood[cptcod]=0;
+      agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
     }
     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
-    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
+    if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
-      if(mobilav==1) mobilavrange=5; /* default */
+      if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
- Line 6784  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8121  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       */
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-          for (i=1; i<=nlstate;i++){
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+            sumnewm[cptcod]=0.;
+            for (i=1; i<=nlstate;i++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
               for (cpt=1;cpt<=(mob-1)/2;cpt++){
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
               }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-            }
+              sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-          }
+            } /* end i */
+            if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
+          } /* end cptcod */
         }/* end age */
       }/* end mob */
-    }else
+    }else{
+      printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
       return -1;
-    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+    }
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
       if(invalidvarcomb[cptcod]){
         printf("\nCombination (%d) ignored because no cases \n",cptcod);
         continue;
       }
-      agemingood[cptcod]=fage-(mob-1)/2;
+      for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
-      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
         sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemingoodr[cptcod]=age;
         }
         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
-          agemingood[cptcod]=age;
+            agemingood[cptcod]=age;
-        }else{ /* bad */
+        }
-          for (i=1; i<=nlstate;i++){
+      } /* age */
-            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
-          } /* i */
-        } /* end bad */
-      }/* age */
-      sum=0.;
-      for (i=1; i<=nlstate;i++){
-        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
-      }
-      if(fabs(sum - 1.) > 1.e-3) { /* bad */
-        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
-        /* for (i=1; i<=nlstate;i++){ */
-        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
-        /* } /\* i *\/ */
-      } /* end bad */
-      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
-      /* From youngest, finding the oldest wrong */
-      agemaxgood[cptcod]=bage+(mob-1)/2;
-      for (age=bage+(mob-1)/2; age<=fage; age++){
         sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemaxgoodr[cptcod]=age;
         }
         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
           agemaxgood[cptcod]=age;
-        }else{ /* bad */
+        }
-          for (i=1; i<=nlstate;i++){
+      } /* age */
-            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
-          } /* i */
+      /* but they will change */
+      firstA1=0;firstA2=0;
+      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
+        sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
+        for (i=1; i<=nlstate;i++){
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
+          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+            agemaxgoodr[cptcod]=age;  /* age min */
+            for (i=1; i<=nlstate;i++)
+              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }else{
+          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemaxgood[cptcod]=age;
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }/* end else */
+        sum=0.;sumr=0.;
+        for (i=1; i<=nlstate;i++){
+          sum+=mobaverage[(int)age][i][cptcod];
+          sumr+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sum - 1.) > 1.e-3) { /* bad */
+          if(!firstA1){
+            firstA1=1;
+            printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
+          }
+          fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
+        } /* end bad */
+        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
+          if(!firstA2){
+            firstA2=1;
+            printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
+          }
+          fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
         } /* end bad */
       }/* age */
-      sum=0.;
-      for (i=1; i<=nlstate;i++){
+      for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
-        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+        sumnewm[cptcod]=0.;
-      }
+        sumnewmr[cptcod]=0.;
-      if(fabs(sum - 1.) > 1.e-3) { /* bad */
+        for (i=1; i<=nlstate;i++){
-        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
+          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-        /* for (i=1; i<=nlstate;i++){ */
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
-        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
+        }
-        /* } /\* i *\/ */
+        if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
-      } /* end bad */
+          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemingoodr[cptcod]=age;
+            for (i=1; i<=nlstate;i++)
+              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
+          }else{ /* bad we change the value with the values of good ages */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }else{
+          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
+            agemingood[cptcod]=age;
+          }else{ /* bad */
+            for (i=1; i<=nlstate;i++){
+              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+            } /* i */
+          } /* end bad */
+        }/* end else */
+        sum=0.;sumr=0.;
+        for (i=1; i<=nlstate;i++){
+          sum+=mobaverage[(int)age][i][cptcod];
+          sumr+=mobaverage[(int)age][i][cptcod];
+        }
+        if(fabs(sum - 1.) > 1.e-3) { /* bad */
+          printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
+        } /* end bad */
+        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
+        if(fabs(sumr - 1.) > 1.e-3) { /* bad */
+          printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
+        } /* end bad */
+      }/* age */
       for (age=bage; age<=fage; age++){
-        printf("%d %d ", cptcod, (int)age);
+        /* printf("%d %d ", cptcod, (int)age); */
         sumnewp[cptcod]=0.;
         sumnewm[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
- Line 6869  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8281  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       }
       /* printf("\n"); */
       /* } */
       /* brutal averaging */
-      for (i=1; i<=nlstate;i++){
+      /* for (i=1; i<=nlstate;i++){ */
-        for (age=1; age<=bage; age++){
+      /*   for (age=1; age<=bage; age++){ */
-          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
-          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
-        }
+      /*   }      */
-        for (age=fage; age<=AGESUP; age++){
+      /*   for (age=fage; age<=AGESUP; age++){ */
-          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
-          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
-        }
+      /*   } */
-      } /* end i status */
+      /* } /\* end i status *\/ */
-      for (i=nlstate+1; i<=nlstate+ndeath;i++){
+      /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
-        for (age=1; age<=AGESUP; age++){
+      /*   for (age=1; age<=AGESUP; age++){ */
-          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
+      /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
-          mobaverage[(int)age][i][cptcod]=0.;
+      /*          mobaverage[(int)age][i][cptcod]=0.; */
-        }
+      /*   } */
-      }
+      /* } */
     }/* end cptcod */
-    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(agemaxgoodr,1, ncovcombmax);
-    free_vector(sumnewp,1, ncovcombmax);
     free_vector(agemaxgood,1, ncovcombmax);
     free_vector(agemingood,1, ncovcombmax);
+    free_vector(agemingoodr,1, ncovcombmax);
+    free_vector(sumnewmr,1, ncovcombmax);
+    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
     return 0;
   }/* End movingaverage */
  /************** Forecasting ******************/
- void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, 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;
- Line 6917  void prevforecast(char fileres[], double
+ Line 8333  void prevforecast(char fileres[], double
    */
    /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
    /*          firstpass, lastpass,  stepm,  weightopt, model); */
    strcpy(fileresf,"F_");
    strcat(fileresf,fileresu);
    if((ficresf=fopen(fileresf,"w"))==NULL) {
      printf("Problem with forecast resultfile: %s\n", fileresf);
      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
    }
-   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
+   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
+   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
+   if (stepm<=12) stepsize=1;
+   if(estepm < stepm){
+     printf ("Problem %d lower than %d\n",estepm, stepm);
+   }
+   else{
+     hstepm=estepm;
+   }
+   if(estepm > stepm){ /* Yes every two year */
+     stepsize=2;
+   }
+   hstepm=hstepm/stepm;
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
+                                fractional in yp1 */
+   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=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(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(k=1; k<=i1;k++){
+     if(i1 != 1 && TKresult[nres]!= k)
+       continue;
+     if(invalidvarcomb[k]){
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
+       continue;
+     }
+     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+     for(j=1;j<=cptcoveff;j++) {
+       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+     }
+     fprintf(ficresf," yearproj age");
+     for(j=1; j<=nlstate+ndeath;j++){
+       for(i=1; i<=nlstate;i++)
+         fprintf(ficresf," p%d%d",i,j);
+       fprintf(ficresf," wp.%d",j);
+     }
+     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficresf,"\n");
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+       /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
+       for (agec=fage; agec>=(bage); agec--){
+         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+         nhstepm = nhstepm/hstepm;
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         oldm=oldms;savm=savms;
+         /* We compute pii at age agec over nhstepm);*/
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
+         /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+         for (h=0; h<=nhstepm; h++){
+           if (h*hstepm/YEARM*stepm ==yearp) {
+             break;
+           }
+         }
+         fprintf(ficresf,"\n");
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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]*prev[(int)agec][i][k];
+             else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+             }
+             fprintf(ficresf," %.3f", p3mat[i][j][h]);
+           } /* end i */
+           fprintf(ficresf," %.3f", ppij);
+         }/* end j */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+       /* diffyear=(int) anproj1+yearp-ageminpar-1; */
+       /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
+     } /* end yearp */
+   } /* end  k */
+   fclose(ficresf);
+   printf("End of Computing forecasting \n");
+   fprintf(ficlog,"End of Computing forecasting\n");
+ }
+ /************** Back Forecasting ******************/
+  void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
+   /* 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 end of backprojection (same day and month as back1).
+      prevacurrent and prev are prevalences.
+   */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
+   double agec; /* generic age */
+   double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+   double *popeffectif,*popcount;
+   double ***p3mat;
+   /* double ***mobaverage; */
+   char fileresfb[FILENAMELENGTH];
+   agelim=AGEINF;
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
+      We still use firstpass and lastpass as another selection.
