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Diff for /imach/src/imach.c between versions 1.237 and 1.268

-version 1.237, 2016/08/26 09:20:19
+version 1.268, 2017/05/18 20:09:32
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.268  2017/05/18 20:09:32  brouard
+   Summary: backprojection and confidence intervals of backprevalence
+   Revision 1.267  2017/05/13 10:25:05  brouard
+   Summary: temporary save for backprojection
+   Revision 1.266  2017/05/13 07:26:12  brouard
+   Summary: Version 0.99r13 (improvements and bugs fixed)
+   Revision 1.265  2017/04/26 16:22:11  brouard
+   Summary: imach 0.99r13 Some bugs fixed
+   Revision 1.264  2017/04/26 06:01:29  brouard
+   Summary: Labels in graphs
+   Revision 1.263  2017/04/24 15:23:15  brouard
+   Summary: to save
+   Revision 1.262  2017/04/18 16:48:12  brouard
+   *** empty log message ***
+   Revision 1.261  2017/04/05 10:14:09  brouard
+   Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
+   Revision 1.260  2017/04/04 17:46:59  brouard
+   Summary: Gnuplot indexations fixed (humm)
+   Revision 1.259  2017/04/04 13:01:16  brouard
+   Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
+   Revision 1.258  2017/04/03 10:17:47  brouard
+   Summary: Version 0.99r12
+   Some cleanings, conformed with updated documentation.
+   Revision 1.257  2017/03/29 16:53:30  brouard
+   Summary: Temp
+   Revision 1.256  2017/03/27 05:50:23  brouard
+   Summary: Temporary
+   Revision 1.255  2017/03/08 16:02:28  brouard
+   Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
+   Revision 1.254  2017/03/08 07:13:00  brouard
+   Summary: Fixing data parameter line
+   Revision 1.253  2016/12/15 11:59:41  brouard
+   Summary: 0.99 in progress
+   Revision 1.252  2016/09/15 21:15:37  brouard
+   *** empty log message ***
+   Revision 1.251  2016/09/15 15:01:13  brouard
+   Summary: not working
+   Revision 1.250  2016/09/08 16:07:27  brouard
+   Summary: continue
+   Revision 1.249  2016/09/07 17:14:18  brouard
+   Summary: Starting values from frequencies
+   Revision 1.248  2016/09/07 14:10:18  brouard
+   *** empty log message ***
+   Revision 1.247  2016/09/02 11:11:21  brouard
+   *** empty log message ***
+   Revision 1.246  2016/09/02 08:49:22  brouard
+   *** empty log message ***
+   Revision 1.245  2016/09/02 07:25:01  brouard
+   *** empty log message ***
+   Revision 1.244  2016/09/02 07:17:34  brouard
+   *** empty log message ***
+   Revision 1.243  2016/09/02 06:45:35  brouard
+   *** empty log message ***
+   Revision 1.242  2016/08/30 15:01:20  brouard
+   Summary: Fixing a lots
+   Revision 1.241  2016/08/29 17:17:25  brouard
+   Summary: gnuplot problem in Back projection to fix
+   Revision 1.240  2016/08/29 07:53:18  brouard
+   Summary: Better
+   Revision 1.239  2016/08/26 15:51:03  brouard
+   Summary: Improvement in Powell output in order to copy and paste
+   Author:
+   Revision 1.238  2016/08/26 14:23:35  brouard
+   Summary: Starting tests of 0.99
    Revision 1.237  2016/08/26 09:20:19  brouard
    Summary: to valgrind
- Line 84
+ Line 181
    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 729  Back prevalence and projections:
+ Line 824  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 874  typedef struct {
+ Line 969  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 897  typedef struct {
+ Line 992  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 990  FILE  *ficresvij;
+ Line 1086  FILE  *ficresvij;
  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
+ FILE  *ficresvbl;
+ char fileresvbl[FILENAMELENGTH];
  char title[MAXLINE];
  char model[MAXLINE]; /**< The model line */
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
- Line 1029  double dval;
+ Line 1127  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 1086  double *agedc;
+ Line 1185  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 1116  int *TvarsQind;
+ Line 1215  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 1145  double *Tvalsel; /**< Selected modality
+ Line 1245  double *Tvalsel; /**< Selected modality
  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
  int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
  int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
+ int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
  int *Tage;
  int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
  int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
- Line 1154  int *Ndum; /** Freq of modality (tricode
+ Line 1256  int *Ndum; /** Freq of modality (tricode
  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
  int **Tvard;
  int *Tprod;/**< Gives the k position of the k1 product */
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
  int *Tposprod; /**< Gives the k1 product from the k position */
- /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
+    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
-    if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
-    Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
- */
  int cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
- Line 2057  void powell(double p[], double **xi, int
+ Line 2158  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 2092  void powell(double p[], double **xi, int
+ Line 2193  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 2170  void powell(double p[], double **xi, int
+ Line 2304  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 2216  void powell(double p[], double **xi, int
+ Line 2351  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 2313  void powell(double p[], double **xi, int
+ Line 2448  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 2496  Earliest age to start was %d-%d=%d, ncvl
+ Line 2631  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 2519  Earliest age to start was %d-%d=%d, ncvl
+ Line 2654  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 2533  Earliest age to start was %d-%d=%d, ncvl
+ Line 2669  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 2555  Earliest age to start was %d-%d=%d, ncvl
+ Line 2691  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 2578  Earliest age to start was %d-%d=%d, ncvl
+ Line 2748  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 2598  Earliest age to start was %d-%d=%d, ncvl
+ Line 2787  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 2610  Earliest age to start was %d-%d=%d, ncvl
+ Line 2799  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 2625  Oldest age to start was %d-%d=%d, ncvloo
+ Line 2819  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 2634  double **pmij(double **ps, double *cov,
+ Line 2828  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 2699  double **pmij(double **ps, double *cov,
+ Line 2894  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 2708  double **pmij(double **ps, double *cov,
+ Line 2903  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 2725  double **pmij(double **ps, double *cov,
+ Line 2920  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 */
+     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 2974  double ***hpxij(double ***po, int nhstep
+ Line 3193  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 2995  double ***hbxij(double ***po, int nhstep
+ Line 3214  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 3019  double ***hbxij(double ***po, int nhstep
+ Line 3239  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 3064  double ***hbxij(double ***po, int nhstep
+ Line 3295  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 3126  double func( double *x)
+ Line 3358  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 3145  double func( double *x)
+ Line 3377  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 3159  double func( double *x)
+ Line 3392  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 3441  double funcone( double *x)
+ Line 3677  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 3468  double funcone( double *x)
+ Line 3705  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 3521  double funcone( double *x)
+ Line 3763  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 3901  double hessij( double x[], double **hess
+ Line 4143  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 3991  void ludcmp(double **a, int n, int *indx
+ Line 4233  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 4057  void pstamp(FILE *fichier)
+ Line 4308  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 4076  void  freqsummary(char fileres[], int ia
+ Line 4331  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 4090  void  freqsummary(char fileres[], int ia
+ Line 4345  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 4100  void  freqsummary(char fileres[], int ia
+ Line 4355  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(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(jk=1; jk <=nlstate ; jk++){
-                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-                                         pp[jk] += freq[jk][m][iage];
-       }
-       for(jk=1; jk <=nlstate ; jk++){
-                                 for(m=-1, pos=0; m <=0 ; m++)
-                                         pos += freq[jk][m][iage];
-                                 if(pp[jk]>=1.e-10){
-                                         if(first==1){
-                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-                                         }
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
-                                 }else{
-                                         if(first==1)
-                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
-                                 }
-       }
-       for(jk=1; jk <=nlstate ; jk++){
-                                 /* posprop[jk]=0; */
-                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
-                                         pp[jk] += freq[jk][m][iage];
-       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
-       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
-                                 pos += pp[jk]; /* pos is the total number of transitions until this age */
-                                 posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
-                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
-                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
-       }
-       for(jk=1; jk <=nlstate ; jk++){
-                                 if(pos>=1.e-5){
-                                         if(first==1)
-                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
-                                 }else{
-                                         if(first==1)
-                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-                                 }
-                                 if( iage <= iagemax){
-                                         if(pos>=1.e-5){
-                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
-                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
-                                                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
-                                         }
-                                         else{
-                                                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
-                                                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
-                                         }
-                                 }
-                                 pospropt[jk] +=posprop[jk];
-       } /* end loop jk */
-       /* pospropt=0.; */
-       for(jk=-1; jk <=nlstate+ndeath; jk++){
-                                 for(m=-1; m <=nlstate+ndeath; m++){
-                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */
-                                                 if(first==1){
-                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
-                                                 }
-                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
-                                         }
-                                         if(jk!=0 && m!=0)
-                                                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
