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Diff for /imach/src/imach.c between versions 1.238 and 1.282

-version 1.238, 2016/08/26 14:23:35
+version 1.282, 2018/02/27 22:50:02
  Line 1
  /* $Id$
    $State$
    $Log$
+   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
- Line 87
+ Line 225
    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 732  Back prevalence and projections:
+ Line 868  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 877  typedef struct {
+ Line 1013  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 900  typedef struct {
+ Line 1036  typedef struct {
  #define YEARM 12. /**< Number of months per year */
  /* #define AGESUP 130 */
  #define AGESUP 150
+ #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 991  FILE *ficrescveij;
+ Line 1128  FILE *ficrescveij;
  char filerescve[FILENAMELENGTH];
  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
- FILE  *ficresvpl;
- char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
  char model[MAXLINE]; /**< The model line */
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
- Line 1032  double dval;
+ Line 1168  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 1089  double *agedc;
+ Line 1226  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 */
- Line 1119  int *TvarsQind;
+ Line 1256  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) */
- Line 2061  void powell(double p[], double **xi, int
+ Line 2199  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 2096  void powell(double p[], double **xi, int
+ Line 2234  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 2174  void powell(double p[], double **xi, int
+ Line 2345  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 2220  void powell(double p[], double **xi, int
+ Line 2392  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 2317  void powell(double p[], double **xi, int
+ Line 2489  void powell(double p[], double **xi, int
              flatd++;
          }
          if(flatd >0){
-           printf("%d flat directions\n",flatd);
+           printf("%d flat directions: ",flatd);
-           fprintf(ficlog,"%d flat directions\n",flatd);
+           fprintf(ficlog,"%d flat directions :",flatd);
            for (j=1;j<=n;j++) {
              if(flatdir[j]>0){
                printf("%d ",j);
- Line 2358  void powell(double p[], double **xi, int
+ Line 2530  void powell(double p[], double **xi, int
    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 combination ij
+     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
-        (and selected quantitative values in nres)
+      *   (and selected quantitative values in nres)
-        by left multiplying the unit
+      *  by left multiplying the unit
-        matrix by transitions matrix until convergence is reached with precision ftolpl */
+      *  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= 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 */
+      * Wx is row vector: population in state 1, population in state 2, population dead
-   /* or prevalence in state 1, prevalence in state 2, 0 */
+      * or prevalence in state 1, prevalence in state 2, 0
-   /* newm is the matrix after multiplications, its rows are identical at a factor */
+      * newm is the matrix after multiplications, its rows are identical at a factor.
-   /* Initial matrix pimij */
+      * 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 2500  Earliest age to start was %d-%d=%d, ncvl
+ Line 2675  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 2523  Earliest age to start was %d-%d=%d, ncvl
+ Line 2698  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 2537  Earliest age to start was %d-%d=%d, ncvl
+ Line 2713  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 2559  Earliest age to start was %d-%d=%d, ncvl
+ Line 2735  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)); */
      }
-     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
+     /* for (k=1; k<=cptcovn;k++) { */
-     for (k=1; k<=cptcovprod;k++) /* Useless */
+     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[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+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
-       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+     /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
+     /* } */
+     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
+                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
+       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
+     }
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
+     /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
+     /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
+     for (k=1; k<=cptcovage;k++){  /* For product with age */
+       if(Dummy[Tvar[Tage[k]]]){
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       } else{
+         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+       }
+       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
+     }
+     for (k=1; k<=cptcovprod;k++){ /* For product without age */
+       /* 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 2582  Earliest age to start was %d-%d=%d, ncvl
+ Line 2792  Earliest age to start was %d-%d=%d, ncvl
      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
+     /* if((int)age == 86 || (int)age == 87){ */
+     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
+     /*   for(i=1; i<=nlstate+ndeath; i++) { */
+     /*  printf("%d newm= ",i); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",newm[i][j]); */
+     /*  } */
+     /*  printf("oldm * "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",oldm[i][j]); */
+     /*  } */
+     /*  printf(" bmmij "); */
+     /*  for(j=1;j<=nlstate+ndeath;j++) { */
+     /*    printf("%f ",pmmij[i][j]); */
+     /*  } */
+     /*  printf("\n"); */
+     /*   } */
+     /* } */
      savm=oldm;
      oldm=newm;
      for(j=1; j<=nlstate; j++){
        max[j]=0.;
        min[j]=1.;
- Line 2602  Earliest age to start was %d-%d=%d, ncvl
+ Line 2831  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 2614  Earliest age to start was %d-%d=%d, ncvl
+ Line 2843  Earliest age to start was %d-%d=%d, ncvl
      }
    } /* age 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 2629  Oldest age to start was %d-%d=%d, ncvloo
+ Line 2863  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 2638  double **pmij(double **ps, double *cov,
+ Line 2872  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 2703  double **pmij(double **ps, double *cov,
+ Line 2938  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 2712  double **pmij(double **ps, double *cov,
+ Line 2947  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 matrixe (in order for B to sum to 1 even for death state) */
    double **dnewm, **dsavm, **doldm;
    double **bbmij;
- Line 2729  double **pmij(double **ps, double *cov,
+ Line 2964  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) */
+   /* 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) */
+   bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
+   /* Diag(Sum_i w^i_x p^ij_x */
+   /* 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); /* 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 2978  double ***hpxij(double ***po, int nhstep
+ Line 3238  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 2999  double ***hbxij(double ***po, int nhstep
+ Line 3259  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 3023  double ***hbxij(double ***po, int nhstep
+ Line 3284  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 3068  double ***hbxij(double ***po, int nhstep
+ Line 3340  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 3130  double func( double *x)
+ Line 3403  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 */
          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)*/
- Line 3149  double func( double *x)
+ Line 3422  double func( double *x)
        */
        for(mi=1; mi<= wav[i]-1; mi++){
          for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
-           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
+           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][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++){
- Line 3163  double func( double *x)
+ Line 3437  double func( double *x)
            if(nagesqr==1)
              cov[3]= agexact*agexact;  /* Should be changed here */
            for (kk=1; kk<=cptcovage;kk++) {
+           if(!FixedV[Tvar[Tage[kk]]])
              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
+           else
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
            }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- Line 3445  double funcone( double *x)
+ Line 3722  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 3472  double funcone( double *x)
+ Line 3750  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 3525  double funcone( double *x)
+ Line 3808  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 3603  void likelione(FILE *ficres,double p[],
+ Line 3886  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 3905  double hessij( double x[], double **hess
+ Line 4188  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 3995  void ludcmp(double **a, int n, int *indx
+ Line 4278  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 4061  void pstamp(FILE *fichier)
+ Line 4353  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 *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;
    double **meanqt;
    double *pp, **prop, *posprop, *pospropt;
- Line 4080  void  freqsummary(char fileres[], int ia
+ Line 4376  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); */
- Line 4094  void  freqsummary(char fileres[], int ia
+ Line 4390  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 4104  void  freqsummary(char fileres[], int ia
+ Line 4400  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 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]; *\/ */
+     first=1;
-             /* }else  if(Tvaraff[z1] ==-10){ */
+     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 */
-             /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
+       posproptt=0.;
-             /* }else  */
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
-             if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
+         scanf("%d", i);*/
-               /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
+       for (i=-5; i<=nlstate+ndeath; i++)
-               bool=0;
+         for (s2=-5; s2<=nlstate+ndeath; s2++)
-               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
+           for(m=iagemin; m <= iagemax+3; m++)
-                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
+             freq[i][s2][m]=0;
-                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+       for (i=1; i<=nlstate; i++)  {
-             } /* Onlyf fixed */
+         for(m=iagemin; m <= iagemax+3; m++)
-           } /* end z1 */
+           prop[i][m]=0;
-         } /* cptcovn > 0 */
+         posprop[i]=0;
-       } /* end any */
+         pospropt[i]=0;
-       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
+       }
-         /* for(m=firstpass; m<=lastpass; m++){ */
+       /* for (z1=1; z1<= nqfveff; z1++) {   */
-         for(mi=1; mi<wav[iind];mi++){ /* For that wave */
+       /*   meanq[z1]+=0.; */
-           m=mw[mi][iind];
+       /*   for(m=1;m<=lastpass;m++){ */
-           if(anyvaryingduminmodel==1){ /* Some are varying covariates */
+       /*        meanqt[m][z1]=0.; */
-             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 */
+       /* dateintsum=0; */
-                   bool=0;
+       /* k2cpt=0; */
-               }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
+       /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
-                   bool=0;
+       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<= nqfveff; z1++) {   */
+               /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
+               /* } */
+               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 that 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){
+               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+                  and mw[mi+1][iind]. dh depends on stepm. */
+               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+               ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+               if(m >=firstpass && m <=lastpass){
+                 k2=anint[m][iind]+(mint[m][iind]/12.);
+                 /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+                 if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+                 if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+                 if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                   prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+                 if (m<lastpass) {
+                   /* if(s[m][iind]==4 && s[m+1][iind]==4) */
+                   /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
+                   if(s[m][iind]==-1)
+                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
+                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+                   /* if((int)agev[m][iind] == 55) */