+   */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
+   /*Do we need to compute prevalence again?*/
+   /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+   strcpy(fileresfb,"FB_");
+   strcat(fileresfb,fileresu);
+   if((ficresfb=fopen(fileresfb,"w"))==NULL) {
+     printf("Problem with back forecast resultfile: %s\n", fileresfb);
+     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
+   }
+   printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
    stepsize=(int) (stepm+YEARM-1)/YEARM;
    if (stepm<=12) stepsize=1;
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
-   else  hstepm=estepm;
+   else{
+     hstepm=estepm;
-   hstepm=hstepm/stepm;
+   }
+   if(estepm >= stepm){ /* Yes every two year */
+     stepsize=2;
+   }
+   hstepm=hstepm/stepm;
    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                 fractional in yp1 */
    anprojmean=yp;
- Line 6947  void prevforecast(char fileres[], double
+ Line 8507  void prevforecast(char fileres[], double
    jprojmean=yp;
    if(jprojmean==0) jprojmean=1;
    if(mprojmean==0) jprojmean=1;
    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(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-   fprintf(ficresf,"#****** Routine prevforecast **\n");
+   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
- /*            if (h==(int)(YEARM*yearp)){ */
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
-   for(k=1;k<=i1;k++){
+   for(k=1; k<=i1;k++){
+     if(i1 != 1 && TKresult[nres]!= k)
+       continue;
      if(invalidvarcomb[k]){
        printf("\nCombination (%d) projection ignored because no cases \n",k);
        continue;
      }
-     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
      for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
      }
-     fprintf(ficresf," yearproj age");
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-     for(j=1; j<=nlstate+ndeath;j++){
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       for(i=1; i<=nlstate;i++)
-         fprintf(ficresf," p%d%d",i,j);
-       fprintf(ficresf," wp.%d",j);
      }
-     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+     fprintf(ficresfb," yearbproj age");
-       fprintf(ficresf,"\n");
+     for(j=1; j<=nlstate+ndeath;j++){
-       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+       for(i=1; i<=nlstate;i++)
-       for (agec=fage; agec>=(ageminpar-1); agec--){
+         fprintf(ficresfb," b%d%d",i,j);
-         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       fprintf(ficresfb," b.%d",j);
-         nhstepm = nhstepm/hstepm;
+     }
+     for (yearp=0; yearp>=(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);
+       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
+       /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
+       for (agec=bage; agec<=fage; agec++){  /* testing */
+         /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
+         nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
+         nhstepm = nhstepm/hstepm;
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+         /* computes hbxij at age agec over 1 to nhstepm */
+         /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
+         hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
+         /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
+         /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+         /* printf(" agec=%.2f\n",agec);fflush(stdout); */
          for (h=0; h<=nhstepm; h++){
-           if (h*hstepm/YEARM*stepm ==yearp) {
+           if (h*hstepm/YEARM*stepm ==-yearp) {
-             fprintf(ficresf,"\n");
+             break;
-             for(j=1;j<=cptcoveff;j++)
+           }
-               fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         }
-             fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+         fprintf(ficresfb,"\n");
-           }
+         for(j=1;j<=cptcoveff;j++)
-           for(j=1; j<=nlstate+ndeath;j++) {
+           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-             ppij=0.;
+         fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
-             for(i=1; i<=nlstate;i++) {
+         for(i=1; i<=nlstate+ndeath;i++) {
-               if (mobilav==1)
+           ppij=0.;ppi=0.;
-                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
+           for(j=1; j<=nlstate;j++) {
-               else {
+             /* if (mobilav==1) */
-                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+             ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
-               }
+             ppi=ppi+prevacurrent[(int)agec][j][k];
-               if (h*hstepm/YEARM*stepm== yearp) {
+             /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
-                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
+             /* ppi=ppi+mobaverage[(int)agec][j][k]; */
-               }
+               /* else { */
-             } /* end i */
+               /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
-             if (h*hstepm/YEARM*stepm==yearp) {
+               /* } */
-               fprintf(ficresf," %.3f", ppij);
+             fprintf(ficresfb," %.3f", p3mat[i][j][h]);
-             }
+           } /* end j */
-           }/* end j */
+           if(ppi <0.99){
-         } /* end h */
+             printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+             fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+           }
+           fprintf(ficresfb," %.3f", ppij);
+         }/* end j */
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        } /* end agec */
      } /* end yearp */
-   } /* end  k */
+   } /* end k */
-   fclose(ficresf);
-   printf("End of Computing forecasting \n");
-   fprintf(ficlog,"End of Computing forecasting\n");
- }
- /* /\************** Back Forecasting ******************\/ */
- /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
- /*   /\* back1, year, month, day of starting backection  */
- /*      agemin, agemax range of age */
- /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
- /*      anback2 year of en of backection (same day and month as back1). */
- /*   *\/ */
- /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
- /*   double agec; /\* generic age *\/ */
- /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
- /*   double *popeffectif,*popcount; */
- /*   double ***p3mat; */
- /*   /\* double ***mobaverage; *\/ */
- /*   char fileresfb[FILENAMELENGTH]; */
- /*   agelim=AGESUP; */
- /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
- /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
- /*      We still use firstpass and lastpass as another selection. */
- /*   *\/ */
- /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
- /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
- /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
- /*   strcpy(fileresfb,"FB_");  */
- /*   strcat(fileresfb,fileresu); */
- /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
- /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
- /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
- /*   } */
- /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
- /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
- /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
- /*   /\* if (mobilav!=0) { *\/ */
- /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
- /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
- /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
- /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
- /*   /\*   } *\/ */
- /*   /\* } *\/ */
- /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
- /*   if (stepm<=12) stepsize=1; */
- /*   if(estepm < stepm){ */
- /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
- /*   } */
- /*   else  hstepm=estepm;    */
- /*   hstepm=hstepm/stepm;  */
- /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
- /*                                fractional in yp1 *\/ */
- /*   anprojmean=yp; */
- /*   yp2=modf((yp1*12),&yp); */
- /*   mprojmean=yp; */
- /*   yp1=modf((yp2*30.5),&yp); */
- /*   jprojmean=yp; */
- /*   if(jprojmean==0) jprojmean=1; */
- /*   if(mprojmean==0) jprojmean=1; */
- /*   i1=cptcoveff; */
- /*   if (cptcovn < 1){i1=1;} */
- /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
+   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
- /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
+   fclose(ficresfb);
+   printf("End of Computing Back forecasting \n");
- /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
+   fprintf(ficlog,"End of Computing Back forecasting\n");
- /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
- /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
- /*       k=k+1; */
- /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
- /*       for(j=1;j<=cptcoveff;j++) { */
- /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
- /*       } */
- /*       fprintf(ficresfb," yearbproj age"); */
- /*       for(j=1; j<=nlstate+ndeath;j++){  */
- /*                              for(i=1; i<=nlstate;i++)               */
- /*           fprintf(ficresfb," p%d%d",i,j); */
- /*                              fprintf(ficresfb," p.%d",j); */
- /*       } */
- /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
- /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
- /*                              fprintf(ficresfb,"\n"); */
- /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
- /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
- /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
- /*                                      nhstepm = nhstepm/hstepm;  */
- /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
- /*                                      oldm=oldms;savm=savms; */
- /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
- /*                                      for (h=0; h<=nhstepm; h++){ */
- /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
- /*               fprintf(ficresfb,"\n"); */
- /*               for(j=1;j<=cptcoveff;j++)  */
- /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
- /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
- /*                                              }  */
- /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
- /*                                                      ppij=0.; */
- /*                                                      for(i=1; i<=nlstate;i++) { */
- /*                                                              if (mobilav==1)  */
- /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
- /*                                                              else { */
- /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
- /*                                                              } */
- /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
- /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
- /*                                                              } */
- /*                                                      } /\* end i *\/ */
- /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
- /*                                                              fprintf(ficresfb," %.3f", ppij); */
- /*                                                      } */
- /*                                              }/\* end j *\/ */
- /*                                      } /\* end h *\/ */
- /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
- /*                              } /\* end agec *\/ */
- /*       } /\* end yearp *\/ */
- /*     } /\* end cptcod *\/ */
- /*   } /\* end  cptcov *\/ */
- /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
- /*   fclose(ficresfb); */
+ }
- /*   printf("End of Computing Back forecasting \n"); */
- /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
+ /* Variance of prevalence limit: varprlim */
+  void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
- /* } */
+     /*------- Variance of forward period (stable) prevalence------*/
+    char fileresvpl[FILENAMELENGTH];
+    FILE *ficresvpl;
+    double **oldm, **savm;
+    double **varpl; /* Variances of prevalence limits by age */
+    int i1, k, nres, j ;
+     strcpy(fileresvpl,"VPL_");
+     strcat(fileresvpl,fileresu);
+     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+       printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
+       exit(0);
+     }
+     printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+     fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       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);
+       oldm=oldms;savm=savms;
+       varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       /*}*/
+     }
+     fclose(ficresvpl);
+     printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
+  }
+ /* Variance of back prevalence: varbprlim */
+  void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
+       /*------- Variance of back (stable) prevalence------*/
+    char fileresvbl[FILENAMELENGTH];
+    FILE  *ficresvbl;
+    double **oldm, **savm;
+    double **varbpl; /* Variances of back prevalence limits by age */
+    int i1, k, nres, j ;
+    strcpy(fileresvbl,"VBL_");
+    strcat(fileresvbl,fileresu);
+    if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
+      printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
+      exit(0);
+    }
+    printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
+    fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
+    i1=pow(2,cptcoveff);
+    if (cptcovn < 1){i1=1;}
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+      for(k=1; k<=i1;k++){
+        if(i1 != 1 && TKresult[nres]!= k)
+          continue;