-                                 }
-       } /* end loop jk */
-       posproptt=0.;
-       for(jk=1; jk <=nlstate; jk++){
-                                 posproptt += pospropt[jk];
-       }
-       fprintf(ficresphtmfr,"</tr>\n ");
-       if(iage <= iagemax){
-                                 fprintf(ficresp,"\n");
-                                 fprintf(ficresphtm,"</tr>\n");
        }
-       if(first==1)
+       fprintf(ficresphtm,"</tr>\n");
-                                 printf("Others in log...\n");
+       fprintf(ficresphtm,"</table>\n");
-       fprintf(ficlog,"\n");
+       fprintf(ficresphtmfr,"</table>\n");
-     } /* end loop age iage */
-     fprintf(ficresphtm,"<tr><th>Tot</th>");
-     for(jk=1; jk <=nlstate ; jk++){
        if(posproptt < 1.e-5){
-                                 fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+         fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
+         printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
+         invalidvarcomb[j1]=1;
        }else{
-                                 fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+         invalidvarcomb[j1]=0;
        }
-     }
+       fprintf(ficresphtmfr,"</table>\n");
-     fprintf(ficresphtm,"</tr>\n");
+       fprintf(ficlog,"\n");
-     fprintf(ficresphtm,"</table>\n");
+       if(j!=0){
-     fprintf(ficresphtmfr,"</table>\n");
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
-     if(posproptt < 1.e-5){
+         for(i=1,s1=1; i <=nlstate; i++){
-       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+           for(k=1; k <=(nlstate+ndeath); k++){
-       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+             if (k != i) {
-       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
-       invalidvarcomb[j1]=1;
+                 if(jj==1){  /* Constant case (in fact cste + age) */
-     }else{
+                   if(j1==1){ /* All dummy covariates to zero */
-       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
-       invalidvarcomb[j1]=0;
+                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
-     }
+                     printf("%d%d ",i,k);
-     fprintf(ficresphtmfr,"</table>\n");
+                     fprintf(ficlog,"%d%d ",i,k);
-   } /* end selected combination of covariate j1 */
+                     printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
-   dateintmean=dateintsum/k2cpt;
+                     fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                     pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
-   fclose(ficresp);
+                   }
-   fclose(ficresphtm);
+                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
-   fclose(ficresphtmfr);
+                   for(iage=iagemin; iage <= iagemax+3; iage++){
-   free_vector(meanq,1,nqfveff);
+                     x[iage]= (double)iage;
-   free_matrix(meanqt,1,lastpass,1,nqtveff);
+                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
-   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
+                     /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
+                   }
+                   /* Some are not finite, but linreg will ignore these ages */
+                   no=0;
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
+                   pstart[s1]=b;
+                   pstart[s1-1]=a;
+                 }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */
+                   printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
+                   printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
+                   pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
+                   printf("%d%d ",i,k);
+                   fprintf(ficlog,"%d%d ",i,k);
+                   printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
+                 }else{ /* Other cases, like quantitative fixed or varying covariates */
+                   ;
+                 }
+                 /* printf("%12.7f )", param[i][jj][k]); */
+                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+                 s1++;
+               } /* end jj */
+             } /* end k!= i */
+           } /* end k */
+         } /* end i, s1 */
+       } /* end j !=0 */
+     } /* end selected combination of covariate j1 */
+     if(j==0){ /* We can estimate starting values from the occurences in each case */
+       printf("#Freqsummary: Starting values for the constants:\n");
+       fprintf(ficlog,"\n");
+       for(i=1,s1=1; i <=nlstate; i++){
+         for(k=1; k <=(nlstate+ndeath); k++){
+           if (k != i) {
+             printf("%d%d ",i,k);
+             fprintf(ficlog,"%d%d ",i,k);
+             for(jj=1; jj <=ncovmodel; jj++){
+               pstart[s1]=p[s1]; /* Setting pstart to p values by default */
+               if(jj==1){ /* Age has to be done */
+                 pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
+                 printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+                 fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
+               }
+               /* printf("%12.7f )", param[i][jj][k]); */
+               /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+               s1++;
+             }
+             printf("\n");
+             fprintf(ficlog,"\n");
+           }
+         }
+       }
+       printf("#Freqsummary\n");
+       fprintf(ficlog,"\n");
+       for(s1=-1; s1 <=nlstate+ndeath; s1++){
+         for(s2=-1; s2 <=nlstate+ndeath; s2++){
+           /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
+           printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
+           /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
+           /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
+           /* } */
+         }
+       } /* end loop s1 */
+       printf("\n");
+       fprintf(ficlog,"\n");
+     } /* end j=0 */
+   } /* end j */
+   if(mle == -2){  /* We want to use these values as starting values */
+     for(i=1, jk=1; i <=nlstate; i++){
+       for(j=1; j <=nlstate+ndeath; j++){
+         if(j!=i){
+           /*ca[0]= k+'a'-1;ca[1]='\0';*/
+           printf("%1d%1d",i,j);
+           fprintf(ficparo,"%1d%1d",i,j);
+           for(k=1; k<=ncovmodel;k++){
+             /*    printf(" %lf",param[i][j][k]); */
+             /*    fprintf(ficparo," %lf",param[i][j][k]); */
+             p[jk]=pstart[jk];
+             printf(" %f ",pstart[jk]);
+             fprintf(ficparo," %f ",pstart[jk]);
+             jk++;
+           }
+           printf("\n");
+           fprintf(ficparo,"\n");
+         }
+       }
+     }
+   } /* end mle=-2 */
+   dateintmean=dateintsum/k2cpt;
+   fclose(ficresp);
+   fclose(ficresphtm);
+   fclose(ficresphtmfr);
+   free_vector(meanq,1,nqfveff);
+   free_matrix(meanqt,1,lastpass,1,nqtveff);
+   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
+   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
    free_vector(pospropt,1,nlstate);
    free_vector(posprop,1,nlstate);
-   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+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 4438  void prevalence(double ***probs, double
+ Line 4953  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 4448  void prevalence(double ***probs, double
+ Line 4963  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 4479  void prevalence(double ***probs, double
+ Line 4994  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 4505  void prevalence(double ***probs, double
+ Line 5020  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 4516  void prevalence(double ***probs, double
+ Line 5034  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 4565  void  concatwav(int wav[], int **dh, int
+ Line 5083  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 4595  void  concatwav(int wav[], int **dh, int
+ Line 5113  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 4614  void  concatwav(int wav[], int **dh, int
+ Line 5128  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 4650  void  concatwav(int wav[], int **dh, int
+ Line 5164  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 4737  void  concatwav(int wav[], int **dh, int
+ Line 5251  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 4918  void  concatwav(int wav[], int **dh, int
+ Line 5432  void  concatwav(int wav[], int **dh, int
    double ***p3mat;
    double eip;
-   pstamp(ficreseij);
+   /* pstamp(ficreseij); */
    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
    fprintf(ficreseij,"# Age");
    for(i=1; i<=nlstate;i++){
- Line 5283  void  concatwav(int wav[], int **dh, int
+ Line 5797  void  concatwav(int wav[], int **dh, int
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
+    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+    }
+    for(j=1;j<=cptcoveff;j++)
+      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
+    fprintf(ficresprobmorprev,"\n");
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
- Line 5352  void  concatwav(int wav[], int **dh, int
+ Line 5874  void  concatwav(int wav[], int **dh, int
           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 5384  void  concatwav(int wav[], int **dh, int
+ Line 5906  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);
-        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 5461  void  concatwav(int wav[], int **dh, int
+ Line 5983  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 5545  void  concatwav(int wav[], int **dh, int
+ Line 6067  void  concatwav(int wav[], int **dh, int
    /* 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 5556  void  concatwav(int wav[], int **dh, int
+ Line 6078  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 5632  void  concatwav(int wav[], int **dh, int
+ Line 6156  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 5655  void  concatwav(int wav[], int **dh, int
+ Line 6181  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 fileres[], 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 5735  void varprob(char optionfilefiname[], do
+ Line 6386  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 5952  To be simple, these graphs help to under
+ Line 6603  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 5963  To be simple, these graphs help to under
+ Line 6614  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(lc1),v12,sqrt(fabs(lc2)),   \
-                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+                            mu2,std,v21,sqrt(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 6000  To be simple, these graphs help to under
+ Line 6651  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 jprev2, double mprev2,double anprev2, double dateprev2){
    int jj1, k1, i1, cpt, k4, nres;
- Line 6038  void printinghtml(char fileresu[], char
+ Line 6689  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 6074  void printinghtml(char fileresu[], char
+ Line 6770  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) up 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, 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) up to stable (mixed) back prevalence in state %d. 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, 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 6177  See page 'Matrix of variance-covariance
+ Line 6880  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 6200  See page 'Matrix of variance-covariance
+ Line 6903  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 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 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 6270  void printinggnuplot(char fileresu[], ch
+ Line 6975  void printinggnuplot(char fileresu[], ch
    strcpy(dirfileres,optionfilefiname);
    strcpy(optfileres,"vpl");
    /* 1eme*/
-   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
+   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
-     for (k1=1; k1<= m ; k1 ++) /* For each valid combination of covariate */
+     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 */
+         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-       if(TKresult[nres]!= k1)