+                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
+                   /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
+                   freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
+                 }
+               } /* end if between passes */
+               if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
+                 dateintsum=dateintsum+k2; /* on all covariates ?*/
+                 k2cpt++;
+                 /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
                }
+             }else{
+               bool=1;
+             }/* 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);*/
+       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");
+       }
+       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 each age */
+       for(iage=iagemin; iage <= iagemax+3; iage++){
+         fprintf(ficresphtm,"<tr>");
+         if(iage==iagemax+1){
+           fprintf(ficlog,"1");
+           fprintf(ficresphtmfr,"<tr><th>0</th> ");
+         }else if(iage==iagemax+2){
+           fprintf(ficlog,"0");
+           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
+         }else if(iage==iagemax+3){
+           fprintf(ficlog,"Total");
+           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
+         }else{
+           if(first==1){
+             first=0;
+             printf("See log file for details...\n");
+           }
+           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
+           fprintf(ficlog,"Age %d", iage);
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
+             pp[s1] += freq[s1][m][iage];
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           for(m=-1, pos=0; m <=0 ; m++)
+             pos += freq[s1][m][iage];
+           if(pp[s1]>=1.e-10){
+             if(first==1){
+               printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
+             }
+             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
+           }else{
+             if(first==1)
+               printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
+             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
+           }
+         }
+         for(s1=1; s1 <=nlstate ; s1++){
+           /* posprop[s1]=0; */
+           for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+             pp[s1] += freq[s1][m][iage];
+         }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
+         for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
+           pos += pp[s1]; /* pos is the total number of transitions until this age */
+           posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
+                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+           pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
+                                           from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+         }
+         /* Writing ficresp */
+         if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
+           if( iage <= iagemax){
+             fprintf(ficresp," %d",iage);
+           }
+         }else if( nj==2){
+           if( iage <= iagemax){
+             fprintf(ficresp," %d",iage);
+             for (z1=1; z1<=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);
              }
-           }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
+           }
-           /* bool =0 we keep that guy which corresponds to the combination of dummy values */
+           pospropt[s1] +=posprop[s1];
-           if(bool==1){
+         } /* end loop s1 */
-             /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+         /* pospropt=0.; */
-                and mw[mi+1][iind]. dh depends on stepm. */
+         for(s1=-1; s1 <=nlstate+ndeath; s1++){
-             agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+           for(m=-1; m <=nlstate+ndeath; m++){
-             ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+             if(freq[s1][m][iage] !=0 ) { /* minimizing output */
-             if(m >=firstpass && m <=lastpass){
+               if(first==1){
-               k2=anint[m][iind]+(mint[m][iind]/12.);
+                 printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
-               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
-               if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
-               if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
-               if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
-                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
-               if (m<lastpass) {
-                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-                 /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
-                 if(s[m][iind]==-1)
-                   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
-                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
-                 /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
-                 freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
                }
-             } /* end if between passes */
+               /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
-             if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
+               fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
-               dateintsum=dateintsum+k2;
-               k2cpt++;
-               /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
              }
-           } /* end bool 2 */
+             if(s1!=0 && m!=0)
-         } /* end m */
+               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
-       } /* end bool */
+           }
-     } /* end iind = 1 to imx */
+         } /* end loop s1 */
-     /* prop[s][age] is feeded for any initial and valid live state as well as
+         posproptt=0.;
-        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
+         for(s1=1; s1 <=nlstate; s1++){
+           posproptt += pospropt[s1];
+         }
-     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+         fprintf(ficresphtmfr,"</tr>\n ");
-     pstamp(ficresp);
+         fprintf(ficresphtm,"</tr>\n");
-     /* if  (ncoveff>0) { */
+         if((cptcoveff==0 && nj==1)|| nj==2 ) {
-     if  (cptcoveff>0) {
+           if(iage <= iagemax)
-       fprintf(ficresp, "\n#********** Variable ");
+             fprintf(ficresp,"\n");
-       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+         }
-       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+         if(first==1)
-       for (z1=1; z1<=cptcoveff; z1++){
+           printf("Others in log...\n");
-         fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         fprintf(ficlog,"\n");
-         fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       } /* end loop age iage */
-         fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       }
+       fprintf(ficresphtm,"<tr><th>Tot</th>");
-       fprintf(ficresp, "**********\n#");
+       for(s1=1; s1 <=nlstate ; s1++){
-       fprintf(ficresphtm, "**********</h3>\n");
+         if(posproptt < 1.e-5){
-       fprintf(ficresphtmfr, "**********</h3>\n");
+           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
-       fprintf(ficlog, "\n#********** Variable ");
+         }else{
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
-       fprintf(ficlog, "**********\n");
+         }
-     }
-     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
-     for(i=1; i<=nlstate;i++) {
-       fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
-       fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-     }
-     fprintf(ficresp, "\n");
-     fprintf(ficresphtm, "\n");
-     /* Header of frequency table by age */
-     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-     fprintf(ficresphtmfr,"<th>Age</th> ");
-     for(jk=-1; jk <=nlstate+ndeath; jk++){
-       for(m=-1; m <=nlstate+ndeath; m++){
-         if(jk!=0 && m!=0)
-           fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
        }
-     }
+       fprintf(ficresphtm,"</tr>\n");
-     fprintf(ficresphtmfr, "\n");
+       fprintf(ficresphtm,"</table>\n");
+       fprintf(ficresphtmfr,"</table>\n");
-     /* For each age */
+       if(posproptt < 1.e-5){
-     for(iage=iagemin; iage <= iagemax+3; iage++){
+         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       fprintf(ficresphtm,"<tr>");
+         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       if(iage==iagemax+1){
+         fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
-                                 fprintf(ficlog,"1");
+         printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
-                                 fprintf(ficresphtmfr,"<tr><th>0</th> ");
+         invalidvarcomb[j1]=1;
-       }else if(iage==iagemax+2){
-                                 fprintf(ficlog,"0");
-                                 fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
-       }else if(iage==iagemax+3){
-                                 fprintf(ficlog,"Total");
-                                 fprintf(ficresphtmfr,"<tr><th>Total</th> ");
        }else{
-                                 if(first==1){
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
-                                         first=0;
+         invalidvarcomb[j1]=0;
-                                         printf("See log file for details...\n");
-                                 }
-                                 fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
-                                 fprintf(ficlog,"Age %d", iage);
        }
-       for(jk=1; jk <=nlstate ; jk++){
+       fprintf(ficresphtmfr,"</table>\n");
-                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+       fprintf(ficlog,"\n");
-                                         pp[jk] += freq[jk][m][iage];
+       if(j!=0){
-       }
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
-       for(jk=1; jk <=nlstate ; jk++){
+         for(i=1,s1=1; i <=nlstate; i++){
-                                 for(m=-1, pos=0; m <=0 ; m++)
+           for(k=1; k <=(nlstate+ndeath); k++){
-                                         pos += freq[jk][m][iage];
+             if (k != i) {
-                                 if(pp[jk]>=1.e-10){
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
-                                         if(first==1){
+                 if(jj==1){  /* Constant case (in fact cste + age) */
-                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+                   if(j1==1){ /* All dummy covariates to zero */
-                                         }
+                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
-                                 }else{
+                     printf("%d%d ",i,k);
-                                         if(first==1)
+                     fprintf(ficlog,"%d%d ",i,k);
-                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                     printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+                     fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
-                                 }
+                     pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
-       }
+                   }
+                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
-       for(jk=1; jk <=nlstate ; jk++){
+                   for(iage=iagemin; iage <= iagemax+3; iage++){
-                                 /* posprop[jk]=0; */
+                     x[iage]= (double)iage;
-                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
+                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
-                                         pp[jk] += freq[jk][m][iage];
+                     /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
-       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
+                   }
+                   /* Some are not finite, but linreg will ignore these ages */
-       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
+                   no=0;
-                                 pos += pp[jk]; /* pos is the total number of transitions until this age */
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
-                                 posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
+                   pstart[s1]=b;
-                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+                   pstart[s1-1]=a;
-                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
+                 }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 */
-                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
+                   printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
-       }
+                   printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
-       for(jk=1; jk <=nlstate ; jk++){
+                   pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
-                                 if(pos>=1.e-5){
+                   printf("%d%d ",i,k);
-                                         if(first==1)
+                   fprintf(ficlog,"%d%d ",i,k);
-                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                   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]));