+        fprintf(ficresvbl,"\n#****** ");
+        printf("\n#****** ");
+        fprintf(ficlog,"\n#****** ");
+        for(j=1;j<=cptcoveff;j++) {
+          fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+        }
+        fprintf(ficresvbl,"******\n");
+        printf("******\n");
+        fprintf(ficlog,"******\n");
+        varbpl=matrix(1,nlstate,(int) bage, (int) fage);
+        oldm=oldms;savm=savms;
+        varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
+        free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
+        /*}*/
+      }
+    fclose(ficresvbl);
+    printf("done variance-covariance of back prevalence\n");fflush(stdout);
+    fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
+  } /* End of varbprlim */
  /************** Forecasting *****not tested NB*************/
  /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
- Line 7572  int readdata(char datafile[], int firsto
+ Line 9139  int readdata(char datafile[], int firsto
    /*-------- data file ----------*/
    FILE *fic;
    char dummy[]="                         ";
-   int i=0, j=0, n=0, iv=0;
+   int i=0, j=0, n=0, iv=0, v;
    int lstra;
    int linei, month, year,iout;
    char line[MAXLINE], linetmp[MAXLINE];
    char stra[MAXLINE], strb[MAXLINE];
    char *stratrunc;
+   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
+   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
+   for(v=1; v <=ncovcol;v++){
+     DummyV[v]=0;
+     FixedV[v]=0;
+   }
+   for(v=ncovcol+1; v <=ncovcol+nqv;v++){
+     DummyV[v]=1;
+     FixedV[v]=0;
+   }
+   for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
+     DummyV[v]=0;
+     FixedV[v]=1;
+   }
+   for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
+     DummyV[v]=1;
+     FixedV[v]=1;
+   }
+   for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
+     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
+     fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
+   }
    if((fic=fopen(datafile,"r"))==NULL)    {
      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
- Line 7609  int readdata(char datafile[], int firsto
+ Line 9198  int readdata(char datafile[], int firsto
      /* Loops on waves */
      for (j=maxwav;j>=1;j--){
        for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
-                                 cutv(stra, strb, line, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                         cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
+           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
-                                         cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
+           cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
-                                         if(isalpha(strb[1])) { /* .m or .d Really Missing value */
+           if(isalpha(strb[1])) { /* .m or .d Really Missing value */
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                 }else{
+         }else{
-                                         errno=0;
+           errno=0;
-                                         /* what_kind_of_number(strb); */
+           /* what_kind_of_number(strb); */
-                                         dval=strtod(strb,&endptr);
+           dval=strtod(strb,&endptr);
-                                         /* if( strb[0]=='\0' || (*endptr != '\0')){ */
+           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
-                                         /* if(strb != endptr && *endptr == '\0') */
+           /* if(strb != endptr && *endptr == '\0') */
-                                         /*    dval=dlval; */
+           /*    dval=dlval; */
-                                         /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
-                                         if( strb[0]=='\0' || (*endptr != '\0')){
+           if( strb[0]=='\0' || (*endptr != '\0')){
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                         cotqvar[j][iv][i]=dval;
+           cotqvar[j][iv][i]=dval;
-                                         cotvar[j][ntv+iv][i]=dval;
+           cotvar[j][ntv+iv][i]=dval;
-                                 }
+         }
-                                 strcpy(line,stra);
+         strcpy(line,stra);
        }/* end loop ntqv */
        for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
-                                 cutv(stra, strb, line, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                 }else{
+         }else{
-                                         errno=0;
+           errno=0;
-                                         lval=strtol(strb,&endptr,10);
+           lval=strtol(strb,&endptr,10);
-                                         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+           /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-                                         if( strb[0]=='\0' || (*endptr != '\0')){
+           if( strb[0]=='\0' || (*endptr != '\0')){
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                 }
+         }
-                                 if(lval <-1 || lval >1){
+         if(lval <-1 || lval >1){
-                                         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
   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 \
+           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;
+           return 1;
-                                 }
+         }
-                                 cotvar[j][iv][i]=(double)(lval);
+         cotvar[j][iv][i]=(double)(lval);
-                                 strcpy(line,stra);
+         strcpy(line,stra);
        }/* end loop ntv */
        /* Statuses  at wave */
        cutv(stra, strb, line, ' ');
        if(strb[0]=='.') { /* Missing value */
-                                 lval=-1;
+         lval=-1;
        }else{
-                                 errno=0;
+         errno=0;
-                                 lval=strtol(strb,&endptr,10);
+         lval=strtol(strb,&endptr,10);
-                                 /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-                                 if( strb[0]=='\0' || (*endptr != '\0')){
+         if( strb[0]=='\0' || (*endptr != '\0')){
-                                         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-                                         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
-                                         return 1;
+           return 1;
-                                 }
+         }
        }
        s[j][i]=lval;
- Line 7847  int readdata(char datafile[], int firsto
+ Line 9436  int readdata(char datafile[], int firsto
    return (1);
  }
- void removespace(char **stri){/*, char stro[]) {*/
+ void removefirstspace(char **stri){/*, char stro[]) {*/
    char *p1 = *stri, *p2 = *stri;
-   do
+   while (*p2 == ' ')
-     while (*p2 == ' ')
+     p2++;
-       p2++;
+   /* while ((*p1++ = *p2++) !=0) */
-   while (*p1++ == *p2++);
+   /*   ; */
-   *stri=p1;
+   /* do */
+   /*   while (*p2 == ' ') */
+   /*     p2++; */
+   /* while (*p1++ == *p2++); */
+   *stri=p2;
  }
- int decoderesult ( char resultline[])
+ int decoderesult ( char resultline[], int nres)
  /**< This routine decode one result line and returns the combination # of dummy covariates only **/
  {
-   int j=0, k=0;
+   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];
-   removespace(&resultline);
+   removefirstspace(&resultline);
    printf("decoderesult:%s\n",resultline);
    if (strstr(resultline,"v") !=0){
- Line 7875  int decoderesult ( char resultline[])
+ Line 9470  int decoderesult ( char resultline[])
    if (strlen(resultsav) >1){
      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
    }
+   if(j == 0){ /* Resultline but no = */
-   for(k=1; k<=j;k++){ /* Loop on total covariates of the model */
+     TKresult[nres]=0; /* Combination for the nresult and the model */
-     cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
+     return (0);
-                                      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 */
+   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 *\/ */
- Line 7889  int decoderesult ( char resultline[])
+ Line 9495  int decoderesult ( char resultline[])
      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);
  }
- int selected( int kvar){ /* Selected combination of covariates */
-   if(Tvarsel[kvar])
-     return (0);
-   else
-     return(1);
- }
  int decodemodel( char model[], int lastobs)
   /**< This routine decodes the model and returns:
          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
- Line 7913  int decodemodel( char model[], int lasto
+ Line 9588  int decodemodel( char model[], int lasto
          * - 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, k3, k4;
    char modelsav[80];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
- Line 7936  int decodemodel( char model[], int lasto
+ Line 9611  int decodemodel( char model[], int lasto
      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");
+         substrchaine(modelsav, model, "+age*age");
        else if (strstr(model,"age*age+") !=0)
-                                 substrchaine(modelsav, model, "age*age+");
+         substrchaine(modelsav, model, "age*age+");
        else
-                                 substrchaine(modelsav, model, "age*age");
+         substrchaine(modelsav, model, "age*age");
      }else
        nagesqr=0;
      if (strlen(modelsav) >1){
- Line 8020  int decodemodel( char model[], int lasto
+ Line 9695  int decodemodel( char model[], int lasto
        }
        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 '+'
+         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
                                           modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
-                                 if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
-                                 /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
-                                 /*scanf("%d",i);*/
+         /*scanf("%d",i);*/
-                                 if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
-                                         cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
-                                         if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
-                                                 /* covar is not filled and then is empty */
+             /* covar is not filled and then is empty */
-                                                 cptcovprod--;
+             cptcovprod--;
-                                                 cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
-                                                 Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
+             Tvar[k]=atoi(stre);  /* V2+V1+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 */
+             Typevar[k]=1;  /* 1 for age product */
-                                                 cptcovage++; /* Sums the number of covariates which include age as a 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 */
+             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
-                                                 /*printf("stre=%s ", stre);*/
+             /*printf("stre=%s ", stre);*/
-                                         } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
-                                                 cptcovprod--;
+             cptcovprod--;
-                                                 cutl(stre,strb,strc,'V');
+             cutl(stre,strb,strc,'V');
-                                                 Tvar[k]=atoi(stre);
+             Tvar[k]=atoi(stre);
-                                                 Typevar[k]=1;  /* 1 for age product */
+             Typevar[k]=1;  /* 1 for age product */
-                                                 cptcovage++;
+             cptcovage++;
-                                                 Tage[cptcovage]=k;
+             Tage[cptcovage]=k;
-                                         } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
+           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
-                                                 /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
-                                                 cptcovn++;
+             cptcovn++;
-                                                 cptcovprodnoage++;k1++;
+             cptcovprodnoage++;k1++;
-                                                 cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
-                                                 Tvar[k]=ncovcol+nqv+ntv+nqtv+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
-                                                                                                                                                                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + 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 */
+             Typevar[k]=2;  /* 2 for double fixed dummy covariates */
-                                                 cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+             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  */
+             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
-                                                 Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
+             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
-                                                 Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