+         if(m != 1 && TKresult[nres]!= k1)
-         continue;
+           continue;
-       /* We are interested in selected combination by the resultline */
+         /* 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);
+         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+         strcpy(gplotlabel,"(");
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
+           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-         printf(" V%d=%d ",Tvaraff[k],vlv);
+           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           /* printf(" V%d=%d ",Tvaraff[k],vlv); */
-       }
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
-         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
-         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-       }
+           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
-       printf("\n#\n");
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       fprintf(ficgp,"\n#\n");
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       if(invalidvarcomb[k1]){
+         }
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         strcpy(gplotlabel+strlen(gplotlabel),")");
-         continue;
+         /* 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 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);
- 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_"),k1-1,k1-1,nres); */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+       /* k1-1 error should be nres-1*/
+         for (i=1; i<= nlstate ; i ++) {
-       for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else        fprintf(ficgp," %%*lf (%%*lf)");
-         else        fprintf(ficgp," %%*lf (%%*lf)");
+         }
-       }
+         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
-       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);
+         for (i=1; i<= nlstate ; i ++) {
-       for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
-         else fprintf(ficgp," %%*lf (%%*lf)");
+         }
-       }
+         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
-       fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+         for (i=1; i<= nlstate ; i ++) {
-       for (i=1; i<= nlstate ; i ++) {
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           else fprintf(ficgp," %%*lf (%%*lf)");
-         else fprintf(ficgp," %%*lf (%%*lf)");
+         }
-       }
+         /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%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:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
-       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
-         /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+         if(cptcoveff ==0){
-         fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
+           fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+(cpt-1),  cpt );
-         if(cptcoveff ==0){
-           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
          }else{
            kl=0;
            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
- Line 6341  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 7049  plot [%.f:%.f] \"%s\" every :::%d::%d u
              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
              if(k==cptcoveff){
-               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
-+(cpt-1),  cpt );  /* 4 or 6 ?*/
++cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
              }else{
                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                kl++;
              }
            } /* end covariate */
          } /* end if no covariate */
-       } /* end if backcast */
-       fprintf(ficgp,"\nset out \n");
+         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
+           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
+           if(cptcoveff ==0){
+             fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
+           }else{
+             kl=0;
+             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
+               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               vlv= nbcode[Tvaraff[k]][lv];
+               kl++;
+               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+               if(k==cptcoveff){
+                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
+               }else{
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+                 kl++;
+               }
+             } /* end covariate */
+           } /* end if no covariate */
+           if(backcast == 1){
+             fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+             /* k1-1 error should be nres-1*/
+             for (i=1; i<= nlstate ; i ++) {
+               if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+               else        fprintf(ficgp," %%*lf (%%*lf)");
+             }
+             fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 0,\"%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 1,\"%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 1");
+           } /* end if backprojcast */
+         } /* end if backcast */
+         fprintf(ficgp,"\nset out ;unset label;\n");
+       } /* nres */
      } /* k1 */
    } /* cpt */
    /*2 eme*/
-   for (k1=1; k1<= m ; k1 ++)
+   for (k1=1; k1<= m ; k1 ++){
-   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
-       continue;
+         continue;
-     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-     for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+       strcpy(gplotlabel,"(");
-       lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       vlv= nbcode[Tvaraff[k]][lv];
-       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-     }
-     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-       printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-     }
-     fprintf(ficgp,"\n#\n");
-     if(invalidvarcomb[k1]){
-       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       continue;
-     }
-     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       if(vpopbased==0)
-         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-       else
-         fprintf(ficgp,"\nreplot ");
-       for (i=1; i<= nlstate+1 ; i ++) {
-         k=2*i;
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         fprintf(ficgp,"\" t\"\" w l lt 0,");
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-       } /* state */
-     } /* vpopbased */
-     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-   } /* k1 end 2 eme*/
-   /*3eme*/
-   for (k1=1; k1<= m ; k1 ++)
-   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     if(TKresult[nres]!= k)
-       continue;
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate dummy combination and each value */
          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
          vlv= nbcode[Tvaraff[k]][lv];
          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
        }
        /* for(k=1; k <= ncovds; k++){ */
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       }
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
        }
-       /*       k=2+nlstate*(2*cpt-2); */
+       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
-       k=2+(nlstate+1)*(cpt-1);
+       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
+         fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
-       fprintf(ficgp,"set ter svg size 640, 480\n\
+         if(vpopbased==0){
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
+           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         }else
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\nreplot ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+         for (i=1; i<= nlstate+1 ; i ++) {
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           k=2*i;
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
+           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           fprintf(ficgp,"\" t\"\" w l lt 0,");
+           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
+           for (j=1; j<= nlstate+1 ; j ++) {
+             if (j==i) fprintf(ficgp," %%lf (%%lf)");
+             else fprintf(ficgp," %%*lf (%%*lf)");
+           }
+           if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+           else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
+         } /* state */
+       } /* vpopbased */
+       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
+     } /* end nres */
+   } /* k1 end 2 eme*/
+   /*3eme*/
+   for (k1=1; k1<= m ; k1 ++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(m != 1 && TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<= nlstate ; cpt ++) {
+         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
+         strcpy(gplotlabel,"(");
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         /*       k=2+nlstate*(2*cpt-2); */
+         k=2+(nlstate+1)*(cpt-1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+         fprintf(ficgp,"set ter svg size 640, 480\n\
+ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
+         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-       */
+         */
-       for (i=1; i< nlstate ; i ++) {
+         for (i=1; i< nlstate ; i ++) {
-         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
+           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+           /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
-       }
+         }
-       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
+         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
-     }
+       }
-   }
+       fprintf(ficgp,"\nunset label;\n");
+     } /* end nres */
+   } /* end kl 3eme */
    /* 4eme */
    /* Survival functions (period) from state i in state j by initial state i */
-   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
-   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     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 */
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
+         strcpy(gplotlabel,"(");
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
- set ter svg size 640, 480\n                                                                                                                                                                                     \
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
- unset log y\n                                                                                                                                                                                                                                           \
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-       k=3;
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       for (i=1; i<= nlstate ; i ++){
+           vlv= nbcode[Tvaraff[k]][lv];
-         if(i==1){
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
-         }else{
-           fprintf(ficgp,", '' ");
          }
-         l=(nlstate+ndeath)*(i-1)+1;
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         for (j=2; j<= nlstate+ndeath ; j ++)
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-           fprintf(ficgp,"+$%d",k+l+j-1);
+         }
-         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         strcpy(gplotlabel+strlen(gplotlabel),")");
-       } /* nlstate */
+         fprintf(ficgp,"\n#\n");
-       fprintf(ficgp,"\nset out\n");
+         if(invalidvarcomb[k1]){
-     } /* end cpt state*/
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-   } /* end covariate */
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
+         for (i=1; i<= nlstate ; i ++){
+           if(i==1){
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           }else{
+             fprintf(ficgp,", '' ");
+           }
+           l=(nlstate+ndeath)*(i-1)+1;
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
+           for (j=2; j<= nlstate+ndeath ; j ++)
+             fprintf(ficgp,"+$%d",k+l+j-1);
+           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end nres */
+   } /* end covariate k1 */
  /* 5eme */
    /* Survival functions (period) from state i in state j by final state j */
-   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