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+                 }else{ /* Other cases, like quantitative fixed or varying covariates */
-                                 }else{
+                   ;
-                                         if(first==1)
+                 }
-                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                 /* printf("%12.7f )", param[i][jj][k]); */
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
-                                 }
+                 s1++;
-                                 if( iage <= iagemax){
+               } /* end jj */
-                                         if(pos>=1.e-5){
+             } /* end k!= i */
-                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+           } /* end k */
-                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
+         } /* end i, s1 */
-                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
+       } /* end j !=0 */
-                                                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
+     } /* end selected combination of covariate j1 */
-                                         }
+     if(j==0){ /* We can estimate starting values from the occurences in each case */
-                                         else{
+       printf("#Freqsummary: Starting values for the constants:\n");
-                                                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
+       fprintf(ficlog,"\n");
-                                                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
+       for(i=1,s1=1; i <=nlstate; i++){
-                                         }
+         for(k=1; k <=(nlstate+ndeath); k++){
-                                 }
+           if (k != i) {
-                                 pospropt[jk] +=posprop[jk];
+             printf("%d%d ",i,k);
-       } /* end loop jk */
+             fprintf(ficlog,"%d%d ",i,k);
-       /* pospropt=0.; */
+             for(jj=1; jj <=ncovmodel; jj++){
-       for(jk=-1; jk <=nlstate+ndeath; jk++){
+               pstart[s1]=p[s1]; /* Setting pstart to p values by default */
-                                 for(m=-1; m <=nlstate+ndeath; m++){
+               if(jj==1){ /* Age has to be done */
-                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+                 pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
-                                                 if(first==1){
+                 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]));
-                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
+                 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]));
-                                                 }
+               }
-                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
+               /* printf("%12.7f )", param[i][jj][k]); */
-                                         }
+               /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
-                                         if(jk!=0 && m!=0)
+               s1++;
-                                                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
+             }
-                                 }
+             printf("\n");
-       } /* end loop jk */
+             fprintf(ficlog,"\n");
-       posproptt=0.;
+           }
-       for(jk=1; jk <=nlstate; jk++){
+         }
-                                 posproptt += pospropt[jk];
-       }
-       fprintf(ficresphtmfr,"</tr>\n ");
-       if(iage <= iagemax){
-                                 fprintf(ficresp,"\n");
-                                 fprintf(ficresphtm,"</tr>\n");
        }
-       if(first==1)
+       printf("#Freqsummary\n");
-                                 printf("Others in log...\n");
        fprintf(ficlog,"\n");
-     } /* end loop age iage */
+       for(s1=-1; s1 <=nlstate+ndeath; s1++){
-     fprintf(ficresphtm,"<tr><th>Tot</th>");
+         for(s2=-1; s2 <=nlstate+ndeath; s2++){
-     for(jk=1; jk <=nlstate ; jk++){
+           /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
-       if(posproptt < 1.e-5){
+           printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
-                                 fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+           fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
-       }else{
+           /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
-                                 fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+           /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /* } */
+         }
+       } /* end loop s1 */
+       printf("\n");
+       fprintf(ficlog,"\n");
+     } /* end j=0 */
+   } /* end j */
+   if(mle == -2){  /* We want to use these values as starting values */
+     for(i=1, jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j!=i){
+           /*ca[0]= k+'a'-1;ca[1]='\0';*/
+           printf("%1d%1d",i,j);
+           fprintf(ficparo,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             /*    printf(" %lf",param[i][j][k]); */
+             /*    fprintf(ficparo," %lf",param[i][j][k]); */
+             p[jk]=pstart[jk];
+             printf(" %f ",pstart[jk]);
+             fprintf(ficparo," %f ",pstart[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficparo,"\n");
+         }
        }
      }
-     fprintf(ficresphtm,"</tr>\n");
+   } /* end mle=-2 */
-     fprintf(ficresphtm,"</table>\n");
-     fprintf(ficresphtmfr,"</table>\n");
-     if(posproptt < 1.e-5){
-       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
-       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
-       invalidvarcomb[j1]=1;
-     }else{
-       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
-       invalidvarcomb[j1]=0;
-     }
-     fprintf(ficresphtmfr,"</table>\n");
-   } /* end selected combination of covariate j1 */
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
    fclose(ficresphtm);
    fclose(ficresphtmfr);
    free_vector(meanq,1,nqfveff);
    free_matrix(meanqt,1,lastpass,1,nqtveff);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
    free_vector(pospropt,1,nlstate);
    free_vector(posprop,1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
    free_vector(pp,1,nlstate);
    /* End of freqsummary */
  }
+ /* Simple linear regression */
+ int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
+   /* y=a+bx regression */
+   double   sumx = 0.0;                        /* sum of x                      */
+   double   sumx2 = 0.0;                       /* sum of x**2                   */
+   double   sumxy = 0.0;                       /* sum of x * y                  */
+   double   sumy = 0.0;                        /* sum of y                      */
+   double   sumy2 = 0.0;                       /* sum of y**2                   */
+   double   sume2 = 0.0;                       /* sum of square or residuals */
+   double yhat;
+   double denom=0;
+   int i;
+   int ne=*no;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     sumx  += x[i];
+     sumx2 += x[i]*x[i];
+     sumxy += x[i] * y[i];
+     sumy  += y[i];
+     sumy2 += y[i]*y[i];
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   denom = (ne * sumx2 - sumx*sumx);
+   if (denom == 0) {
+     // vertical, slope m is infinity
+     *b = INFINITY;
+     *a = 0;
+     if (r) *r = 0;
+     return 1;
+   }
+   *b = (ne * sumxy  -  sumx * sumy) / denom;
+   *a = (sumy * sumx2  -  sumx * sumxy) / denom;
+   if (r!=NULL) {
+     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
+       sqrt((sumx2 - sumx*sumx/ne) *
+            (sumy2 - sumy*sumy/ne));
+   }
+   *no=ne;
+   for ( i=ifi, ne=0;i<=ila;i++) {
+     if(!isfinite(x[i]) || !isfinite(y[i])){
+       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+       continue;
+     }
+     ne=ne+1;
+     yhat = y[i] - *a -*b* x[i];
+     sume2  += yhat * yhat ;
+     denom = (ne * sumx2 - sumx*sumx);
+     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+   }
+   *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
+   *sa= *sb * sqrt(sumx2/ne);
+   return 0;
+ }
  /************ Prevalence ********************/
  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
  {
- Line 4442  void prevalence(double ***probs, double
+ Line 4998  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;
- Line 4452  void prevalence(double ***probs, double
+ Line 5008  void prevalence(double ***probs, double
    first=1;
    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 4483  void prevalence(double ***probs, double
+ Line 5039  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 4509  void prevalence(double ***probs, double
+ Line 5065  void prevalence(double ***probs, double
            } else{
              if(first==1){
                first=0;
-               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others 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]);
+               fprintf(ficlog,"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\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
              }
            }
          }
- Line 4520  void prevalence(double ***probs, double
+ Line 5079  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 4569  void  concatwav(int wav[], int **dh, int
+ Line 5128  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 4599  void  concatwav(int wav[], int **dh, int
+ Line 5158  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 4618  void  concatwav(int wav[], int **dh, int
+ Line 5173  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 4654  void  concatwav(int wav[], int **dh, int
+ Line 5209  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 4741  void  concatwav(int wav[], int **dh, int
+ Line 5296  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 */
-   /* Loop on covariates without age and products and no quantitative variable */
+    /* Loop on covariates without age and products and no quantitative variable */
-   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
+    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
-   for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
+    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;
+      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-     if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
+      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-       switch(Fixed[k]) {
+        switch(Fixed[k]) {
-       case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
+        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-                                 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*/
+          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*/
-                                         ij=(int)(covar[Tvar[k]][i]);
+            ij=(int)(covar[Tvar[k]][i]);
-                                         /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
+            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-                                          * If product of Vn*Vm, still boolean *:
+             * If product of Vn*Vm, still boolean *:
-                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
+             * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
+             * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-                                         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
+            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-                                                  modality of the nth covariate of individual i. */
+               modality of the nth covariate of individual i. */
-                                         if (ij > modmaxcovj)
+            if (ij > modmaxcovj)
-                                                 modmaxcovj=ij;
+              modmaxcovj=ij;
-                                         else if (ij < modmincovj)
+            else if (ij < modmincovj)
-                                                 modmincovj=ij;
+              modmincovj=ij;
-                                         if ((ij < -1) && (ij > NCOVMAX)){
+            if ((ij < -1) && (ij > NCOVMAX)){
-                                                 printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
+              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-                                                 exit(1);
+              exit(1);
-                                         }else
+            }else
-                                                 Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
+              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-                                         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
+            /*  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);*/
+            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-                                         /* getting the maximum value of the modality of the covariate
+            /* getting the maximum value of the modality of the covariate
-                                                  (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-                                                  female ies 1, then modmaxcovj=1.