-                                                 Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
-                                                 k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
+             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   */
+             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
-                                                 for (i=1; i<=lastobs;i++){
+             for (i=1; i<=lastobs;i++){
-                                                         /* Computes the new covariate which is a product of
+               /* 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 */
+                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
-                                                         covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
-                                                 }
+             }
-                                         } /* End age is not in the model */
+           } /* End age is not in the model */
-                                 } /* End if model includes a product */
+         } /* End if model includes a product */
-                                 else { /* no more sum */
+         else { /* no more sum */
-                                         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
-                                         /*  scanf("%d",i);*/
+           /*  scanf("%d",i);*/
-                                         cutl(strd,strc,strb,'V');
+           cutl(strd,strc,strb,'V');
-                                         ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
+           ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
-                                         cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
+           cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
-                                         Tvar[k]=atoi(strd);
+           Tvar[k]=atoi(strd);
-                                         Typevar[k]=0;  /* 0 for simple covariates */
+           Typevar[k]=0;  /* 0 for simple covariates */
-                                 }
+         }
-                                 strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                                    scanf("%d",i);*/
        } /* end of loop + on total covariates */
- Line 8119  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9794  Dummy[k] 0=dummy (0 1), 1 quantitative (
  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, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
+   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 || Typevar[k]==2)){ /* Simple or product fixed dummy (<=ncovcol) covariates */
+     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;
+       modell[k].maintype= FTYPE;
-                         TvarF[ncovf]=Tvar[k];
+       TvarF[ncovf]=Tvar[k];
-                         TvarFind[ncovf]=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 */
+     }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].maintype= FTYPE;
-                         modell[k].subtype= FQ;
+       modell[k].subtype= FQ;
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
        ncovf++;
-                         TvarF[ncovf]=Tvar[k];
+       TvarF[ncovf]=Tvar[k];
-                         TvarFind[ncovf]=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){
+     }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].maintype= VTYPE;
-                         modell[k].subtype= VD;
+       modell[k].subtype= VD;
-                         ncovv++; /* Only simple time varying variables */
+       nsd++;
-                         TvarV[ncovv]=Tvar[k];
+       TvarsD[nsd]=Tvar[k];
-                         TvarVind[ncovv]=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;
+       Fixed[k]= 1;
-                         Dummy[k]= 1;
+       Dummy[k]= 1;
-                         nqtveff++;
+       nqtveff++;
-                         modell[k].maintype= VTYPE;
+       modell[k].maintype= VTYPE;
-                         modell[k].subtype= VQ;
+       modell[k].subtype= VQ;
-                         ncovv++; /* Only simple time varying variables */
+       ncovv++; /* Only simple time varying variables */
-                         TvarV[ncovv]=Tvar[k];
+       nsq++;
-                         TvarVind[ncovv]=k;
+       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 */
+       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
-                         /* Tmodeliqind[k]=nqtveff;/\* 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 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++;
+       ncova++;
-                         TvarA[ncova]=Tvar[k];
+       TvarA[ncova]=Tvar[k];
-                         TvarAind[ncova]=k;
+       TvarAind[ncova]=k;
        if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
-                                 Fixed[k]= 2;
+         Fixed[k]= 2;
-                                 Dummy[k]= 2;
+         Dummy[k]= 2;
-                                 modell[k].maintype= ATYPE;
+         modell[k].maintype= ATYPE;
-                                 modell[k].subtype= APFD;
+         modell[k].subtype= APFD;
-                                 /* ncoveff++; */
+         /* ncoveff++; */
        }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
-                                 Fixed[k]= 2;
+         Fixed[k]= 2;
-                                 Dummy[k]= 3;
+         Dummy[k]= 3;
-                                 modell[k].maintype= ATYPE;
+         modell[k].maintype= ATYPE;
-                                 modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
+         modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
-                                 /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
+         /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
        }else if( Tvar[k] <=ncovcol+nqv+ntv ){
-                                 Fixed[k]= 3;
+         Fixed[k]= 3;
-                                 Dummy[k]= 2;
+         Dummy[k]= 2;
-                                 modell[k].maintype= ATYPE;
+         modell[k].maintype= ATYPE;
-                                 modell[k].subtype= APVD;                /*      Product age * varying dummy */
+         modell[k].subtype= APVD;                /*      Product age * varying dummy */
-                                 /* ntveff++; /\* Only simple time varying dummy variable *\/ */
+         /* ntveff++; /\* Only simple time varying dummy variable *\/ */
        }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
-                                 Fixed[k]= 3;
+         Fixed[k]= 3;
-                                 Dummy[k]= 3;
+         Dummy[k]= 3;
-                                 modell[k].maintype= ATYPE;
+         modell[k].maintype= ATYPE;
-                                 modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
+         modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
-                                 /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
+         /* 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){
+         if(Tvard[k1][2] <=ncovcol){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 0;
+           Dummy[k]= 0;
-                                         modell[k].maintype= FTYPE;
+           modell[k].maintype= FTYPE;
-                                         modell[k].subtype= FPDD;                /*      Product fixed dummy * fixed dummy */
+           modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
-                                         ncovf++; /* Fixed variables without age */
+           ncovf++; /* Fixed variables without age */
-                                         TvarF[ncovf]=Tvar[k];
+           TvarF[ncovf]=Tvar[k];
-                                         TvarFind[ncovf]=k;
+           TvarFind[ncovf]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
-                                         Fixed[k]= 0;  /* or 2 ?*/
+           Fixed[k]= 0;  /* or 2 ?*/
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= FTYPE;
+           modell[k].maintype= FTYPE;
-                                         modell[k].subtype= FPDQ;                /*      Product fixed dummy * fixed quantitative */
+           modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
-                                         ncovf++; /* Varying variables without age */
+           ncovf++; /* Varying variables without age */
-                                         TvarF[ncovf]=Tvar[k];
+           TvarF[ncovf]=Tvar[k];
-                                         TvarFind[ncovf]=k;
+           TvarFind[ncovf]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 0;
+           Dummy[k]= 0;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDD;                /*      Product fixed dummy * varying dummy */
+           modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDQ;                /*      Product fixed dummy * varying quantitative */
+           modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }
+         }
        }else if(Tvard[k1][1] <=ncovcol+nqv){
-                                 if(Tvard[k1][2] <=ncovcol){
+         if(Tvard[k1][2] <=ncovcol){
-                                         Fixed[k]= 0;  /* or 2 ?*/
+           Fixed[k]= 0;  /* or 2 ?*/
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= FTYPE;
+           modell[k].maintype= FTYPE;
-                                         modell[k].subtype= FPDQ;                /*      Product fixed quantitative * fixed dummy */
+           modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
-                                         ncovf++; /* Fixed variables without age */
+           ncovf++; /* Fixed variables without age */
-                                         TvarF[ncovf]=Tvar[k];
+           TvarF[ncovf]=Tvar[k];
-                                         TvarFind[ncovf]=k;
+           TvarFind[ncovf]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDQ;                /*      Product fixed quantitative * varying dummy */
+           modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPQQ;                /*      Product fixed quantitative * varying quantitative */
+           modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }
+         }
        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
-                                 if(Tvard[k1][2] <=ncovcol){
+         if(Tvard[k1][2] <=ncovcol){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDD;                /*      Product time varying dummy * fixed dummy */
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDQ;                /*      Product time varying dummy * fixed quantitative */
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 0;
+           Dummy[k]= 0;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDD;                /*      Product time varying dummy * time varying dummy */
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDQ;                /*      Product time varying dummy * time varying quantitative */
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }
+         }
        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
-                                 if(Tvard[k1][2] <=ncovcol){
+         if(Tvard[k1][2] <=ncovcol){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDQ;                /*      Product time varying quantitative * fixed dummy */
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPQQ;                /*      Product time varying quantitative * fixed quantitative */
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPDQ;                /*      Product time varying quantitative * time varying dummy */
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=k;
+           TvarVind[ncovv]=k;
-                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
-                                         Fixed[k]= 1;
+           Fixed[k]= 1;
-                                         Dummy[k]= 1;
+           Dummy[k]= 1;
-                                         modell[k].maintype= VTYPE;
+           modell[k].maintype= VTYPE;
-                                         modell[k].subtype= VPQQ;                /*      Product time varying quantitative * time varying quantitative */
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
-                                         ncovv++; /* Varying variables without age */
+           ncovv++; /* Varying variables without age */
-                                         TvarV[ncovv]=Tvar[k];
+           TvarV[ncovv]=Tvar[k];
-                                         TvarVind[ncovv]=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]);
+         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]);
+         fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
-       } /* end k1 */
+       } /*end k1*/
      }else{
        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
- Line 8347  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10044  Dummy[k] 0=dummy (0 1), 1 quantitative (
    /* Searching for doublons in the model */
    for(k1=1; k1<= cptcovt;k1++){
      for(k2=1; k2 <k1;k2++){
-       if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
+       /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
-                                 if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
+       if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
-                                         if(Tvar[k1]==Tvar[k2]){
+         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
-                                                 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]]);