-   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     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  */
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+         strcpy(gplotlabel,"(");
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
- set ter svg size 640, 480\n                                             \
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
- unset log y\n                                                           \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         k=3;
-       k=3;
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           if(j==1)
-         if(j==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           else
-         else
+             fprintf(ficgp,", '' ");
-           fprintf(ficgp,", '' ");
+           l=(nlstate+ndeath)*(cpt-1) +j;
-         l=(nlstate+ndeath)*(cpt-1) +j;
+           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+           /* for (i=2; i<= nlstate+ndeath ; i ++) */
-         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+         } /* nlstate */
-       } /* nlstate */
+         fprintf(ficgp,", '' ");
-       fprintf(ficgp,", '' ");
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           l=(nlstate+ndeath)*(cpt-1) +j;
-         l=(nlstate+ndeath)*(cpt-1) +j;
+           if(j < nlstate)
-         if(j < nlstate)
+             fprintf(ficgp,"$%d +",k+l);
-           fprintf(ficgp,"$%d +",k+l);
+           else
-         else
+             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         }
-       }
+         fprintf(ficgp,"\nset out; unset label;\n");
-       fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
-     } /* end cpt state*/
+     } /* end covariate */
-   } /* end covariate */
+   } /* end nres */
  /* 6eme */
    /* CV preval stable (period) for each covariate */
    for (k1=1; k1<= m ; k1 ++) /* For each covariate combination 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 6581  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7356  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
          vlv= nbcode[Tvaraff[k]][lv];
          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
        }
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
        }
+       strcpy(gplotlabel+strlen(gplotlabel),")");
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
        }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
+       fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
        k=3; /* Offset */
-       for (i=1; i<= nlstate ; i ++){
+       for (i=1; i<= nlstate ; i ++){ /* State of origin */
          if(i==1)
            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
          else
            fprintf(ficgp,", '' ");
-         l=(nlstate+ndeath)*(i-1)+1;
+         l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
          for (j=2; j<= nlstate ; j ++)
            fprintf(ficgp,"+$%d",k+l+j-1);
          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
        } /* nlstate */
-       fprintf(ficgp,"\nset out\n");
+       fprintf(ficgp,"\nset out; unset label;\n");
      } /* end cpt state*/
    } /* end covariate */
- Line 6618  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7395  plot [%.f:%.f]  ", ageminpar, agemaxpar)
      /* 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 6629  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7407  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
            vlv= nbcode[Tvaraff[k]][lv];
            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
            continue;
          }
-         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
          k=3; /* Offset */
-         for (i=1; i<= nlstate ; i ++){
+         for (i=1; i<= nlstate ; i ++){ /* State of arrival */
            if(i==1)
              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
            else
              fprintf(ficgp,", '' ");
            /* l=(nlstate+ndeath)*(i-1)+1; */
-           l=(nlstate+ndeath)*(cpt-1)+1;
+           l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
-           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
            /* for (j=2; j<= nlstate ; j ++) */
            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
-           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
          } /* nlstate */
-         fprintf(ficgp,"\nset out\n");
+         fprintf(ficgp,"\nset out; unset label;\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if backcast */
- Line 6671  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7451  plot [%.f:%.f]  ", ageminpar, agemaxpar)
      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 6682  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7463  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
            vlv= nbcode[Tvaraff[k]][lv];
            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
+         strcpy(gplotlabel+strlen(gplotlabel),")");
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
- Line 6693  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7477  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          }
          fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
-         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
-         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+         istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+         /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+         for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
            /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
            /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
            /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-           if(i==1){
+           if(i==istart){
              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
            }else{
              fprintf(ficgp,",\\\n '' ");
- Line 6715  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7502  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
              /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
              fprintf(ficgp," u %d:(", ioffset);
-             if(i==nlstate+1)
+             if(i==nlstate+1){
-               fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
+               fprintf(ficgp," $%d/(1.-$%d)):5 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," (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 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 */
- Line 6750  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7542  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
              if(i==nlstate+1){
-               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):5 t 'p.%d' with line lc variable", gplotcondition, \
                        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,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \
+                      offyear,                           \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
+ /*  '' 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)):5 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," (($5-$6) == %d ) ? $%d : 1/0):5 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 */
+             if(cptcoveff ==1){
+               ioffset=4; /* Age is in 4 */
+             }else{
+               ioffset=6; /* Age is in 6 */
+               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+             }
+             fprintf(ficgp," u %d:(",ioffset);
+             kl=0;
+             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):5 t 'bw%d' with line lc variable", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),cpt );
+               fprintf(ficgp,",\\\n '' ");
+               fprintf(ficgp," u %d:(",ioffset);
+               /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
+               fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d : 1/0):5 with labels center not ", gplotcondition, \
+                      offbyear,                          \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
+ /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
+             }else{
+               /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
+               fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
+             }
+           } /* end if covariate */
+         } /* nlstate */
+         fprintf(ficgp,"\nset out; unset label;\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* End if backcast */
-   /* proba elementaires */
+   /* 9eme writing MLE parameters */
-   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
+   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
    for(i=1,jk=1; i <=nlstate; i++){
      fprintf(ficgp,"# initial state %d\n",i);
      for(k=1; k <=(nlstate+ndeath); k++){
- Line 6782  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7697  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"##############\n#\n");
    /*goto avoid;*/
-   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
+   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
+   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
- Line 6797  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7713  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
    fprintf(ficgp,"#\n");
    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year \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,"# ng=%d\n",ng);
+     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 label \"%s\" at graph 0.98,0.5 center rotate 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 6854  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7784  plot [%.f:%.f]  ", ageminpar, agemaxpar)
              /* 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(Dummy[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(Dummy[Tvard[ijp][1]]==0){/* Vn is dummy */
-                     if(Dummy[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(Dummy[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++;
                    }
-                 }
+                 } /* 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 6902  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7837  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            if(ng != 1){
              fprintf(ficgp,")/(1");
-             for(k1=1; k1 <=nlstate; k1++){
+             for(cpt=1; cpt <=nlstate; cpt++){
                if(nagesqr==0)
-                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
                else /* nagesqr =1 */
-                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
+                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                ij=1;
                for(j=3; j <=ncovmodel-nagesqr; j++){
-                 if((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,")");
              }
- Line 6938  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7874  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            i=i+ncovmodel;
          } /* end k */
        } /* end k2 */
-       fprintf(ficgp,"\n set out\n");
+       fprintf(ficgp,"\n set out; unset label;\n");
-     } /* end jk */
+     } /* end k1 */
    } /* end ng */
    /* avoid: */
    fflush(ficgp);
- Line 6955  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7891  plot [%.f:%.f]  ", ageminpar, agemaxpar)
     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  */
- Line 6966  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7903  plot [%.f:%.f]  ", ageminpar, agemaxpar)
     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 6990  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7930  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       */
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
-          for (i=1; i<=nlstate;i++){
+          for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
-            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+            sumnewm[cptcod]=0.;
+            for (i=1; i<=nlstate;i++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
               for (cpt=1;cpt<=(mob-1)/2;cpt++){
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
               }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