+               female ies 1, then modmaxcovj=1.
-                                         */
+            */
-                                 } /* end for loop on individuals i */
+          } /* end for loop on individuals i */
-                                 printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+          printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-                                 fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
+          fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-                                 cptcode=modmaxcovj;
+          cptcode=modmaxcovj;
-                                 /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-                                 /*for (i=0; i<=cptcode; i++) {*/
+          /*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 */
+          for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
-                                         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
+            printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-                                         fprintf(ficlog, "Frequencies of covariates %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]);
-                                         if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
+            if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-                                                 if( j != -1){
+              if( j != -1){
-                                                         ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
+                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
-                                                                                                                                  covariate for which somebody answered excluding
+                                   covariate for which somebody answered excluding
-                                                                                                                                  undefined. Usually 2: 0 and 1. */
+                                   undefined. Usually 2: 0 and 1. */
-                                                 }
+              }
-                                                 ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
+              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
-                                                                                                                                                 covariate for which somebody answered including
+                                      covariate for which somebody answered including
-                                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */
+                                      undefined. Usually 3: -1, 0 and 1. */
-                                         }       /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
+            }    /* 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 */
+                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-                                 } /* Ndum[-1] number of undefined modalities */
+          } /* 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*/
+          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 */
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-                   break;
+              break;
-                 }
+            }
-                                         ij++;
+            ij++;
-                                         nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
+            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*/
-                                         cptcode = ij; /* New max modality for covar j */
+            cptcode = ij; /* New max modality for covar j */
-                                 } /* end of loop on modality i=-1 to 1 or more */
+          } /* end of loop on modality i=-1 to 1 or more */
-                                 break;
+          break;
-       case 1: /* Testing on varying covariate, could be simple and
+        case 1: /* Testing on varying covariate, could be simple and
-                * should look at waves or product of fixed *
+                 * should look at waves or product of fixed *
-                * varying. No time to test -1, assuming 0 and 1 only */
+                 * varying. No time to test -1, assuming 0 and 1 only */
-                                 ij=0;
+          ij=0;
-                                 for(i=0; i<=1;i++){
+          for(i=0; i<=1;i++){
-                                         nbcode[Tvar[k]][++ij]=i;
+            nbcode[Tvar[k]][++ij]=i;
-                                 }
+          }
-                                 break;
+          break;
-       default:
+        default:
-                                 break;
+          break;
-       } /* end switch */
+        } /* end switch */
-     } /* end dummy test */
+      } /* end dummy test */
-     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-     /*  /\*recode from 0 *\/ */
+      /*         /\*recode from 0 *\/ */
-     /*                               k is a modality. If we have model=V1+V1*sex  */
+      /*                                      k is a modality. If we have model=V1+V1*sex  */
-     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
+      /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
-     /*  } */
+      /*         } */
-     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+      /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
-     /*  if (ij > ncodemax[j]) { */
+      /*         if (ij > ncodemax[j]) { */
-     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-     /*    break; */
+      /*           break; */
-     /*  } */
+      /*         } */
-     /*   }  /\* end of loop on modality k *\/ */
+      /*   }  /\* end of loop on modality k *\/ */
-   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
-   for (k=-1; k< maxncov; k++) Ndum[k]=0;
+    for (k=-1; k< maxncov; k++) Ndum[k]=0;
-   /* Look at fixed dummy (single or product) covariates to check empty modalities */
+    /* Look at fixed dummy (single or product) covariates to check empty modalities */
-   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
+    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-     ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
+      ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
-     Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
+      Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
-     /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
+      /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
-   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
-   ij=0;
+    ij=0;
-   /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
+    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
-   for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
-     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-     /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
+      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
+      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-       /* If product not in single variable we don't print results */
+        /* If product not in single variable we don't print results */
-       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-       ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
+        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
-       Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
+        Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
-       Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
+        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
-       TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
+        TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
-       if(Fixed[k]!=0)
+        if(Fixed[k]!=0)
-         anyvaryingduminmodel=1;
+          anyvaryingduminmodel=1;
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
-                         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
+        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
-                         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
-                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
-                         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
-     }
+      }
-   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
-   /* ij--; */
+    /* ij--; */
-   /* cptcoveff=ij; /\*Number of total covariates*\/ */
+    /* cptcoveff=ij; /\*Number of total covariates*\/ */
-   *cptcov=ij; /*Number of total real effective covariates: effective
+    *cptcov=ij; /*Number of total real effective covariates: effective
-                                                          * because they can be excluded from the model and real
+                 * because they can be excluded from the model and real
-                                                          * if in the model but excluded because missing values, but how to get k from ij?*/
+                 * if in the model but excluded because missing values, but how to get k from ij?*/
-   for(j=ij+1; j<= cptcovt; j++){
+    for(j=ij+1; j<= cptcovt; j++){
-     Tvaraff[j]=0;
+      Tvaraff[j]=0;
-     Tmodelind[j]=0;
+      Tmodelind[j]=0;
-   }
+    }
-   for(j=ntveff+1; j<= cptcovt; j++){
+    for(j=ntveff+1; j<= cptcovt; j++){
-     TmodelInvind[j]=0;
+      TmodelInvind[j]=0;
-   }
+    }
-   /* To be sorted */
+    /* To be sorted */
-   ;
+    ;
- }
+  }
  /*********** Health Expectancies ****************/
- Line 4953  void  concatwav(int wav[], int **dh, int
+ Line 5508  void  concatwav(int wav[], int **dh, int
    /* 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 5184  void  concatwav(int wav[], int **dh, int
+ Line 5739  void  concatwav(int wav[], int **dh, int
            /* 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 5199  void  concatwav(int wav[], int **dh, int
+ Line 5755  void  concatwav(int wav[], int **dh, int
      }
      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 5232  void  concatwav(int wav[], int **dh, int
+ Line 5789  void  concatwav(int wav[], int **dh, int
  /************ 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[], 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;
- Line 5243  void  concatwav(int wav[], int **dh, int
+ Line 5801  void  concatwav(int wav[], int **dh, int
     int i, j, nhstepm, hstepm, h, nstepm ;
     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 5308  void  concatwav(int wav[], int **dh, int
+ Line 5866  void  concatwav(int wav[], int **dh, int
     /* 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 5363  void  concatwav(int wav[], int **dh, int
+ Line 5921  void  concatwav(int wav[], int **dh, int
         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, nresult);
+         * 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 5375  void  concatwav(int wav[], int **dh, int
+ Line 5936  void  concatwav(int wav[], int **dh, int
               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,nres);  /* 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, nresult);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
         if (popbased==1) {
           if(mobilav ==0){
- Line 5424  void  concatwav(int wav[], int **dh, int
+ Line 5990  void  concatwav(int wav[], int **dh, int
           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 5447  void  concatwav(int wav[], int **dh, int
+ Line 6017  void  concatwav(int wav[], int **dh, int
       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 5464  void  concatwav(int wav[], int **dh, int
+ Line 6040  void  concatwav(int wav[], int **dh, int
         }
       }
-      /* 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 5473  void  concatwav(int wav[], int **dh, int
+ Line 6053  void  concatwav(int wav[], int **dh, int
       /* end ppptj */
       /*  x centered again */
-      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
       if (popbased==1) {
         if(mobilav ==0){
- Line 5552  void  concatwav(int wav[], int **dh, int
+ Line 6132  void  concatwav(int wav[], int **dh, int
   }  /* 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[], int nres)
+  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 5568  void  concatwav(int wav[], int **dh, int
+ Line 6148  void  concatwav(int wav[], int **dh, int
    pstamp(ficresvpl);