+           if(Tvar[k1]==Tvar[k2]){
-                                                 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);
+             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
-                                                 return(1);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
-                                         }
+             return(1);
-                                 }else if (Typevar[k1] ==2){
+           }
-                                         k3=Tposprod[k1];
+         }else if (Typevar[k1] ==2){
-                                         k4=Tposprod[k2];
+           k3=Tposprod[k1];
-                                         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])) ){
+           k4=Tposprod[k2];
-                                                 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]]);
+           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])) ){
-                                                 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);
+             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]]);
-                                                 return(1);
+             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\n",ncovf,ncovv,ncova);
+   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\n",ncovf,ncovv,ncova);
+   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: ");
- Line 8377  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 10075  Dummy[k] 0=dummy (0 1), 1 quantitative (
  }
  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
- {
+ {/* Check ages at death */
    int i, m;
    int firstone=0;
- Line 8392  int calandcheckages(int imx, int maxwav,
+ Line 10090  int calandcheckages(int imx, int maxwav,
          *nberr = *nberr + 1;
          if(firstone == 0){
            firstone=1;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
          }
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
-         s[m][i]=-1;
+         s[m][i]=-1;  /* Droping the death status */
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
          (*nberr)++;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+         s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
        }
      }
    }
- Line 8523  BOOL IsWow64()
+ Line 10221  BOOL IsWow64()
  #endif
  void syscompilerinfo(int logged)
-  {
+ {
-    /* #include "syscompilerinfo.h"*/
+ #include <stdint.h>
+   /* #include "syscompilerinfo.h"*/
     /* command line Intel compiler 32bit windows, XP compatible:*/
     /* /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
- Line 8559  void syscompilerinfo(int logged)
+ Line 10259  void syscompilerinfo(int logged)
        /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
        /NOLOGO /TLBID:1
     */
  #if defined __INTEL_COMPILER
  #if defined(__GNUC__)
          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
- Line 8575  void syscompilerinfo(int logged)
+ Line 10277  void syscompilerinfo(int logged)
     }
  #endif
- #include <stdint.h>
     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
  #if defined(__clang__)
     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
- Line 8662  void syscompilerinfo(int logged)
+ Line 10362  void syscompilerinfo(int logged)
  #endif
  #endif
-    //   void main()
+    //   void main ()
     //   {
  #if defined(_MSC_VER)
     if (IsWow64()){
- Line 8683  void syscompilerinfo(int logged)
+ Line 10383  void syscompilerinfo(int logged)
  }
  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
-   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
+   /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
-   int i, j, k, i1 ;
+   int i, j, k, i1, k4=0, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
    double tot;
- Line 8692  int prevalence_limit(double *p, double *
+ Line 10392  int prevalence_limit(double *p, double *
    strcpy(filerespl,"PL_");
    strcat(filerespl,fileresu);
    if((ficrespl=fopen(filerespl,"w"))==NULL) {
-     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
-     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
+     fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
    }
-   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
    pstamp(ficrespl);
-   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
    fprintf(ficrespl,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
    fprintf(ficrespl,"\n");
- Line 8709  int prevalence_limit(double *p, double *
+ Line 10409  int prevalence_limit(double *p, double *
    agelim=agemaxpar;
    /* i1=pow(2,ncoveff); */
-   i1=pow(2,cptcoveff); /* Number of dummy covariates */
+   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
    if (cptcovn < 1){i1=1;}
-   for(k=1; k<=i1;k++){
+   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
-   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       if(i1 != 1 && TKresult[nres]!= k)
-     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         continue;
-     /* k=k+1; */
-     /* to clean */
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     fprintf(ficrespl,"#******");
-     printf("#******");
-     fprintf(ficlog,"#******");
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
-     fprintf(ficrespl,"******\n");
-     printf("******\n");
-     fprintf(ficlog,"******\n");
-     if(invalidvarcomb[k]){
-       printf("\nCombination (%d) ignored because no case \n",k);
-       fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
-       fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
-                                                 continue;
-     }
-     fprintf(ficrespl,"#Age ");
+       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-     for(j=1;j<=cptcoveff;j++) {
+       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
-       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     }
+       /* k=k+1; */
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       /* to clean */
-     fprintf(ficrespl,"Total Years_to_converge\n");
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       fprintf(ficrespl,"#******");
+       printf("#******");
+       fprintf(ficlog,"#******");
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       fprintf(ficrespl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       if(invalidvarcomb[k]){
+         printf("\nCombination (%d) ignored because no case \n",k);
+         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
+         continue;
+       }
+       fprintf(ficrespl,"#Age ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       fprintf(ficrespl,"Total Years_to_converge\n");
-     for (age=agebase; age<=agelim; age++){
+       for (age=agebase; age<=agelim; age++){
-       /* for (age=agebase; age<=agebase; age++){ */
+         /* for (age=agebase; age<=agebase; age++){ */
-       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
-       fprintf(ficrespl,"%.0f ",age );
+         fprintf(ficrespl,"%.0f ",age );
-       for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       tot=0.;
+         tot=0.;
-       for(i=1; i<=nlstate;i++){
+         for(i=1; i<=nlstate;i++){
-         tot +=  prlim[i][i];
+           tot +=  prlim[i][i];
-         fprintf(ficrespl," %.5f", prlim[i][i]);
+           fprintf(ficrespl," %.5f", prlim[i][i]);
-       }
+         }
-       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
-     } /* Age */
+       } /* Age */
-     /* was end of cptcod */
+       /* was end of cptcod */
-   } /* cptcov */
+     } /* cptcov */
+   } /* nres */
    return 0;
  }
  int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
-         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
+         /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
          /* Computes the back prevalence limit  for any combination      of covariate values
     * at any age between ageminpar and agemaxpar
           */
-   int i, j, k, i1 ;
+   int i, j, k, i1, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
    double tot;
- Line 8778  int back_prevalence_limit(double *p, dou
+ Line 10488  int back_prevalence_limit(double *p, dou
    strcpy(fileresplb,"PLB_");
    strcat(fileresplb,fileresu);
    if((ficresplb=fopen(fileresplb,"w"))==NULL) {
-     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
-     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
+     fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
    }
-   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
-   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
+   fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
    pstamp(ficresplb);
-   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
+   fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
    fprintf(ficresplb,"#Age ");
    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
    fprintf(ficresplb,"\n");
- Line 8799  int back_prevalence_limit(double *p, dou
+ Line 10509  int back_prevalence_limit(double *p, dou
    i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-   for(k=1; k<=i1;k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-     fprintf(ficresplb,"#******");
+      if(i1 != 1 && TKresult[nres]!= k)
-     printf("#******");
+         continue;
-     fprintf(ficlog,"#******");
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       fprintf(ficresplb,"#******");
-       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       printf("#******");
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficlog,"#******");
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-     }
+         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     fprintf(ficresplb,"******\n");
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     printf("******\n");
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     fprintf(ficlog,"******\n");
+       }
-     if(invalidvarcomb[k]){
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-       printf("\nCombination (%d) ignored because no cases \n",k);
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       continue;
+       }
-     }
+       fprintf(ficresplb,"******\n");
+       printf("******\n");
-     fprintf(ficresplb,"#Age ");
+       fprintf(ficlog,"******\n");
-     for(j=1;j<=cptcoveff;j++) {
+       if(invalidvarcomb[k]){
-       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("\nCombination (%d) ignored because no cases \n",k);
-     }
+         fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
-     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
+         fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
-     fprintf(ficresplb,"Total Years_to_converge\n");
+         continue;
+       }
-     for (age=agebase; age<=agelim; age++){
+       fprintf(ficresplb,"#Age ");
-       /* for (age=agebase; age<=agebase; age++){ */
+       for(j=1;j<=cptcoveff;j++) {
-       if(mobilavproj > 0){
+         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         /* 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);
-       }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);
        }
-       fprintf(ficresplb,"%.0f ",age );
+       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
-       for(j=1;j<=cptcoveff;j++)
+       fprintf(ficresplb,"Total Years_to_converge\n");
-         fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       tot=0.;
-       for(i=1; i<=nlstate;i++){
+       for (age=agebase; age<=agelim; age++){
-         tot +=  bprlim[i][i];
+         /* for (age=agebase; age<=agebase; age++){ */
-         fprintf(ficresplb," %.5f", bprlim[i][i]);
+         if(mobilavproj > 0){
-       }
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
-       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-     } /* Age */
+           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
-     /* was end of cptcod */
+         }else if (mobilavproj == 0){
-   } /* cptcov */
+           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);
+           /* printf("TOTOT\n"); */
+           /* exit(1); */
+         }
+         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); */
- Line 8867  int hPijx(double *p, int bage, int fage)
+ Line 10588  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 8894  int hPijx(double *p, int bage, int fage)
+ Line 10615  int hPijx(double *p, int bage, int fage)
                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                  /*      k=k+1;  */
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
        fprintf(ficrespij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       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 8908  int hPijx(double *p, int bage, int fage)
+ Line 10636  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 8938  int hPijx(double *p, int bage, int fage)
+ Line 10666  int hPijx(double *p, int bage, int fage)
          int ageminl;
    int hstepm;
    int nhstepm;
-   int h, i, i1, j, k;
+   int h, i, i1, j, k, nres;
    double agedeb;
    double ***p3mat;
- Line 8955  int hPijx(double *p, int bage, int fage)
+ Line 10683  int hPijx(double *p, int bage, int fage)
    /*if (stepm<=24) stepsize=2;*/
    /* agelim=AGESUP; */
-   ageminl=30;
+   ageminl=AGEINF; /* was 30 */
    hstepm=stepsize*YEARM; /* Every year of age */
    hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
    /* hstepm=1;   aff par mois*/
    pstamp(ficrespijb);
-   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
+   fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
    i1= pow(2,cptcoveff);
    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*    k=k+1;  */
-   for (k=1; k <= (int) pow(2,cptcoveff); k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     fprintf(ficrespijb,"\n#****** ");