-            }
+              sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
-          }
+            } /* end i */
+            if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
+          } /* end cptcod */
         }/* end age */
       }/* end mob */
-    }else
+    }else{
+      printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
       return -1;
-    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
+    }
+    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
       if(invalidvarcomb[cptcod]){
         printf("\nCombination (%d) ignored because no cases \n",cptcod);
         continue;
       }
-      agemingood[cptcod]=fage-(mob-1)/2;
+      for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
-      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
         sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemingoodr[cptcod]=age;
         }
         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
-          agemingood[cptcod]=age;
+            agemingood[cptcod]=age;
-        }else{ /* bad */
+        }
-          for (i=1; i<=nlstate;i++){
+      } /* age */
-            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
-          } /* i */
-        } /* end bad */
-      }/* age */
-      sum=0.;
-      for (i=1; i<=nlstate;i++){
-        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
-      }
-      if(fabs(sum - 1.) > 1.e-3) { /* bad */
-        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
-        /* for (i=1; i<=nlstate;i++){ */
-        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
-        /* } /\* i *\/ */
-      } /* end bad */
-      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
-      /* From youngest, finding the oldest wrong */
-      agemaxgood[cptcod]=bage+(mob-1)/2;
-      for (age=bage+(mob-1)/2; age<=fage; age++){
         sumnewm[cptcod]=0.;
+        sumnewmr[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
+          sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
+        }
+        if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
+          agemaxgoodr[cptcod]=age;
         }
         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
           agemaxgood[cptcod]=age;
-        }else{ /* bad */
+        }
-          for (i=1; i<=nlstate;i++){
+      } /* age */
-            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
-          } /* i */
+      /* but they will change */
+      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 7075  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8081  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       }
       /* printf("\n"); */
       /* } */
       /* brutal averaging */
-      for (i=1; i<=nlstate;i++){
+      /* for (i=1; i<=nlstate;i++){ */
-        for (age=1; age<=bage; age++){
+      /*   for (age=1; age<=bage; age++){ */
-          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
-          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
-        }
+      /*   }      */
-        for (age=fage; age<=AGESUP; age++){
+      /*   for (age=fage; age<=AGESUP; age++){ */
-          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
+      /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
-          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
+      /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
-        }
+      /*   } */
-      } /* end i status */
+      /* } /\* end i status *\/ */
-      for (i=nlstate+1; i<=nlstate+ndeath;i++){
+      /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
-        for (age=1; age<=AGESUP; age++){
+      /*   for (age=1; age<=AGESUP; age++){ */
-          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
+      /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
-          mobaverage[(int)age][i][cptcod]=0.;
+      /*          mobaverage[(int)age][i][cptcod]=0.; */
-        }
+      /*   } */
-      }
+      /* } */
     }/* end cptcod */
-    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(agemaxgoodr,1, ncovcombmax);
-    free_vector(sumnewp,1, ncovcombmax);
     free_vector(agemaxgood,1, ncovcombmax);
     free_vector(agemingood,1, ncovcombmax);
+    free_vector(agemingoodr,1, ncovcombmax);
+    free_vector(sumnewmr,1, ncovcombmax);
+    free_vector(sumnewm,1, ncovcombmax);
+    free_vector(sumnewp,1, ncovcombmax);
     return 0;
   }/* End movingaverage */
  /************** Forecasting ******************/
-  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+ void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double 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 7164  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8174  plot [%.f:%.f]  ", ageminpar, agemaxpar)
  /*            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 7175  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8185  plot [%.f:%.f]  ", ageminpar, agemaxpar)
        fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
      }
      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-       printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
      }
      fprintf(ficresf," yearproj age");
      for(j=1; j<=nlstate+ndeath;j++){
- Line 7192  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8201  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          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]*mobaverage[(int)agec][i][k];
-               if (h*hstepm/YEARM*stepm== yearp) {
+             /* else { */ /* even if mobilav==-1 we use mobaverage */
-                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
+             /*  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
-               }
+             /* } */
-             } /* end i */
+             fprintf(ficresf," %.3f", p3mat[i][j][h]);
-             if (h*hstepm/YEARM*stepm==yearp) {
+           } /* end i */
-               fprintf(ficresf," %.3f", ppij);
+           fprintf(ficresf," %.3f", ppij);
-             }
+         }/* end j */
-           }/* end j */
-         } /* end h */
          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 7230  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 8240  plot [%.f:%.f]  ", ageminpar, agemaxpar)
  }
  /* /\************** 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 en of backection (same day and month as back1).
- /*   *\/ */
+   */
- /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
+   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
- /*   double agec; /\* generic age *\/ */
+   double agec; /* generic age */
- /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
+   double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
- /*   double *popeffectif,*popcount; */
+   double *popeffectif,*popcount;
- /*   double ***p3mat; */
+   double ***p3mat;
- /*   /\* double ***mobaverage; *\/ */
+   /* double ***mobaverage; */
- /*   char fileresfb[FILENAMELENGTH]; */
+   char fileresfb[FILENAMELENGTH];
- /*   agelim=AGESUP; */
+   agelim=AGEINF;
- /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
- /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
- /*      We still use firstpass and lastpass as another selection. */
+      We still use firstpass and lastpass as another selection.
- /*   *\/ */
+   */
- /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
+   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
- /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
+   /*          firstpass, lastpass,  stepm,  weightopt, model); */
- /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+   /*Do we need to compute prevalence again?*/
- /*   strcpy(fileresfb,"FB_");  */
- /*   strcat(fileresfb,fileresu); */
+   /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
- /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
- /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
+   strcpy(fileresfb,"FB_");
- /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
+   strcat(fileresfb,fileresu);
- /*   } */
+   if((ficresfb=fopen(fileresfb,"w"))==NULL) {
- /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
+     printf("Problem with back forecast resultfile: %s\n", fileresfb);
- /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
+     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
+   }
- /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
+   printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
+   fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
- /*   /\* if (mobilav!=0) { *\/ */
- /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+   if (cptcoveff==0) ncodemax[cptcoveff]=1;
- /*   /\*   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);
- /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
+   }
- /*   if (stepm<=12) stepsize=1; */
+   else  hstepm=estepm;
- /*   if(estepm < stepm){ */
- /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
+   hstepm=hstepm/stepm;
- /*   } */
+   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
- /*   else  hstepm=estepm;    */
+                                fractional in yp1 */
+   anprojmean=yp;
- /*   hstepm=hstepm/stepm;  */
+   yp2=modf((yp1*12),&yp);
- /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
+   mprojmean=yp;
- /*                                fractional in yp1 *\/ */
+   yp1=modf((yp2*30.5),&yp);
- /*   anprojmean=yp; */
+   jprojmean=yp;
- /*   yp2=modf((yp1*12),&yp); */
+   if(jprojmean==0) jprojmean=1;
- /*   mprojmean=yp; */
+   if(mprojmean==0) jprojmean=1;
- /*   yp1=modf((yp2*30.5),&yp); */
- /*   jprojmean=yp; */
+   i1=pow(2,cptcoveff);
- /*   if(jprojmean==0) jprojmean=1; */
+   if (cptcovn < 1){i1=1;}
- /*   if(mprojmean==0) jprojmean=1; */
- /*   i1=cptcoveff; */
- /*   if (cptcovn < 1){i1=1;} */
- /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
+   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
- /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
+   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
- /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
+   /*          if (h==(int)(YEARM*yearp)){ */
- /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
+   /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
- /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
+   /*   for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
- /*       k=k+1; */
+   /*     k=k+1; */
- /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
- /*       for(j=1;j<=cptcoveff;j++) { */
+   for(k=1; k<=i1;k++){
- /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
+     if(i1 != 1 && TKresult[nres]!= k)
- /*       } */
+       continue;
- /*       fprintf(ficresfb," yearbproj age"); */
+     if(invalidvarcomb[k]){
- /*       for(j=1; j<=nlstate+ndeath;j++){  */
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
- /*                              for(i=1; i<=nlstate;i++)               */
+       continue;
- /*           fprintf(ficresfb," p%d%d",i,j); */
+     }
- /*                              fprintf(ficresfb," p.%d",j); */
+     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
- /*       } */
+     for(j=1;j<=cptcoveff;j++) {
- /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
+       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
+     }
- /*                              fprintf(ficresfb,"\n"); */
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
- /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
- /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
+     }
- /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
+     fprintf(ficresfb," yearbproj age");
- /*                                      nhstepm = nhstepm/hstepm;  */
+     for(j=1; j<=nlstate+ndeath;j++){
- /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+       for(i=1; i<=nlstate;i++)
- /*                                      oldm=oldms;savm=savms; */
+         fprintf(ficresfb," b%d%d",i,j);
- /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
+       fprintf(ficresfb," b.%d",j);
- /*                                      for (h=0; h<=nhstepm; h++){ */
+     }
- /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
+     for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
- /*               fprintf(ficresfb,"\n"); */