    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+   fprintf(ficresvpl,"# Age ");
+   if(nresult >=1)
+     fprintf(ficresvpl," Result# ");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
    fprintf(ficresvpl,"\n");
    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 5644  void  concatwav(int wav[], int **dh, int
+ Line 6226  void  concatwav(int wav[], int **dh, int
      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 );
+     if(nresult >=1)
+       fprintf(ficresvpl,"%d ",nres );
      for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      fprintf(ficresvpl,"\n");
- Line 5667  void  concatwav(int wav[], int **dh, int
+ Line 6251  void  concatwav(int wav[], int **dh, int
    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 5747  void varprob(char optionfilefiname[], do
+ Line 6456  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. %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 5944  To be simple, these graphs help to under
+ Line 6653  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 5964  To be simple, these graphs help to under
+ Line 6678  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 5975  To be simple, these graphs help to under
+ Line 6689  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 6012  To be simple, these graphs help to under
+ Line 6726  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, k4, nres;
     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
- Line 6050  void printinghtml(char fileresu[], char
+ Line 6764  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;
+    fprintf(fichtm," \n<ul>");
     for(nres=1; nres <= nresult; nres++) /* For each resultline */
-    for(k1=1; k1<=m;k1++){
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
-      if(TKresult[nres]!= k1)
+      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 ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
- Line 6086  void printinghtml(char fileresu[], char
+ Line 6845  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. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
       }
       /* State specific survival functions (period) */
       for(cpt=1; cpt<=nlstate;cpt++){
         fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
   Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
-  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
+  <a href=\"%s_%d-%d-%d.svg\">%s_%d%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
       }
       /* Period (stable) prevalence in each health state */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability 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 */
         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 */
         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- 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) 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.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", 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- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
+  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 6189  See page 'Matrix of variance-covariance
+ Line 6958  See page 'Matrix of variance-covariance
     jj1=0;
-    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k1=1; k1<=m;k1++){
-      if(TKresult[nres]!= k1)
+      if(m != 1 && TKresult[nres]!= k1)
         continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
- Line 6212  See page 'Matrix of variance-covariance
+ Line 6981  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,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 6250  void printinggnuplot(char fileresu[], ch
+ Line 7023  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 6286  void printinggnuplot(char fileresu[], ch
+ Line 7073  void printinggnuplot(char fileresu[], ch
      for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-         if(TKresult[nres]!= k1)
+         if(m != 1 && TKresult[nres]!= k1)
            continue;
          /* We are interested in selected combination by the resultline */
-         printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
+         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
          fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
+         strcpy(gplotlabel,"(");
          for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
            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 */
- Line 6298  void printinggnuplot(char fileresu[], ch
+ Line 7086  void printinggnuplot(char fileresu[], ch
            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
            vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
            /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-           printf(" V%d=%d ",Tvaraff[k],vlv);
+           /* printf(" V%d=%d ",Tvaraff[k],vlv); */
            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 */
-           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           /* 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]);
-         printf("\n#\n");
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         /* printf("\n#\n"); */
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
+           /*k1=k1-1;*/ /* To be checked */
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
            continue;
          }
-         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
-         fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
+         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
-         fprintf(ficgp,"set xlabel \"Age\" \n\
+         /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
- set ylabel \"Probability\" \n             \
+         fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
- set ter svg size 640, 480\n                                             \
+         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);
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+         /* 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); */
+       /* 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\"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);
+         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
          for (i=1; i<= nlstate ; i ++) {
            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
            else fprintf(ficgp," %%*lf (%%*lf)");
          }
-         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+         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\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
-         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
-           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
-           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
+         if(cptcoveff ==0){
-           if(cptcoveff ==0){
+           fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
-             fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",        2+(cpt-1),  cpt );
+         }else{
-           }else{
+           kl=0;
-             kl=0;
+           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
-             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
+             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-               /* 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(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)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
+             }else{
+               fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+               kl++;
+             }
+           } /* end covariate */
+         } /* end if no covariate */
+         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%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++;
- Line 6353  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7172  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)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
-+(cpt-1),  cpt );  /* 4 or 6 ?*/
++cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
                }else{
                  fprintf(ficgp,"$%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 \n");
+         /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+         fprintf(ficgp,"\nset out ;unset title;\n");
        } /* nres */
      } /* k1 */
    } /* cpt */
- Line 6371  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7210  plot [%.f:%.f] \"%s\" every :::%d::%d u
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++){
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
+       strcpy(gplotlabel,"(");
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6381  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7221  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;
        }
-       fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-         if(vpopbased==0)
+         fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
+         if(vpopbased==0){
            fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-         else
+         }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);
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
            for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," %%lf (%%lf)");
              else fprintf(ficgp," %%*lf (%%*lf)");
            }
            if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
            else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
+           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_"),k1-1,k1-1,vpopbased);
+           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)");
- Line 6423  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7267  plot [%.f:%.f] \"%s\" every :::%d::%d u
            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 */
+       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*/
- Line 6431  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7275  plot [%.f:%.f] \"%s\" every :::%d::%d u
    /*3eme*/
    for (k1=1; k1<= m ; k1 ++){
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        for (cpt=1; cpt<= nlstate ; cpt ++) {
-         fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, 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 */
- Line 6443  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7288  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 (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 6455  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7303  plot [%.f:%.f] \"%s\" every :::%d::%d u
          /*       k=2+nlstate*(2*cpt-2); */
          k=2+(nlstate+1)*(cpt-1);
-         fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
+         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_"),k1-1,k1-1,k,cpt);
+ 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);
- Line 6467  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7316  plot [%.f:%.f] \"%s\" every :::%d::%d u
          */
          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.\" 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 */
- Line 6480  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7330  plot [%.f:%.f] \"%s\" every :::%d::%d u
    /* Survival functions (period) from state i in state j by initial state i */
    for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
+         strcpy(gplotlabel,"(");
          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 */
- Line 6491  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7342  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 (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,"LIJ_"),cpt,k1);
+         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;
- Line 6517  set ter svg size 640, 480\nunset log y\n
+ Line 7372  set ter svg size 640, 480\nunset log y\n
              fprintf(ficgp,"+$%d",k+l+j-1);
            fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
          } /* nlstate */
-         fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end nres */
    } /* end covariate k1 */
- Line 6526  set ter svg size 640, 480\nunset log y\n
+ Line 7381  set ter svg size 640, 480\nunset log y\n
    /* Survival functions (period) from state i in state j by final state j */
    for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= 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 */
- Line 6537  set ter svg size 640, 480\nunset log y\n
+ Line 7393  set ter svg size 640, 480\nunset log y\n
            /* 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 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;
- Line 6571  set ter svg size 640, 480\nunset log y\n
+ Line 7431  set ter svg size 640, 480\nunset log y\n