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-     for(j=1;j<=cptcoveff;j++)
+       if(i1 != 1 && TKresult[nres]!= k)
-       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         continue;
-     fprintf(ficrespijb,"******\n");
+       fprintf(ficrespijb,"\n#****** ");
-     if(invalidvarcomb[k]){
+       for(j=1;j<=cptcoveff;j++)
-       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       continue;
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-     }
+         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
-     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       fprintf(ficrespijb,"******\n");
-     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       if(invalidvarcomb[k]){  /* Is it necessary here? */
-       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
-       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         continue;
-       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+       }
-       /*          nhstepm=nhstepm*YEARM; aff par mois*/
+       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
-       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
-       /* oldm=oldms;savm=savms; */
+         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
-       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
-       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-       fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
-       for(i=1; i<=nlstate;i++)
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
-         for(j=1; j<=nlstate+ndeath;j++)
+         /* and memory limitations if stepm is small */
-           fprintf(ficrespijb," %1d-%1d",i,j);
-       fprintf(ficrespijb,"\n");
+         /* oldm=oldms;savm=savms; */
-       for (h=0; h<=nhstepm; h++){
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
-         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
+         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
+             fprintf(ficrespijb," %1d-%1d",i,j);
          fprintf(ficrespijb,"\n");
-       }
+         for (h=0; h<=nhstepm; h++){
-       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-       fprintf(ficrespijb,"\n");
+           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
-     }
+           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
-     /*}*/
+           for(i=1; i<=nlstate;i++)
-   }
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
+           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 9026  int main(int argc, char *argv[])
+ Line 10762  int main(int argc, char *argv[])
    double ssval;
  #endif
    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
-   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
+   int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
+   /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
    int ncvyear=0; /* Number of years needed for the period prevalence to converge */
    int jj, ll, li, lj, lk;
    int numlinepar=0; /* Current linenumber of parameter file */
- Line 9034  int main(int argc, char *argv[])
+ Line 10771  int main(int argc, char *argv[])
    int itimes;
    int NDIM=2;
    int vpopbased=0;
+   int nres=0;
+   int endishere=0;
+   int noffset=0;
+   int ncurrv=0; /* Temporary variable */
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
    /* FILE *ficgp;*/ /*Gnuplot File */
- Line 9052  int main(int argc, char *argv[])
+ Line 10793  int main(int argc, char *argv[])
    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;
+   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
    int c,  h , cpt, c2;
    int jl=0;
    int i1, j1, jk, stepsize=0;
- Line 9065  int main(int argc, char *argv[])
+ Line 10806  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 backcast=0; /* defined as global for mlikeli and mle*/
    int mobilav=0,popforecast=0;
    int hstepm=0, nhstepm=0;
    int agemortsup;
- Line 9078  int main(int argc, char *argv[])
+ Line 10819  int main(int argc, char *argv[])
    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 */
    double *delti; /* Scale */
    double ***eij, ***vareij;
    double **varpl; /* Variances of prevalence limits by age */
    double *epj, vepp;
-   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
+   double dateprev1, dateprev2;
-   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
+   double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
+   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
    double **ximort;
    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
- Line 9166  int main(int argc, char *argv[])
+ Line 10910  int main(int argc, char *argv[])
        if(pathr[0] == '\0') break; /* Dirty */
      }
    }
+   else if (argc<=2){
+     strcpy(pathtot,argv[1]);
+   }
    else{
      strcpy(pathtot,argv[1]);
+     strcpy(z,argv[2]);
+     printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
    }
    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
    /*cygwin_split_path(pathtot,path,optionfile);
- Line 9245  int main(int argc, char *argv[])
+ Line 10994  int main(int argc, char *argv[])
      exit(70);
    }
    strcpy(filereso,"o");
    strcat(filereso,fileresu);
    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
- Line 9255  int main(int argc, char *argv[])
+ Line 11002  int main(int argc, char *argv[])
      fflush(ficlog);
      goto end;
    }
+       /*-------- Rewriting parameter file ----------*/
+   strcpy(rfileres,"r");    /* "Rparameterfile */
+   strcat(rfileres,optionfilefiname);    /* Parameter file first name */
+   strcat(rfileres,".");    /* */
+   strcat(rfileres,optionfilext);    /* Other files have txt extension */
+   if((ficres =fopen(rfileres,"w"))==NULL) {
+     printf("Problem writing new parameter file: %s\n", rfileres);goto end;
+     fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
+     fflush(ficlog);
+     goto end;
+   }
+   fprintf(ficres,"#IMaCh %s\n",version);
    /* Reads comments: lines beginning with '#' */
    numlinepar=0;
+   /* Is it a BOM UTF-8 Windows file? */
-     /* First parameter line */
+   /* First parameter line */
    while(fgets(line, MAXLINE, ficpar)) {
+     noffset=0;
+     if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
+     {
+       noffset=noffset+3;
+       printf("# File is an UTF8 Bom.\n"); // 0xBF
+     }
+     else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
+     {
+       noffset=noffset+2;
+       printf("# File is an UTF16BE BOM file\n");
+     }
+     else if( line[0] == 0 && line[1] == 0)
+     {
+       if( line[2] == (char)0xFE && line[3] == (char)0xFF){
+         noffset=noffset+4;
+         printf("# File is an UTF16BE BOM file\n");
+       }
+     } else{
+       ;/*printf(" Not a BOM file\n");*/
+     }
      /* If line starts with a # it is a comment */
-     if (line[0] == '#') {
+     if (line[noffset] == '#') {
        numlinepar++;
        fputs(line,stdout);
        fputs(line,ficparo);
+       fputs(line,ficres);
        fputs(line,ficlog);
        continue;
      }else
- Line 9275  int main(int argc, char *argv[])
+ Line 11057  int main(int argc, char *argv[])
                          title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
      if (num_filled != 5) {
        printf("Should be 5 parameters\n");
+       fprintf(ficlog,"Should be 5 parameters\n");
      }
      numlinepar++;
      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
    }
    /* Second parameter line */
    while(fgets(line, MAXLINE, ficpar)) {
-     /* If line starts with a # it is a comment */
+     /* while(fscanf(ficpar,"%[^\n]", line)) { */
+     /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
      if (line[0] == '#') {
        numlinepar++;
-       fputs(line,stdout);
+       printf("%s",line);
-       fputs(line,ficparo);
+       fprintf(ficres,"%s",line);
-       fputs(line,ficlog);
+       fprintf(ficparo,"%s",line);
+       fprintf(ficlog,"%s",line);
        continue;
      }else
        break;
- Line 9296  int main(int argc, char *argv[])
+ Line 11084  int main(int argc, char *argv[])
      if (num_filled != 11) {
        printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
        printf("but line=%s\n",line);
+       fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+       fprintf(ficlog,"but line=%s\n",line);
+     }
+     if( lastpass > maxwav){
+       printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+       fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+       fflush(ficlog);
+       goto end;
      }
-     printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+       printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+     fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+     fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
+     fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
    }
    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
- Line 9306  int main(int argc, char *argv[])
+ Line 11105  int main(int argc, char *argv[])
      /* If line starts with a # it is a comment */
      if (line[0] == '#') {
        numlinepar++;
-       fputs(line,stdout);
+       printf("%s",line);
-       fputs(line,ficparo);
+       fprintf(ficres,"%s",line);
-       fputs(line,ficlog);
+       fprintf(ficparo,"%s",line);
+       fprintf(ficlog,"%s",line);
        continue;
      }else
        break;
    }
    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
-     if (num_filled == 0)
+     if (num_filled != 1){
-             model[0]='\0';
+       printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
-     else if (num_filled != 1){
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
-       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
-       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
        model[0]='\0';
        goto end;
      }
- Line 9331  int main(int argc, char *argv[])
+ Line 11129  int main(int argc, char *argv[])
      }
      /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
      printf("model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
+     fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
    }
    /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
    /* numlinepar=numlinepar+3; /\* In general *\/ */
    /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
-   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+   /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
-   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+   /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
    fflush(ficlog);
    /* if(model[0]=='#'|| model[0]== '\0'){ */
    if(model[0]=='#'){
-     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
+     printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
-  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
+  'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
-  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \
+  'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
      if(mle != -1){
-       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
        exit(1);
      }
    }
- Line 9364  int main(int argc, char *argv[])
+ Line 11165  int main(int argc, char *argv[])
    ungetc(c,ficpar);
-   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
+   covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
-   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
+   if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
-   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
+   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
-   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
+   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
       v1+v2*age+v2*v3 makes cptcovn = 3
- Line 9389  int main(int argc, char *argv[])
+ Line 11190  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 9418  int main(int argc, char *argv[])
+ Line 11225  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;
+       j=0;
        for(jj=1; jj <=nlstate+ndeath; jj++){
-                                 if(jj==i) continue;
+         if(jj==i) continue;
-                                 j++;
+         j++;
-                                 fscanf(ficpar,"%1d%1d",&i1,&j1);
+         while((c=getc(ficpar))=='#' && c!= EOF){
-                                 if ((i1 != i) || (j1 != jj)){
+           ungetc(c,ficpar);
-                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+           fgets(line, MAXLINE, ficpar);
+           numlinepar++;
+           fputs(line,stdout);
+           fputs(line,ficparo);
+           fputs(line,ficlog);
+         }
+         ungetc(c,ficpar);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
+         if ((i1 != i) || (j1 != jj)){
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
  It might be a problem of design; if ncovcol and the model are correct\n \
  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-                                         exit(1);
+           exit(1);
-                                 }
+         }
-                                 fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-                                 if(mle==1)
+         if(mle==1)
-                                         printf("%1d%1d",i,jj);
+           printf("%1d%1d",i,jj);
-                                 fprintf(ficlog,"%1d%1d",i,jj);
+         fprintf(ficlog,"%1d%1d",i,jj);
-                                 for(k=1; k<=ncovmodel;k++){
+         for(k=1; k<=ncovmodel;k++){
-                                         fscanf(ficpar," %lf",&param[i][j][k]);
+           fscanf(ficpar," %lf",&param[i][j][k]);
-                                         if(mle==1){