+       /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
- /*               for(j=1;j<=cptcoveff;j++)  */
+       fprintf(ficresfb,"\n");
- /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
+       fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
- /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
+       printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
- /*                                              }  */
+       /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
- /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
+       /*        nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
- /*                                                      ppij=0.; */
+       for (agec=bage; agec<=agemax-1; agec++){  /* testing */
- /*                                                      for(i=1; i<=nlstate;i++) { */
+         /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
- /*                                                              if (mobilav==1)  */
+         nhstepm=(int) rint((agec-agelim)*YEARM/stepm);
- /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
+         nhstepm = nhstepm/hstepm;
- /*                                                              else { */
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
+         oldm=oldms;savm=savms;
- /*                                                              } */
+         /* computes hbxij at age agec over 1 to nhstepm */
- /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
+         hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
- /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
+         /* 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 */
- /*                                                      } /\* end i *\/ */
+         /* printf(" agec=%.2f\n",agec);fflush(stdout); */
- /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
+         for (h=0; h<=nhstepm; h++){
- /*                                                              fprintf(ficresfb," %.3f", ppij); */
+           if (h*hstepm/YEARM*stepm ==-yearp) {
- /*                                                      } */
+             break;
- /*                                              }/\* end j *\/ */
+           }
- /*                                      } /\* end h *\/ */
+         }
- /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
+         fprintf(ficresfb,"\n");
- /*                              } /\* end agec *\/ */
+         for(j=1;j<=cptcoveff;j++)
- /*       } /\* end yearp *\/ */
+           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- /*     } /\* end cptcod *\/ */
+         fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
- /*   } /\* end  cptcov *\/ */
+         for(i=1; i<=nlstate+ndeath;i++) {
+           ppij=0.;ppi=0.;
- /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
+           for(j=1; j<=nlstate;j++) {
+             /* if (mobilav==1) */
- /*   fclose(ficresfb); */
+             ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k];
- /*   printf("End of Computing Back forecasting \n"); */
+             ppi=ppi+mobaverage[(int)agec][j][k];
- /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
+               /* 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");
- /* } */
+ }
  /************** 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 7785  int readdata(char datafile[], int firsto
+ Line 8812  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 7822  int readdata(char datafile[], int firsto
+ Line 8871  int readdata(char datafile[], int firsto
      /* Loops on waves */
      for (j=maxwav;j>=1;j--){
        for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
-                                 cutv(stra, strb, line, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                         cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
+           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
-                                         cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
+           cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
-                                         if(isalpha(strb[1])) { /* .m or .d Really Missing value */
+           if(isalpha(strb[1])) { /* .m or .d Really Missing value */
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                 }else{
+         }else{
-                                         errno=0;
+           errno=0;
-                                         /* what_kind_of_number(strb); */
+           /* what_kind_of_number(strb); */
-                                         dval=strtod(strb,&endptr);
+           dval=strtod(strb,&endptr);
-                                         /* if( strb[0]=='\0' || (*endptr != '\0')){ */
+           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
-                                         /* if(strb != endptr && *endptr == '\0') */
+           /* if(strb != endptr && *endptr == '\0') */
-                                         /*    dval=dlval; */
+           /*    dval=dlval; */
-                                         /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
+           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
-                                         if( strb[0]=='\0' || (*endptr != '\0')){
+           if( strb[0]=='\0' || (*endptr != '\0')){
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                         cotqvar[j][iv][i]=dval;
+           cotqvar[j][iv][i]=dval;
-                                         cotvar[j][ntv+iv][i]=dval;
+           cotvar[j][ntv+iv][i]=dval;
-                                 }
+         }
-                                 strcpy(line,stra);
+         strcpy(line,stra);
        }/* end loop ntqv */
        for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
-                                 cutv(stra, strb, line, ' ');
+         cutv(stra, strb, line, ' ');
-                                 if(strb[0]=='.') { /* Missing value */
+         if(strb[0]=='.') { /* Missing value */
-                                         lval=-1;
+           lval=-1;
-                                 }else{
+         }else{
-                                         errno=0;
+           errno=0;
-                                         lval=strtol(strb,&endptr,10);
+           lval=strtol(strb,&endptr,10);
-                                         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+           /*    if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-                                         if( strb[0]=='\0' || (*endptr != '\0')){
+           if( strb[0]=='\0' || (*endptr != '\0')){
-                                                 printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
+             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
-                                                 fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
+             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
-                                                 return 1;
+             return 1;
-                                         }
+           }
-                                 }
+         }
-                                 if(lval <-1 || lval >1){
+         if(lval <-1 || lval >1){
-                                         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-  For example, for multinomial values like 1, 2 and 3,\n                                                                 \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \n                                                                                                                                                                            \
+         V1=1 V2=0 for (2) \n                                            \
   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-  output of IMaCh is often meaningless.\n                                                                                                                                \
+  output of IMaCh is often meaningless.\n                                \
   Exiting.\n",lval,linei, i,line,j);
-                                         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
+           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
-  For example, for multinomial values like 1, 2 and 3,\n                                                                 \
+  For example, for multinomial values like 1, 2 and 3,\n                 \
-  build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
+  build V1=0 V2=0 for the reference value (1),\n                         \
-         V1=1 V2=0 for (2) \n                                                                                                                                                                            \
+         V1=1 V2=0 for (2) \n                                            \
   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
-  output of IMaCh is often meaningless.\n                                                                                                                                \
+  output of IMaCh is often meaningless.\n                                \
   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
-                                         return 1;
+           return 1;
-                                 }
+         }
-                                 cotvar[j][iv][i]=(double)(lval);
+         cotvar[j][iv][i]=(double)(lval);
-                                 strcpy(line,stra);
+         strcpy(line,stra);
        }/* end loop ntv */
        /* Statuses  at wave */
        cutv(stra, strb, line, ' ');
        if(strb[0]=='.') { /* Missing value */
-                                 lval=-1;
+         lval=-1;
        }else{
-                                 errno=0;
+         errno=0;
-                                 lval=strtol(strb,&endptr,10);
+         lval=strtol(strb,&endptr,10);
-                                 /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
-                                 if( strb[0]=='\0' || (*endptr != '\0')){
+         if( strb[0]=='\0' || (*endptr != '\0')){
-                                         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
+           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
-                                         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
-                                         return 1;
+           return 1;
-                                 }
+         }
        }
        s[j][i]=lval;
- Line 8094  int decoderesult ( char resultline[], in
+ Line 9143  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 8207  int decodemodel( char model[], int lasto
+ Line 9261  int decodemodel( char model[], int lasto
          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
          */
  {
-   int i, j, k, ks;
+   int i, j, k, ks, v;
    int  j1, k1, k2, k3, k4;
    char modelsav[80];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
- Line 8413  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9467  Dummy[k] 0=dummy (0 1), 1 quantitative (
  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
    for(k=1, ncovf=0, 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 8438  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9492  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 8452  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9506  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 8463  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9517  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 8479  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9533  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 8491  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9545  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 8693  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 9747  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 8708  int calandcheckages(int imx, int maxwav,
+ Line 9762  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 9028  int prevalence_limit(double *p, double *
+ Line 10082  int prevalence_limit(double *p, double *