            else
              fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
          }
-         fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* end nres */
- Line 6580  set ter svg size 640, 480\nunset log y\n
+ Line 7440  set ter svg size 640, 480\nunset log y\n
    /* CV preval stable (period) for each covariate */
    for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     if(TKresult[nres]!= k1)
+     if(m != 1 && TKresult[nres]!= k1)
        continue;
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
+       strcpy(gplotlabel,"(");
        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
- Line 6592  set ter svg size 640, 480\nunset log y\n
+ Line 7452  set ter svg size 640, 480\nunset log y\n
          /* 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\nunset log y\nplot [%.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 */
- Line 6627  set ter svg size 640, 480\nunset log y\n
+ Line 7491  set ter svg size 640, 480\nunset log y\n
      /* CV back preval stable (period) for each covariate */
      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
-       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
-         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6638  set ter svg size 640, 480\nunset log y\n
+ Line 7503  set ter svg size 640, 480\nunset log y\n
            /* 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\nunset log y\nplot [%.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 */
- Line 6678  set ter svg size 640, 480\nunset log y\n
+ Line 7547  set ter svg size 640, 480\nunset log y\n
      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+         strcpy(gplotlabel,"(");
          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
- Line 6689  set ter svg size 640, 480\nunset log y\n
+ Line 7559  set ter svg size 640, 480\nunset log y\n
            /* 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 6700  set ter svg size 640, 480\nunset log y\n
+ Line 7573  set ter svg size 640, 480\nunset log y\n
          }
          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\nunset log y\nplot [%.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 6720  set ter svg size 640, 480\nunset log y\n
+ Line 7598  set ter svg size 640, 480\nunset log y\n
              /*# 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 6755  set ter svg size 640, 480\nunset log y\n
+ Line 7636  set ter svg size 640, 480\nunset log y\n
              /*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 */
    /* 9eme writing MLE parameters */
    fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
- Line 6806  set ter svg size 640, 480\nunset log y\n
+ Line 7808  set ter svg size 640, 480\nunset log y\n
      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
      fprintf(ficgp,"#model=%s \n",model);
      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
-     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
+     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
-     for(jk=1; jk <=m; jk++)  /* For each combination of covariate */
+     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= jk)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
-       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
+       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.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
+       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 6860  set ter svg size 640, 480\nunset log y\n
+ Line 7878  set ter svg size 640, 480\nunset log y\n
              /* 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(j==Tage[ij]) { /* Product by age */
+               if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                 if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+                 if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
-                   if(DummyV[j]==0){
+                   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+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+                     if(DummyV[j]==0){
-                   }else{ /* quantitative */
+                       fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
-                     fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                     }else{ /* quantitative */
-                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                       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(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(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
-                       fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
-                     }else{ /* Vn is dummy and Vm is quanti */
-                       /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
-                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                      }
-                   }else{ /* Vn*Vm Vn is quanti */
+                     ij++;
-                     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 */
+               }else if(cptcovprod >0){
-                       fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                 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++;
                    }
-                   ijp++;
+                 } /* end Tprod */
-                 }
                } else{  /* simple covariate */
-                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */
+                 /* 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(jk,Tvar[j-2])]); */
+                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                  }
                } /* end simple */
              } /* end j */
- Line 6909  set ter svg size 640, 480\nunset log y\n
+ Line 7931  set ter svg size 640, 480\nunset log y\n
            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((j-2)==Tage[ij]) { /* Bug valgrind */
+                  if(cptcovage >0){
-                   if(ij <=cptcovage) { /* 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 6945  set ter svg size 640, 480\nunset log y\n
+ Line 7968  set ter svg size 640, 480\nunset log y\n
            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 6962  set ter svg size 640, 480\nunset log y\n
+ Line 7986  set ter svg size 640, 480\nunset log y\n
     int mobilavrange, mob;
     int iage=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 6997  set ter svg size 640, 480\nunset log y\n
+ Line 8025  set ter svg size 640, 480\nunset log y\n
       */
       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 */
+      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 */
+          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\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 */
+          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\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); */
- Line 7082  set ter svg size 640, 480\nunset log y\n
+ Line 8176  set ter svg size 640, 480\nunset log y\n
       }
       /* 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, k4, nres=0;
+   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 7148  set ter svg size 640, 480\nunset log y\n
+ Line 8246  set ter svg size 640, 480\nunset log y\n
    if(estepm < stepm){
      printf ("Problem %d lower than %d\n",estepm, stepm);
    }
-   else  hstepm=estepm;
+   else{
+     hstepm=estepm;
+   }
+   if(estepm > stepm){ /* Yes every two year */
+     stepsize=2;
+   }
    hstepm=hstepm/stepm;
    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
- Line 7171  set ter svg size 640, 480\nunset log y\n
+ Line 8274  set ter svg size 640, 480\nunset log y\n
  /*            if (h==(int)(YEARM*yearp)){ */
    for(nres=1; nres <= nresult; nres++) /* For each resultline */
    for(k=1; k<=i1;k++){
-     if(TKresult[nres]!= k)
+     if(i1 != 1 && TKresult[nres]!= k)
        continue;
      if(invalidvarcomb[k]){
        printf("\nCombination (%d) projection ignored because no cases \n",k);
- Line 7193  set ter svg size 640, 480\nunset log y\n
+ Line 8296  set ter svg size 640, 480\nunset log y\n
      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>=(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) {
-             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(ficresf,"\n");
-           }
+         for(j=1;j<=cptcoveff;j++)
-           for(j=1; j<=nlstate+ndeath;j++) {
+           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-             ppij=0.;
+         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-             for(i=1; i<=nlstate;i++) {
-               if (mobilav==1)
+         for(j=1; j<=nlstate+ndeath;j++) {
-                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
+           ppij=0.;
-               else {
+           for(i=1; i<=nlstate;i++) {
-                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
+             if (mobilav>=1)
-               }
+              ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
-               if (h*hstepm/YEARM*stepm== yearp) {
+             else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
-                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
-               }
-             } /* end i */
-             if (h*hstepm/YEARM*stepm==yearp) {
-               fprintf(ficresf," %.3f", ppij);
              }
-           }/* end j */
+             fprintf(ficresf," %.3f", p3mat[i][j][h]);
-         } /* end 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 */
- Line 7235  set ter svg size 640, 480\nunset log y\n
+ Line 8340  set ter svg size 640, 480\nunset log y\n
  }
- /* /\************** Back Forecasting ******************\/ */
+ /************** 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){ */
+  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  */
+   /* back1, year, month, day of starting backection
- /*      agemin, agemax range of age */
+      agemin, agemax range of age
- /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
+      dateprev1 dateprev2 range of dates during which prevalence is computed
- /*      anback2 year of en of backection (same day and month as back1). */
+      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; */
+   */
- /*   double agec; /\* generic age *\/ */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
- /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
+   double agec; /* generic age */
- /*   double *popeffectif,*popcount; */
+   double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
- /*   double ***p3mat; */
+   double *popeffectif,*popcount;
- /*   /\* double ***mobaverage; *\/ */
+   double ***p3mat;
- /*   char fileresfb[FILENAMELENGTH]; */
+   /* double ***mobaverage; */
+   char fileresfb[FILENAMELENGTH];
- /*   agelim=AGESUP; */
- /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
+   agelim=AGEINF;
- /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
- /*      We still use firstpass and lastpass as another selection. */
+      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); *\/ */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
- /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
- /*   strcpy(fileresfb,"FB_");  */
+   /*Do we need to compute prevalence again?*/
- /*   strcat(fileresfb,fileresu); */
- /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
+   /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
- /*     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);  */
+   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);
- /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
- /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
- /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
+   stepsize=(int) (stepm+YEARM-1)/YEARM;
- /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
+   if (stepm<=12) stepsize=1;
- /*       k=k+1; */
+   if(estepm < stepm){
- /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
+     printf ("Problem %d lower than %d\n",estepm, stepm);
- /*       for(j=1;j<=cptcoveff;j++) { */
+   }
- /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
+   else{
- /*       } */
+     hstepm=estepm;
- /*       fprintf(ficresfb," yearbproj age"); */
+   }
- /*       for(j=1; j<=nlstate+ndeath;j++){  */
+   if(estepm >= stepm){ /* Yes every two year */
- /*                              for(i=1; i<=nlstate;i++)               */
+     stepsize=2;
- /*           fprintf(ficresfb," p%d%d",i,j); */
+   }
- /*                              fprintf(ficresfb," p.%d",j); */
- /*       } */
+   hstepm=hstepm/stepm;
- /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