+           if(mle==1){
-                                                 printf(" %lf",param[i][j][k]);
+             printf(" %lf",param[i][j][k]);
-                                                 fprintf(ficlog," %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
-                                         }
+           }
-                                         else
+           else
-                                                 fprintf(ficlog," %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
-                                         fprintf(ficparo," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
-                                 }
+         }
-                                 fscanf(ficpar,"\n");
+         fscanf(ficpar,"\n");
-                                 numlinepar++;
+         numlinepar++;
-                                 if(mle==1)
+         if(mle==1)
-                                         printf("\n");
+           printf("\n");
-                                 fprintf(ficlog,"\n");
+         fprintf(ficlog,"\n");
-                                 fprintf(ficparo,"\n");
+         fprintf(ficparo,"\n");
        }
      }
      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 9470  run imach with mle=-1 to get a correct t
+ Line 11288  run imach with mle=-1 to get a correct t
      for(i=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath-1; j++){
-                                 fscanf(ficpar,"%1d%1d",&i1,&j1);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-                                 if ( (i1-i) * (j1-j) != 0){
+         if ( (i1-i) * (j1-j) != 0){
-                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-                                         exit(1);
+           exit(1);
-                                 }
+         }
-                                 printf("%1d%1d",i,j);
+         printf("%1d%1d",i,j);
-                                 fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-                                 fprintf(ficlog,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-                                 for(k=1; k<=ncovmodel;k++){
+         for(k=1; k<=ncovmodel;k++){
-                                         fscanf(ficpar,"%le",&delti3[i][j][k]);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-                                         printf(" %le",delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
-                                         fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-                                         fprintf(ficlog," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-                                 }
+         }
-                                 fscanf(ficpar,"\n");
+         fscanf(ficpar,"\n");
-                                 numlinepar++;
+         numlinepar++;
-                                 printf("\n");
+         printf("\n");
-                                 fprintf(ficparo,"\n");
+         fprintf(ficparo,"\n");
-                                 fprintf(ficlog,"\n");
+         fprintf(ficlog,"\n");
        }
      }
      fflush(ficlog);
      /* Reads covariance matrix */
      delti=delti3[1][1];
- Line 9558  Please run with mle=-1 to get a correct
+ Line 11376  Please run with mle=-1 to get a correct
      fflush(ficlog);
-     /*-------- Rewriting parameter file ----------*/
-     strcpy(rfileres,"r");    /* "Rparameterfile */
-     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
-     strcat(rfileres,".");    /* */
-     strcat(rfileres,optionfilext);    /* Other files have txt extension */
-     if((ficres =fopen(rfileres,"w"))==NULL) {
-       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
-       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
-     }
-     fprintf(ficres,"#%s\n",version);
    }    /* End of mle != -3 */
    /*  Main data
     */
-   n= lastobs;
+   nobs=lastobs-firstobs+1; /* was = lastobs;*/
-   num=lvector(1,n);
+   /* num=lvector(1,n); */
-   moisnais=vector(1,n);
+   /* moisnais=vector(1,n); */
-   annais=vector(1,n);
+   /* annais=vector(1,n); */
-   moisdc=vector(1,n);
+   /* moisdc=vector(1,n); */
-   andc=vector(1,n);
+   /* andc=vector(1,n); */
-   weight=vector(1,n);
+   /* weight=vector(1,n); */
-   agedc=vector(1,n);
+   /* agedc=vector(1,n); */
-   cod=ivector(1,n);
+   /* cod=ivector(1,n); */
-   for(i=1;i<=n;i++){
+   /* for(i=1;i<=n;i++){ */
-                 num[i]=0;
+   num=lvector(firstobs,lastobs);
-                 moisnais[i]=0;
+   moisnais=vector(firstobs,lastobs);
-                 annais[i]=0;
+   annais=vector(firstobs,lastobs);
-                 moisdc[i]=0;
+   moisdc=vector(firstobs,lastobs);
-                 andc[i]=0;
+   andc=vector(firstobs,lastobs);
-                 agedc[i]=0;
+   weight=vector(firstobs,lastobs);
-                 cod[i]=0;
+   agedc=vector(firstobs,lastobs);
-                 weight[i]=1.0; /* Equal weights, 1 by default */
+   cod=ivector(firstobs,lastobs);
-         }
+   for(i=firstobs;i<=lastobs;i++){
-   mint=matrix(1,maxwav,1,n);
+     num[i]=0;
-   anint=matrix(1,maxwav,1,n);
+     moisnais[i]=0;
-   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
+     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,firstobs,lastobs);
+   anint=matrix(1,maxwav,firstobs,lastobs);
+   s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
    tab=ivector(1,NCOVMAX);
    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
- Line 9603  Please run with mle=-1 to get a correct
+ Line 11420  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. */
+   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); /*  */
- Line 9691  Please run with mle=-1 to get a correct
+ Line 11512  Please run with mle=-1 to get a correct
    agegomp=(int)agemin;
-   free_vector(moisnais,1,n);
+   free_vector(moisnais,firstobs,lastobs);
-   free_vector(annais,1,n);
+   free_vector(annais,firstobs,lastobs);
    /* free_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n);*/
    /* free_vector(moisdc,1,n); */
- Line 9716  Please run with mle=-1 to get a correct
+ Line 11537  Please run with mle=-1 to get a correct
    */
    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
-   /* */
+   /* Concatenates waves */
-   free_vector(moisdc,1,n);
+   free_vector(moisdc,firstobs,lastobs);
-   free_vector(andc,1,n);
+   free_vector(andc,firstobs,lastobs);
    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
    nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
- Line 9897  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 11718  Title=%s <br>Datafile=%s Firstpass=%d La
    /* Calculates basic frequencies. Computes observed prevalence at single age
                   and for any valid combination of covariates
       and prints on file fileres'p'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
+   freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
                firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
-   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
+   fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
+           ftol, stepm);
+   fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
+   ncurrv=1;
+   for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
+   ncurrv=i;
+   for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
+   fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
+            nlstate, ndeath, maxwav, mle, weightopt);
+   fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
+ <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
+   fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
-           imx,agemin,agemax,jmin,jmax,jmean);
+   imx,agemin,agemax,jmin,jmax,jmean);
    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
    /* For Powell, parameters are in a vector p[] starting at p[1]
       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
- Line 9919  Interval (in months) between two waves:
+ Line 11761  Interval (in months) between two waves:
    /* For mortality only */
    if (mle==-3){
      ximort=matrix(1,NDIM,1,NDIM);
-                 for(i=1;i<=NDIM;i++)
+     for(i=1;i<=NDIM;i++)
-                         for(j=1;j<=NDIM;j++)
+       for(j=1;j<=NDIM;j++)
-                                 ximort[i][j]=0.;
+         ximort[i][j]=0.;
      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
-     cens=ivector(1,n);
+     cens=ivector(firstobs,lastobs);
-     ageexmed=vector(1,n);
+     ageexmed=vector(firstobs,lastobs);
-     agecens=vector(1,n);
+     agecens=vector(firstobs,lastobs);
-     dcwave=ivector(1,n);
+     dcwave=ivector(firstobs,lastobs);
      for (i=1; i<=imx; i++){
        dcwave[i]=-1;
- Line 10140  Please run with mle=-1 to get a correct
+ Line 11982  Please run with mle=-1 to get a correct
      free_vector(lpop,1,AGESUP);
      free_vector(tpop,1,AGESUP);
      free_matrix(ximort,1,NDIM,1,NDIM);
-     free_ivector(cens,1,n);
+     free_ivector(dcwave,firstobs,lastobs);
-     free_vector(agecens,1,n);
+     free_vector(agecens,firstobs,lastobs);
-     free_ivector(dcwave,1,n);
+     free_vector(ageexmed,firstobs,lastobs);
+     free_ivector(cens,firstobs,lastobs);
  #ifdef GSL
  #endif
    } /* Endof if mle==-3 mortality only */
- Line 10157  Please run with mle=-1 to get a correct
+ Line 12000  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 10172  Please run with mle=-1 to get a correct
+ Line 12019  Please run with mle=-1 to get a correct
      printf("\n");
      /*--------- results files --------------*/
-     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
+     /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- Line 10372  Please run with mle=-1 to get a correct
+ Line 12219  Please run with mle=-1 to get a correct
      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
      /* Other stuffs, more or less useful */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     while(fgets(line, MAXLINE, ficpar)) {
-       ungetc(c,ficpar);
+       /* If line starts with a # it is a comment */
-       fgets(line, MAXLINE, ficpar);
+       if (line[0] == '#') {
-       fputs(line,stdout);
+         numlinepar++;
-       fputs(line,ficparo);
+         fputs(line,stdout);
-     }
+         fputs(line,ficparo);
-     ungetc(c,ficpar);
+         fputs(line,ficlog);
+         continue;
-     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);
+       }else
-     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);
+         break;
-     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("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       fputs(line,stdout);
-       fputs(line,ficparo);
-     }
-     ungetc(c,ficpar);
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
-     fprintf(ficlog,"pop_based=%d\n",popbased);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
-     fprintf(ficres,"pop_based=%d\n",popbased);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       fputs(line,stdout);
-       fputs(line,ficparo);
      }
-     ungetc(c,ficpar);
+     if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
-     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+       if (num_filled != 7) {
-     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         goto end;
-     /* day and month of proj2 are not used but only year anproj2.*/
+       }
+       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       ungetc(c,ficpar);
+       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       fputs(line,stdout);
-       fputs(line,ficparo);
      }
-     ungetc(c,ficpar);
-     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
-     fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     /* day and month of proj2 are not used but only year anproj2.*/
-     /* Results */
      while(fgets(line, MAXLINE, ficpar)) {
        /* If line starts with a # it is a comment */
        if (line[0] == '#') {
- Line 10444  Please run with mle=-1 to get a correct
+ Line 12255  Please run with mle=-1 to get a correct
        }else
          break;
      }
-     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
-       if (num_filled == 0)
-         resultline[0]='\0';
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-       else if (num_filled != 1){
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
-       }
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
-       printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
+       if (num_filled != 1) {
-       decoderesult(resultline);
+         printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-       while(fgets(line, MAXLINE, ficpar)) {
+         fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-         /* If line starts with a # it is a comment */
+         goto end;
-         if (line[0] == '#') {
-           numlinepar++;
-           fputs(line,stdout);
-           fputs(line,ficparo);
-           fputs(line,ficlog);
-           continue;
-         }else
-           break;
        }
-       if (feof(ficpar))
+       printf("pop_based=%d\n",popbased);
-         break;
+       fprintf(ficlog,"pop_based=%d\n",popbased);
-       else{ /* Processess output results for this combination of covariate values */
+       fprintf(ficparo,"pop_based=%d\n",popbased);
-       }
+       fprintf(ficres,"pop_based=%d\n",popbased);
      }
+     /* Results */
+     nresult=0;
+     do{
+       if(!fgets(line, MAXLINE, ficpar)){
+         endishere=1;
+         parameterline=14;
+       }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.*/
+           dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
+           dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
+         }