    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 each combination k of dummy covariates in the model */
-   for(k=1; k<=i1;k++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     if(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
-       continue;
+         continue;
-   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
-     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     /* k=k+1; */
+       /* k=k+1; */
-     /* to clean */
+       /* to clean */
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     fprintf(ficrespl,"#******");
+       fprintf(ficrespl,"#******");
-     printf("#******");
+       printf("#******");
-     fprintf(ficlog,"#******");
+       fprintf(ficlog,"#******");
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
+       }
-     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       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(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-     }
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-     fprintf(ficrespl,"******\n");
+       }
-     printf("******\n");
+       fprintf(ficrespl,"******\n");
-     fprintf(ficlog,"******\n");
+       printf("******\n");
-     if(invalidvarcomb[k]){
+       fprintf(ficlog,"******\n");
-       printf("\nCombination (%d) ignored because no case \n",k);
+       if(invalidvarcomb[k]){
-       fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
+         printf("\nCombination (%d) ignored because no case \n",k);
-       fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
+         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
-                                                 continue;
+         fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
-     }
+         continue;
+       }
-     fprintf(ficrespl,"#Age ");
+       fprintf(ficrespl,"#Age ");
-     for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
+       }
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
-     fprintf(ficrespl,"Total Years_to_converge\n");
+       fprintf(ficrespl,"Total Years_to_converge\n");
-     for (age=agebase; age<=agelim; age++){
+       for (age=agebase; age<=agelim; age++){
-       /* for (age=agebase; age<=agebase; age++){ */
+         /* for (age=agebase; age<=agebase; age++){ */
-       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
-       fprintf(ficrespl,"%.0f ",age );
+         fprintf(ficrespl,"%.0f ",age );
-       for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       tot=0.;
+         tot=0.;
-       for(i=1; i<=nlstate;i++){
+         for(i=1; i<=nlstate;i++){
-         tot +=  prlim[i][i];
+           tot +=  prlim[i][i];
-         fprintf(ficrespl," %.5f", prlim[i][i]);
+           fprintf(ficrespl," %.5f", prlim[i][i]);
-       }
+         }
-       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
-     } /* Age */
+       } /* Age */
-     /* was end of cptcod */
+       /* was end of cptcod */
-   } /* cptcov */
+     } /* cptcov */
+   } /* nres */
    return 0;
  }
- Line 9123  int back_prevalence_limit(double *p, dou
+ Line 10179  int back_prevalence_limit(double *p, dou
    i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-   for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+     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;
+         continue;
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     fprintf(ficresplb,"#******");
+       fprintf(ficresplb,"#******");
-     printf("#******");
+       printf("#******");
-     fprintf(ficlog,"#******");
+       fprintf(ficlog,"#******");
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
+       }
-     for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-       printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-     }
+       }
-     fprintf(ficresplb,"******\n");
+       fprintf(ficresplb,"******\n");
-     printf("******\n");
+       printf("******\n");
-     fprintf(ficlog,"******\n");
+       fprintf(ficlog,"******\n");
-     if(invalidvarcomb[k]){
+       if(invalidvarcomb[k]){
-       printf("\nCombination (%d) ignored because no cases \n",k);
+         printf("\nCombination (%d) ignored because no cases \n",k);
-       fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
-       fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
-       continue;
+         continue;
-     }
+       }
-     fprintf(ficresplb,"#Age ");
+       fprintf(ficresplb,"#Age ");
-     for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
+       }
-     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
+       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
-     fprintf(ficresplb,"Total Years_to_converge\n");
+       fprintf(ficresplb,"Total Years_to_converge\n");
-     for (age=agebase; age<=agelim; age++){
+       for (age=agebase; age<=agelim; age++){
-       /* for (age=agebase; age<=agebase; age++){ */
+         /* for (age=agebase; age<=agebase; age++){ */
-       if(mobilavproj > 0){
+         if(mobilavproj > 0){
-         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
-         /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-         bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
+           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
-       }else if (mobilavproj == 0){
+         }else if (mobilavproj == 0){
-         printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
-         fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
-         exit(1);
+           exit(1);
-       }else{
+         }else{
-         /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-         bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
+           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
-       }
+           /* printf("TOTOT\n"); */
-       fprintf(ficresplb,"%.0f ",age );
+           /* exit(1); */
-       for(j=1;j<=cptcoveff;j++)
+         }
-         fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb,"%.0f ",age );
-       tot=0.;
+         for(j=1;j<=cptcoveff;j++)
-       for(i=1; i<=nlstate;i++){
+           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-         tot +=  bprlim[i][i];
+         tot=0.;
-         fprintf(ficresplb," %.5f", bprlim[i][i]);
+         for(i=1; i<=nlstate;i++){
-       }
+           tot +=  bprlim[i][i];
-       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+           fprintf(ficresplb," %.5f", bprlim[i][i]);
-     } /* Age */
+         }
-     /* was end of cptcod */
+         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
-   } /* cptcov */
+       } /* Age */
+       /* was end of cptcod */
+       /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
+     } /* end of any combination */
+   } /* end of nres */
    /* hBijx(p, bage, fage); */
    /* fclose(ficrespijb); */
- Line 9228  int hPijx(double *p, int bage, int fage)
+ Line 10287  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 9277  int hPijx(double *p, int bage, int fage)
+ Line 10336  int hPijx(double *p, int bage, int fage)
          int ageminl;
    int hstepm;
    int nhstepm;
-   int h, i, i1, j, k;
+   int h, i, i1, j, k, nres;
    double agedeb;
    double ***p3mat;
- Line 9300  int hPijx(double *p, int bage, int fage)
+ Line 10359  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 (k=1; k <= (int) pow(2,cptcoveff); k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     fprintf(ficrespijb,"\n#****** ");
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-     for(j=1;j<=cptcoveff;j++)
+       if(i1 != 1 && TKresult[nres]!= k)
-       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         continue;
-     fprintf(ficrespijb,"******\n");
+       fprintf(ficrespijb,"\n#****** ");
-     if(invalidvarcomb[k]){
+       for(j=1;j<=cptcoveff;j++)
-       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       continue;
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-     }
+         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
-     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       fprintf(ficrespijb,"******\n");
-     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
+       if(invalidvarcomb[k]){  /* Is it necessary here? */
-       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
+         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
-       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+         continue;
-       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
+       }
-       /*          nhstepm=nhstepm*YEARM; aff par mois*/
+       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
+       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
-       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
-       /* oldm=oldms;savm=savms; */
+         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
-       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
+         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
-       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
-       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
+         /*        nhstepm=nhstepm*YEARM; aff par mois*/
-       fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
-       for(i=1; i<=nlstate;i++)
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
-         for(j=1; j<=nlstate+ndeath;j++)
+         /* and memory limitations if stepm is small */
-           fprintf(ficrespijb," %1d-%1d",i,j);
-       fprintf(ficrespijb,"\n");
+         /* oldm=oldms;savm=savms; */
-       for (h=0; h<=nhstepm; h++){
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
-         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
+         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
-             fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
+             fprintf(ficrespijb," %1d-%1d",i,j);
          fprintf(ficrespijb,"\n");
-       }
+         for (h=0; h<=nhstepm; h++){
-       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
-       fprintf(ficrespijb,"\n");
+           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
-     }
+           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
-     /*}*/
+           for(i=1; i<=nlstate;i++)
-   }
+             for(j=1; j<=nlstate+ndeath;j++)
+               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
+           fprintf(ficrespijb,"\n");
+         }
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+         fprintf(ficrespijb,"\n");
+       } /* end age deb */
+     } /* end combination */
+   } /* end nres */
    return 0;
   } /*  hBijx */
- Line 9374  int main(int argc, char *argv[])
+ Line 10441  int main(int argc, char *argv[])
    int NDIM=2;
    int vpopbased=0;
    int nres=0;
+   int endishere=0;
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
- Line 9418  int main(int argc, char *argv[])
+ Line 10486  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 **varbpl; /* Variances of back prevalence limits by age */
    double *epj, vepp;
    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
- Line 9654  int main(int argc, char *argv[])
+ Line 10724  int main(int argc, char *argv[])
        break;
    }
    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
-     if (num_filled == 0)
+     if (num_filled == 0){
-             model[0]='\0';
+       printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
-     else if (num_filled != 1){
+       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
+       model[0]='\0';
+       goto end;
+     } else if (num_filled != 1){
        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';
- Line 9705  int main(int argc, char *argv[])
+ Line 10778  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 9729  int main(int argc, char *argv[])
+ Line 10802  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 9758  int main(int argc, char *argv[])
+ Line 10837  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 9794  run imach with mle=-1 to get a correct t
+ Line 10874  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 10060  Please run with mle=-1 to get a correct
+ Line 11141  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 10241  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 11322  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");
- Line 10250  Youngest age at first (selected) pass %.