- /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
+                                fractional in yp1 */
- /*                              fprintf(ficresfb,"\n"); */
+   anprojmean=yp;
- /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
+   yp2=modf((yp1*12),&yp);
- /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
+   mprojmean=yp;
- /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
+   yp1=modf((yp2*30.5),&yp);
- /*                                      nhstepm = nhstepm/hstepm;  */
+   jprojmean=yp;
- /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+   if(jprojmean==0) jprojmean=1;
- /*                                      oldm=oldms;savm=savms; */
+   if(mprojmean==0) jprojmean=1;
- /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
- /*                                      for (h=0; h<=nhstepm; h++){ */
+   i1=pow(2,cptcoveff);
- /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
+   if (cptcovn < 1){i1=1;}
- /*               fprintf(ficresfb,"\n"); */
- /*               for(j=1;j<=cptcoveff;j++)  */
+   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
- /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
+   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
- /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
- /*                                              }  */
+   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
- /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
- /*                                                      ppij=0.; */
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
- /*                                                      for(i=1; i<=nlstate;i++) { */
+   for(k=1; k<=i1;k++){
- /*                                                              if (mobilav==1)  */
+     if(i1 != 1 && TKresult[nres]!= k)
- /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
+       continue;
- /*                                                              else { */
+     if(invalidvarcomb[k]){
- /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
- /*                                                              } */
+       continue;
- /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
+     }
- /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
+     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
- /*                                                              } */
+     for(j=1;j<=cptcoveff;j++) {
- /*                                                      } /\* end i *\/ */
+       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
+     }
- /*                                                              fprintf(ficresfb," %.3f", ppij); */
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
- /*                                                      } */
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
- /*                                              }/\* end j *\/ */
+     }
- /*                                      } /\* end h *\/ */
+     fprintf(ficresfb," yearbproj age");
- /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+     for(j=1; j<=nlstate+ndeath;j++){
- /*                              } /\* end agec *\/ */
+       for(i=1; i<=nlstate;i++)
- /*       } /\* end yearp *\/ */
+         fprintf(ficresfb," b%d%d",i,j);
- /*     } /\* end cptcod *\/ */
+       fprintf(ficresfb," b.%d",j);
- /*   } /\* end  cptcov *\/ */
+     }
+     for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
- /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
+       fprintf(ficresfb,"\n");
- /*   fclose(ficresfb); */
+       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
- /*   printf("End of Computing Back forecasting \n"); */
+       /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
- /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
+       /* 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;
+         /* 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) {
+             break;
+           }
+         }
+         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(i=1; i<=nlstate+ndeath;i++) {
+           ppij=0.;ppi=0.;
+           for(j=1; j<=nlstate;j++) {
+             /* if (mobilav==1) */
+             ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
+             ppi=ppi+prevacurrent[(int)agec][j][k];
+             /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
+             /* ppi=ppi+mobaverage[(int)agec][j][k]; */
+               /* else { */
+               /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
+               /* } */
+             fprintf(ficresfb," %.3f", p3mat[i][j][h]);
+           } /* end j */
+           if(ppi <0.99){
+             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 */
+   /* 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 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 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++){*/
+     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 period prevalence\n");fflush(stdout);
+     fprintf(ficlog,"done variance-covariance of 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 7791  int readdata(char datafile[], int firsto
+ Line 9034  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 8100  int decoderesult ( char resultline[], in
+ Line 9365  int decoderesult ( char resultline[], in
    if (strlen(resultsav) >1){
      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
    }
+   if(j == 0){ /* Resultline but no = */
+     TKresult[nres]=0; /* Combination for the nresult and the model */
+     return (0);
+   }
    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
      printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
      fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
- Line 8419  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9689  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(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("Decodemodel: V%d, Dummy(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
-     fprintf(ficlog,"Decodemodel: V%d, Dummy(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
-   }
    for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
        Fixed[k]= 0;
- Line 8464  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9714  Dummy[k] 0=dummy (0 1), 1 quantitative (
        TvarFind[ncovf]=k;
        TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
        TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ /* Only simple fixed quantitative variable */
+     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
        Fixed[k]= 0;
        Dummy[k]= 1;
        nqfveff++;
- Line 8478  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9728  Dummy[k] 0=dummy (0 1), 1 quantitative (
        TvarFind[ncovf]=k;
        TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
        TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
-     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */
+     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
        Fixed[k]= 1;
        Dummy[k]= 0;
        ntveff++; /* Only simple time varying dummy variable */
- Line 8489  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9739  Dummy[k] 0=dummy (0 1), 1 quantitative (
        TvarsDind[nsd]=k;
        ncovv++; /* Only simple time varying variables */
        TvarV[ncovv]=Tvar[k];
-       TvarVind[ncovv]=k;
+       TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
        TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
        TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
        printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
- Line 8505  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9755  Dummy[k] 0=dummy (0 1), 1 quantitative (
        TvarsQ[nsq]=Tvar[k];
        TvarsQind[nsq]=k;
        TvarV[ncovv]=Tvar[k];
-       TvarVind[ncovv]=k;
+       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
        TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
        TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
        TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
- Line 8517  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9767  Dummy[k] 0=dummy (0 1), 1 quantitative (
        TvarA[ncova]=Tvar[k];
        TvarAind[ncova]=k;
        if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
          Fixed[k]= 2;
          Dummy[k]= 2;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APFD;
          /* ncoveff++; */
        }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
          Fixed[k]= 2;
          Dummy[k]= 3;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
          /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
        }else if( Tvar[k] <=ncovcol+nqv+ntv ){
          Fixed[k]= 3;
          Dummy[k]= 2;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APVD;                /*      Product age * varying dummy */
          /* ntveff++; /\* Only simple time varying dummy variable *\/ */
        }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
          Fixed[k]= 3;
          Dummy[k]= 3;
          modell[k].maintype= ATYPE;
          modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
          /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
        }
      }else if (Typevar[k] == 2) {  /* product without age */
        k1=Tposprod[k];
        if(Tvard[k1][1] <=ncovcol){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 1;
            Dummy[k]= 0;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
            ncovf++; /* Fixed variables without age */
            TvarF[ncovf]=Tvar[k];
            TvarFind[ncovf]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv){
            Fixed[k]= 0;  /* or 2 ?*/
            Dummy[k]= 1;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
            ncovf++; /* Varying variables without age */
            TvarF[ncovf]=Tvar[k];
            TvarFind[ncovf]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 0;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else if(Tvard[k1][1] <=ncovcol+nqv){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 0;  /* or 2 ?*/
            Dummy[k]= 1;
            modell[k].maintype= FTYPE;
            modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
            ncovf++; /* Fixed variables without age */
            TvarF[ncovf]=Tvar[k];
            TvarFind[ncovf]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 0;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
          if(Tvard[k1][2] <=ncovcol){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
            Fixed[k]= 1;
            Dummy[k]= 1;
            modell[k].maintype= VTYPE;
            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
            ncovv++; /* Varying variables without age */
            TvarV[ncovv]=Tvar[k];
            TvarVind[ncovv]=k;
          }
        }else{
          printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
          fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
-       } /* end k1 */
+       } /*end k1*/
      }else{
        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
- Line 8719  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9969  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 8734  int calandcheckages(int imx, int maxwav,
+ Line 9984  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 9056  int prevalence_limit(double *p, double *
+ Line 10306  int prevalence_limit(double *p, double *
    for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
- Line 9153  int back_prevalence_limit(double *p, dou
+ Line 10403  int back_prevalence_limit(double *p, dou
    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(TKresult[nres]!= k)
+      if(i1 != 1 && TKresult[nres]!= k)
          continue;
        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
        fprintf(ficresplb,"#******");
- Line 9192  int back_prevalence_limit(double *p, dou
+ Line 10442  int back_prevalence_limit(double *p, dou
          if(mobilavproj > 0){
            /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
            /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
+           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
          }else if (mobilavproj == 0){
            printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
            fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
            exit(1);
          }else{
            /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
+           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++)