+         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.*/
+           dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
+           dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
+         }
+         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); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
- Line 10483  Please run with mle=-1 to get a correct
+ Line 12377  Please run with mle=-1 to get a correct
  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
      }else{
-       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
+       /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
+       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
      }
      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
-                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+                  jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
- Line 10496  Please run with mle=-1 to get a correct
+ Line 12391  Please run with mle=-1 to get a correct
      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
      /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
      /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
-     free_lvector(num,1,n);
+     free_lvector(num,firstobs,lastobs);
-     free_vector(agedc,1,n);
+     free_vector(agedc,firstobs,lastobs);
      /*free_matrix(covar,0,NCOVMAX,1,n);*/
      /*free_matrix(covar,1,NCOVMAX,1,n);*/
      fclose(ficparo);
- Line 10523  Please run with mle=-1 to get a correct
+ Line 12418  Please run with mle=-1 to get a correct
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-     /* Prevalence for each covariates in probs[age][status][cov] */
+     /* Prevalence for each covariate combination in probs[age][status][cov] */
-     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+     probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-     for(i=1;i<=AGESUP;i++)
+     for(i=AGEINF;i<=AGESUP;i++)
        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
          for(k=1;k<=ncovcombmax;k++)
            probs[i][j][k]=0.;
-     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
+                ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
      if (mobilav!=0 ||mobilavproj !=0 ) {
-       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+       mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-       for(i=1;i<=AGESUP;i++)
+       for(i=AGEINF;i<=AGESUP;i++)
-         for(j=1;j<=nlstate;j++)
+         for(j=1;j<=nlstate+ndeath;j++)
            for(k=1;k<=ncovcombmax;k++)
              mobaverages[i][j][k]=0.;
        mobaverage=mobaverages;
        if (mobilav!=0) {
+         printf("Movingaveraging observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging observed prevalence\n");
          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
-       }
+       } else if (mobilavproj !=0) {
-       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
+         printf("Movingaveraging projected observed prevalence\n");
-       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+         fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
-       else if (mobilavproj !=0) {
          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
          }
+       }else{
+         printf("Internal error moving average\n");
+         fflush(stdout);
+         exit(1);
        }
      }/* end if moving average */
      /*---------- Forecasting ------------------*/
-     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
      if(prevfcast==1){
        /*    if(stepm ==1){*/
-       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
      }
+     /* Backcasting */
      if(backcast==1){
        ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
        ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
- Line 10567  Please run with mle=-1 to get a correct
+ Line 12469  Please run with mle=-1 to get a correct
        /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
        bprlim=matrix(1,nlstate,1,nlstate);
        back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
        fclose(ficresplb);
        hBijx(p, bage, fage, mobaverage);
        fclose(ficrespijb);
-       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
-       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
+       prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
-          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
+                        mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
+       varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
+       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
-     }
+     }    /* end  Backcasting */
      /* ------ Other prevalence ratios------------ */
- Line 10600  Please run with mle=-1 to get a correct
+ Line 12506  Please run with mle=-1 to get a correct
      }
      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
+     pstamp(ficreseij);
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+       if(i1 != 1 && TKresult[nres]!= k)
+         continue;
        fprintf(ficreseij,"\n#****** ");
+       printf("\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         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");
        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);
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
      }
      fclose(ficreseij);
      printf("done evsij\n");fflush(stdout);
      fprintf(ficlog,"done evsij\n");fflush(ficlog);
      /*---------- State-specific expectancies and variances ------------*/
      strcpy(filerest,"T_");
      strcat(filerest,fileresu);
      if((ficrest=fopen(filerest,"w"))==NULL) {
- Line 10629  Please run with mle=-1 to get a correct
+ Line 12550  Please run with mle=-1 to get a correct
      }
      printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
      fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
      strcpy(fileresstde,"STDE_");
      strcat(fileresstde,fileresu);
      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
- Line 10658  Please run with mle=-1 to get a correct
+ Line 12577  Please run with mle=-1 to get a correct
      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
-     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+     if (cptcovn < 1){i1=1;}
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
-       printf("\n#****** ");
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-       fprintf(ficrest,"\n#****** ");
+       if(i1 != 1 && TKresult[nres]!= k)
-       fprintf(ficlog,"\n#****** ");
+         continue;
+       printf("\n#****** 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");
- Line 10680  Please run with mle=-1 to get a correct
+ Line 12607  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 combination#=%d, ",k);
+       printf(" cvevsij ");
-       fprintf(ficlog, " cvevsij combination#=%d, ",k);
+       fprintf(ficlog, " cvevsij ");
-       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
        printf(" end cvevsij \n ");
        fprintf(ficlog, " end cvevsij \n ");
- Line 10703  Please run with mle=-1 to get a correct
+ Line 12638  Please run with mle=-1 to get a correct
        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        pstamp(ficrest);
+       epj=vector(1,nlstate+1);
        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
          cptcod= 0; /* To be deleted */
          printf("varevsij vpopbased=%d \n",vpopbased);
          fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
          if(vpopbased==1)
            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
          else
-           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
          fprintf(ficrest,"\n");
          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
-         epj=vector(1,nlstate+1);
+         printf("Computing age specific forward period (stable) prevalences in each health state \n");
-         printf("Computing age specific period (stable) prevalences in each health state \n");
+         fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
-         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
          for(age=bage; age <=fage ;age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
            if (vpopbased==1) {
              if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
- Line 10757  Please run with mle=-1 to get a correct
+ Line 12691  Please run with mle=-1 to get a correct
            fprintf(ficrest,"\n");
          }
        } /* End vpopbased */
+       free_vector(epj,1,nlstate+1);
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
-       free_vector(epj,1,nlstate+1);
+       printf("done selection\n");fflush(stdout);
-       printf("done \n");fflush(stdout);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
-       fprintf(ficlog,"done\n");fflush(ficlog);
-       /*}*/
+     } /* End k selection */
-     } /* End k */
      printf("done State-specific expectancies\n");fflush(stdout);
      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
-     /*------- Variance of period (stable) prevalence------*/
+     /* variance-covariance of forward period prevalence*/
+     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
-     strcpy(fileresvpl,"VPL_");
-     strcat(fileresvpl,fileresu);
-     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
-       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
-       exit(0);
-     }
-     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
-     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
-     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
-       fprintf(ficresvpl,"\n#****** ");
-       printf("\n#****** ");
-       fprintf(ficlog,"\n#****** ");
-       for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       }
-       fprintf(ficresvpl,"******\n");
-       printf("******\n");
-       fprintf(ficlog,"******\n");
-       varpl=matrix(1,nlstate,(int) bage, (int) fage);
-       oldm=oldms;savm=savms;
-       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
-       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-       /*}*/
-     }
-     fclose(ficresvpl);
-     printf("done variance-covariance of period prevalence\n");fflush(stdout);
-     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
-     free_vector(weight,1,n);
+     free_vector(weight,firstobs,lastobs);
      free_imatrix(Tvard,1,NCOVMAX,1,2);
-     free_imatrix(s,1,maxwav+1,1,n);
+     free_imatrix(s,1,maxwav+1,firstobs,lastobs);
-     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(anint,1,maxwav,firstobs,lastobs);
-     free_matrix(mint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,firstobs,lastobs);
-     free_ivector(cod,1,n);
+     free_ivector(cod,firstobs,lastobs);
      free_ivector(tab,1,NCOVMAX);
      fclose(ficresstdeij);
      fclose(ficrescveij);
- Line 10823  Please run with mle=-1 to get a correct
+ Line 12722  Please run with mle=-1 to get a correct
      /*---------- End : free ----------------*/
      if (mobilav!=0 ||mobilavproj !=0)
-       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
+       free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
-     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+     free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
    }  /* mle==-3 arrives here for freeing */
- Line 10832  Please run with mle=-1 to get a correct
+ Line 12731  Please run with mle=-1 to get a correct
    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
+   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
-   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
+   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
-   free_matrix(coqvar,1,maxwav,1,n);
+   if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
-   free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
    free_matrix(matcov,1,npar,1,npar);
    free_matrix(hess,1,npar,1,npar);
    /*free_vector(delti,1,npar);*/
    free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
    free_matrix(agev,1,maxwav,1,imx);
+   free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
    free_ivector(ncodemax,1,NCOVMAX);
    free_ivector(ncodemaxwundef,1,NCOVMAX);
    free_ivector(Dummy,-1,NCOVMAX);
    free_ivector(Fixed,-1,NCOVMAX);
+   free_ivector(DummyV,1,NCOVMAX);
+   free_ivector(FixedV,1,NCOVMAX);
    free_ivector(Typevar,-1,NCOVMAX);
    free_ivector(Tvar,1,NCOVMAX);
+   free_ivector(TvarsQ,1,NCOVMAX);
+   free_ivector(TvarsQind,1,NCOVMAX);
+   free_ivector(TvarsD,1,NCOVMAX);
+   free_ivector(TvarsDind,1,NCOVMAX);
    free_ivector(TvarFD,1,NCOVMAX);
    free_ivector(TvarFDind,1,NCOVMAX);
    free_ivector(TvarF,1,NCOVMAX);
- Line 10911  Please run with mle=-1 to get a correct
+ Line 12817  Please run with mle=-1 to get a correct
    fclose(ficlog);
    /*------ End -----------*/
+ /* Executes gnuplot */
    printf("Before Current directory %s!\n",pathcd);
  #ifdef WIN32
- Line 10946  Please run with mle=-1 to get a correct
+ Line 12854  Please run with mle=-1 to get a correct
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+   strcpy(pplotcmd,plotcmd);
    if((outcmd=system(plotcmd)) != 0){
-     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+     printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
-     if((outcmd=system(plotcmd)) != 0)
+     if((outcmd=system(plotcmd)) != 0){
        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+       strcpy(plotcmd,pplotcmd);
+     }
    }
    printf(" Successful, please wait...");
    while (z[0] != 'q') {
- Line 10979  end:
+ Line 12890  end:
      printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
+   printf("End\n");
+   exit(0);
  }

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