+ Line 11331  Youngest age at first (selected) pass %.
  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
            imx,agemin,agemax,jmin,jmax,jmean);
    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
-         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
    /* For Powell, parameters are in a vector p[] starting at p[1]
       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
- Line 10263  Interval (in months) between two waves:
+ Line 11344  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 10501  Please run with mle=-1 to get a correct
+ Line 11582  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 10716  Please run with mle=-1 to get a correct
+ Line 11801  Please run with mle=-1 to get a correct
      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
      /* Other stuffs, more or less useful */
-     while((c=getc(ficpar))=='#' && c!= EOF){
+     while(fgets(line, MAXLINE, ficpar)) {
-       ungetc(c,ficpar);
+       /* If line starts with a # it is a comment */
-       fgets(line, MAXLINE, ficpar);
+       if (line[0] == '#') {
-       fputs(line,stdout);
+         numlinepar++;
-       fputs(line,ficparo);
+         fputs(line,stdout);
-     }
+         fputs(line,ficparo);
-     ungetc(c,ficpar);
+         fputs(line,ficlog);
+         continue;
-     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+       }else
-     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
+         break;
-     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       fputs(line,stdout);
-       fputs(line,ficparo);
-     }
-     ungetc(c,ficpar);
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
-     fprintf(ficlog,"pop_based=%d\n",popbased);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
-     fprintf(ficres,"pop_based=%d\n",popbased);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       fputs(line,stdout);
-       fputs(line,ficparo);
      }
-     ungetc(c,ficpar);
+     if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
-     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
-     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+       if (num_filled != 7) {
-     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
-     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+         goto end;
-     /* day and month of proj2 are not used but only year anproj2.*/
+       }
+       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       ungetc(c,ficpar);
+       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       fgets(line, MAXLINE, ficpar);
+       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-       fputs(line,stdout);
-       fputs(line,ficparo);
      }
-     ungetc(c,ficpar);
-     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
-     fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     /* day and month of proj2 are not used but only year anproj2.*/
-     /* Results */
-     nresult=0;
      while(fgets(line, MAXLINE, ficpar)) {
        /* If line starts with a # it is a comment */
        if (line[0] == '#') {
- Line 10789  Please run with mle=-1 to get a correct
+ Line 11837  Please run with mle=-1 to get a correct
        }else
          break;
      }
-     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
-       if (num_filled == 0)
-         resultline[0]='\0';
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-       else if (num_filled != 1){
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
-       }
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
-       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);
-       while(fgets(line, MAXLINE, ficpar)) {
+       fprintf(ficlog,"pop_based=%d\n",popbased);
+       fprintf(ficparo,"pop_based=%d\n",popbased);
+       fprintf(ficres,"pop_based=%d\n",popbased);
+     }
+     /* Results */
+     nresult=0;
+     do{
+       if(!fgets(line, MAXLINE, ficpar)){
+         endishere=1;
+         parameterline=14;
+       }else if (line[0] == '#') {
          /* If line starts with a # it is a comment */
-         if (line[0] == '#') {
+         numlinepar++;
-           numlinepar++;
+         fputs(line,stdout);
-           fputs(line,stdout);
+         fputs(line,ficparo);
-           fputs(line,ficparo);
+         fputs(line,ficlog);
-           fputs(line,ficlog);
+         continue;
-           continue;
+       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
-         }else
+         parameterline=11;
-           break;
+       else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
+         parameterline=12;
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp))
+         parameterline=13;
+       else{
+         parameterline=14;
        }
-       if (feof(ficpar))
+       switch (parameterline){
+       case 11:
+         if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){
+           if (num_filled != 8) {
+             printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             goto end;
+           }
+           fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
+           /* day and month of proj2 are not used but only year anproj2.*/
+         }
          break;
-       else{ /* Processess output results for this combination of covariate values */
+       case 12:
-       }
+         /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/
-     }
+         if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
+           if (num_filled != 8) {
+             printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             goto end;
+           }
+           printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           /* day and month of proj2 are not used but only year anproj2.*/
+         }
+         break;
+       case 13:
+         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+           if (num_filled == 0){
+             resultline[0]='\0';
+             printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             break;
+           } else if (num_filled != 1){
+             printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+             fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+           }
+           nresult++; /* Sum of resultlines */
+           printf("Result %d: result=%s\n",nresult, resultline);
+           if(nresult > MAXRESULTLINES){
+             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             goto end;
+           }
+           decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+           fprintf(ficparo,"result: %s\n",resultline);
+           fprintf(ficres,"result: %s\n",resultline);
+           fprintf(ficlog,"result: %s\n",resultline);
+           break;
+         case 14:
+           if(ncovmodel >2 && nresult==0 ){
+             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+             goto end;
+           }
+           break;
+         default:
+           nresult=1;
+           decoderesult(".",nresult ); /* No covariate */
+         }
+       } /* End switch parameterline */
+     }while(endishere==0); /* End do */
      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
- Line 10834  Please run with mle=-1 to get a correct
+ Line 11954  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);
      }
      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);
      /*------------ free_vector  -------------*/
- Line 10884  Please run with mle=-1 to get a correct
+ Line 12004  Please run with mle=-1 to get a correct
      if (mobilav!=0 ||mobilavproj !=0 ) {
        mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
        for(i=1;i<=AGESUP;i++)
-         for(j=1;j<=nlstate;j++)
+         for(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);
          }
        }
-       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
+       /* else if(mobilavproj==-1){ /\* Forcing raw observed prevalences *\/ */
-       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
+       /*        for(i=1;i<=AGESUP;i++) */
+       /*          for(j=1;j<=nlstate;j++) */
+       /*            for(k=1;k<=ncovcombmax;k++) */
+       /*              mobaverages[i][j][k]=probs[i][j][k]; */
+       /*        /\* /\\* 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);
- Line 10925  Please run with mle=-1 to get a correct
+ Line 12053  Please run with mle=-1 to get a correct
        hBijx(p, bage, fage, mobaverage);
        fclose(ficrespijb);
-       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
+       /* free_matrix(bprlim,1,nlstate,1,nlstate); /\*here or after loop ? *\/ */
+       prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
+          bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
+       /*------- Variance of back (stable) prevalence------*/
+       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);
+       /*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(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(fileres, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, &ncvyear, 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);
-       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
-          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
      }
+     free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
      /* ------ Other prevalence ratios------------ */
- Line 10953  Please run with mle=-1 to get a correct
+ Line 12133  Please run with mle=-1 to get a correct
      }
      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
+     pstamp(ficreseij);
      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;
        fprintf(ficreseij,"\n#****** ");
        printf("\n#****** ");
- Line 11032  Please run with mle=-1 to get a correct
+ Line 12214  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;
-       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 11065  Please run with mle=-1 to get a correct
+ Line 12247  Please run with mle=-1 to get a correct
        fprintf(ficrescveij,"******\n");
        fprintf(ficresvij,"\n#****** ");
+       /* pstamp(ficresvij); */
        for(j=1;j<=cptcoveff;j++)
          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
- Line 11172  Please run with mle=-1 to get a correct
+ Line 12355  Please run with mle=-1 to get a correct
      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(ficresvpl,"\n#****** ");
        printf("\n#****** ");
- Line 11201  Please run with mle=-1 to get a correct
+ Line 12384  Please run with mle=-1 to get a correct
      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 11227  Please run with mle=-1 to get a correct
+ Line 12411  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);
- Line 11242  Please run with mle=-1 to get a correct
+ Line 12426  Please run with mle=-1 to get a correct
    free_ivector(ncodemaxwundef,1,NCOVMAX);
    free_ivector(Dummy,-1,NCOVMAX);
    free_ivector(Fixed,-1,NCOVMAX);
+   free_ivector(DummyV,1,NCOVMAX);
+   free_ivector(FixedV,1,NCOVMAX);
    free_ivector(Typevar,-1,NCOVMAX);
    free_ivector(Tvar,1,NCOVMAX);
    free_ivector(TvarsQ,1,NCOVMAX);

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

Removed from v.1.237
changed lines
	Added in v.1.268