- Line 9212  int back_prevalence_limit(double *p, dou
+ Line 10464  int back_prevalence_limit(double *p, dou
          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); */
- Line 9256  int hPijx(double *p, int bage, int fage)
+ Line 10509  int hPijx(double *p, int bage, int fage)
                  /*      k=k+1;  */
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k=1; k<=i1;k++){
-       if(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
        fprintf(ficrespij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
- Line 9328  int hPijx(double *p, int bage, int fage)
+ Line 10581  int hPijx(double *p, int bage, int fage)
    /* 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(nres=1; nres <= nresult; nres++){ /* For each resultline */
      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-       if(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
        fprintf(ficrespijb,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
- Line 9344  int hPijx(double *p, int bage, int fage)
+ Line 10597  int hPijx(double *p, int bage, int fage)
          fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
        }
        fprintf(ficrespijb,"******\n");
-       if(invalidvarcomb[k]){
+       if(invalidvarcomb[k]){  /* Is it necessary here? */
          fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
          continue;
        }
- Line 9357  int hPijx(double *p, int bage, int fage)
+ Line 10610  int hPijx(double *p, int bage, int fage)
          /*        nhstepm=nhstepm*YEARM; aff par mois*/
-         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
+         /* and memory limitations if stepm is small */
          /* oldm=oldms;savm=savms; */
          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
+         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
+         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
              fprintf(ficrespijb," %1d-%1d",i,j);
- Line 9408  int main(int argc, char *argv[])
+ Line 10663  int main(int argc, char *argv[])
    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 9452  int main(int argc, char *argv[])
+ Line 10710  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 9540  int main(int argc, char *argv[])
+ Line 10801  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 9619  int main(int argc, char *argv[])
+ Line 10885  int main(int argc, char *argv[])
      exit(70);
    }
    strcpy(filereso,"o");
    strcat(filereso,fileresu);
    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
- Line 9629  int main(int argc, char *argv[])
+ Line 10893  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 9660  int main(int argc, char *argv[])
+ Line 10959  int main(int argc, char *argv[])
        numlinepar++;
        fputs(line,stdout);
        fputs(line,ficparo);
+       fputs(line,ficres);
        fputs(line,ficlog);
        continue;
      }else
- Line 9682  int main(int argc, char *argv[])
+ Line 10982  int main(int argc, char *argv[])
        numlinepar++;
        fputs(line,stdout);
        fputs(line,ficparo);
+       fputs(line,ficres);
        fputs(line,ficlog);
        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 9714  int main(int argc, char *argv[])
+ Line 11013  int main(int argc, char *argv[])
    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 9739  int main(int argc, char *argv[])
+ Line 11038  int main(int argc, char *argv[])
    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
-   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
+   if(nqv>=1)coqvar=matrix(1,nqv,1,n);  /**< 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,1,n);  /**< 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,1,n);  /**< 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 9763  int main(int argc, char *argv[])
+ Line 11062  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 9792  int main(int argc, char *argv[])
+ Line 11097  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+     paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      for(i=1; i <=nlstate; i++){
        j=0;
        for(jj=1; jj <=nlstate+ndeath; jj++){
- Line 9828  run imach with mle=-1 to get a correct t
+ Line 11134  run imach with mle=-1 to get a correct t
      }
      fflush(ficlog);
-     /* Reads scales values */
+     /* Reads parameters values */
      p=param[1][1];
+     pstart=paramstart[1][1];
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
- Line 9932  Please run with mle=-1 to get a correct
+ Line 11239  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
- Line 10009  Please run with mle=-1 to get a correct
+ Line 11306  Please run with mle=-1 to get a correct
    Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
    Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
    Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
-   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
-   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
    /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
        For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
- Line 10096  Please run with mle=-1 to get a correct
+ Line 11391  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(andc,1,n);
- Line 10277  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 11572  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=%f \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) 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 quantitative time varying 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 10299  Interval (in months) between two waves:
+ Line 11615  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);
      ageexmed=vector(1,n);
- Line 10537  Please run with mle=-1 to get a correct
+ Line 11853  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 10752  Please run with mle=-1 to get a correct
+ Line 12072  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,ficres);
-       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);
-       fputs(line,ficres);
      }
-     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 */
-     nresult=0;
      while(fgets(line, MAXLINE, ficpar)) {
        /* If line starts with a # it is a comment */
        if (line[0] == '#') {
- Line 10823  Please run with mle=-1 to get a correct
+ Line 12104  Please run with mle=-1 to get a correct
          fputs(line,stdout);
          fputs(line,ficparo);
          fputs(line,ficlog);
-         fputs(line,ficres);
          continue;
        }else
          break;
      }
-     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
-       if (num_filled == 0)
-         resultline[0]='\0';
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-       else if (num_filled != 1){
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
-       }
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
-       nresult++; /* Sum of resultlines */
+       if (num_filled != 1) {
-       printf("Result %d: result=%s\n",nresult, 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);
-       if(nresult > MAXRESULTLINES){
+         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);
-         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 */
+       printf("pop_based=%d\n",popbased);
-       fprintf(ficparo,"result: %s\n",resultline);
+       fprintf(ficlog,"pop_based=%d\n",popbased);
-       fprintf(ficres,"result: %s\n",resultline);
+       fprintf(ficparo,"pop_based=%d\n",popbased);
-       fprintf(ficlog,"result: %s\n",resultline);
+       fprintf(ficres,"pop_based=%d\n",popbased);
-       while(fgets(line, MAXLINE, ficpar)) {
+     }
+     /* 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 */
-         if (line[0] == '#') {
+         numlinepar++;
-           numlinepar++;
+         fputs(line,stdout);
-           fputs(line,stdout);
+         fputs(line,ficparo);
-           fputs(line,ficparo);
+         fputs(line,ficlog);
-           fputs(line,ficres);
+         continue;
-           fputs(line,ficlog);
+       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
-           continue;
+         parameterline=11;
-         }else
+       else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
-           break;
+         parameterline=12;
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp))
+         parameterline=13;
+       else{
+         parameterline=14;
        }
-       if (feof(ficpar))
+       switch (parameterline){
-         break;
+       case 11:
-       else{ /* Processess output results for this combination of covariate values */
+         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 10877  Please run with mle=-1 to get a correct
+ Line 12230  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 10917  Please run with mle=-1 to get a correct
+ Line 12271  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] *\/ */
-       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
-       else if (mobilavproj !=0) {
          printf("Movingaveraging projected observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
          }
+       }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 10963  Please run with mle=-1 to get a correct
+ Line 12322  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 11004  Please run with mle=-1 to get a correct
+ Line 12367  Please run with mle=-1 to get a correct
      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(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
        fprintf(ficreseij,"\n#****** ");
        printf("\n#****** ");
- Line 11028  Please run with mle=-1 to get a correct
+ Line 12391  Please run with mle=-1 to get a correct
      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 11040  Please run with mle=-1 to get a correct
+ Line 12403  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 11069  Please run with mle=-1 to get a correct
+ Line 12430  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++){
-       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
      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(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
-       printf("\n#****** Selected:");
+       printf("\n#****** Result for:");
-       fprintf(ficrest,"\n#****** Selected:");
+       fprintf(ficrest,"\n#****** Result for:");
-       fprintf(ficlog,"\n#****** Selected:");
+       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)]);
- Line 11133  Please run with mle=-1 to get a correct
+ Line 12491  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 */
- Line 11149  Please run with mle=-1 to get a correct
+ Line 12507  Please run with mle=-1 to get a correct
          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 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++){
- Line 11187  Please run with mle=-1 to get a correct
+ Line 12544  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);
        fprintf(ficlog,"done selection\n");fflush(ficlog);
-       /*}*/
      } /* End k selection */
      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 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++){*/
-     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(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(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
-       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
-       /*}*/
-     }
-     fclose(ficresvpl);
-     printf("done variance-covariance of period prevalence\n");fflush(stdout);
-     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
      free_vector(weight,1,n);
      free_imatrix(Tvard,1,NCOVMAX,1,2);
- Line 11264  Please run with mle=-1 to get a correct
+ Line 12575  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 11273  Please run with mle=-1 to get a correct
+ Line 12584  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,1,n);
-   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
+   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
-   free_matrix(coqvar,1,maxwav,1,n);
+   if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
    free_matrix(covar,0,NCOVMAX,1,n);
    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);
- Line 11358  Please run with mle=-1 to get a correct
+ Line 12670  Please run with mle=-1 to get a correct
    fclose(ficlog);
    /*------ End -----------*/
+ /* Executes gnuplot */
    printf("Before Current directory %s!\n",pathcd);
  #ifdef WIN32
- Line 11426  end:
+ Line 12740  end:
      printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);
    }
+   exit(0);
  }

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>

Removed from v.1.238
changed lines
	Added in v.1.282