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Diff for /imach/src/imach.c between versions 1.227 and 1.248

-version 1.227, 2016/07/21 08:43:33
+version 1.248, 2016/09/07 14:10:18
  Line 1
  /* $Id$
    $State$
    $Log$
-   Revision 1.227  2016/07/21 08:43:33  brouard
+   Revision 1.248  2016/09/07 14:10:18  brouard
-   Summary: 0.99 working (more or less) for Asian Workshop on multitate methods
+   *** empty log message ***
+   Revision 1.247  2016/09/02 11:11:21  brouard
+   *** empty log message ***
+   Revision 1.246  2016/09/02 08:49:22  brouard
+   *** empty log message ***
+   Revision 1.245  2016/09/02 07:25:01  brouard
+   *** empty log message ***
+   Revision 1.244  2016/09/02 07:17:34  brouard
+   *** empty log message ***
+   Revision 1.243  2016/09/02 06:45:35  brouard
+   *** empty log message ***
+   Revision 1.242  2016/08/30 15:01:20  brouard
+   Summary: Fixing a lots
+   Revision 1.241  2016/08/29 17:17:25  brouard
+   Summary: gnuplot problem in Back projection to fix
+   Revision 1.240  2016/08/29 07:53:18  brouard
+   Summary: Better
+   Revision 1.239  2016/08/26 15:51:03  brouard
+   Summary: Improvement in Powell output in order to copy and paste
+   Author:
+   Revision 1.238  2016/08/26 14:23:35  brouard
+   Summary: Starting tests of 0.99
+   Revision 1.237  2016/08/26 09:20:19  brouard
+   Summary: to valgrind
+   Revision 1.236  2016/08/25 10:50:18  brouard
+   *** empty log message ***
+   Revision 1.235  2016/08/25 06:59:23  brouard
+   *** empty log message ***
+   Revision 1.234  2016/08/23 16:51:20  brouard
+   *** empty log message ***
+   Revision 1.233  2016/08/23 07:40:50  brouard
+   Summary: not working
+   Revision 1.232  2016/08/22 14:20:21  brouard
+   Summary: not working
+   Revision 1.231  2016/08/22 07:17:15  brouard
+   Summary: not working
+   Revision 1.230  2016/08/22 06:55:53  brouard
+   Summary: Not working
+   Revision 1.229  2016/07/23 09:45:53  brouard
+   Summary: Completing for func too
+   Revision 1.228  2016/07/22 17:45:30  brouard
+   Summary: Fixing some arrays, still debugging
    Revision 1.226  2016/07/12 18:42:34  brouard
    Summary: temp
- Line 902  int cptcovsnq=0; /**< cptcovsnq number o
+ Line 964  int cptcovsnq=0; /**< cptcovsnq number o
  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
  int cptcovprodnoage=0; /**< Number of covariate products without age */
  int cptcoveff=0; /* Total number of covariates to vary for printing results */
- int ncoveff=0; /* Total number of effective covariates in the model */
+ int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
+ int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
+ int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
+ int nsd=0; /**< Total number of single dummy variables (output) */
+ int nsq=0; /**< Total number of single quantitative variables (output) */
+ int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
  int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
  int ntveff=0; /**< ntveff number of effective time varying variables */
  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
- Line 927  int **dh; /* dh[mi][i] is number of step
+ Line 994  int **dh; /* dh[mi][i] is number of step
  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
             * wave mi and wave mi+1 is not an exact multiple of stepm. */
  int countcallfunc=0;  /* Count the number of calls to func */
+ int selected(int kvar); /* Is covariate kvar selected for printing results */
  double jmean=1; /* Mean space between 2 waves */
  double **matprod2(); /* test */
  double **oldm, **newm, **savm; /* Working pointers to matrices */
- Line 957  char fileresv[FILENAMELENGTH];
+ Line 1026  char fileresv[FILENAMELENGTH];
  FILE  *ficresvpl;
  char fileresvpl[FILENAMELENGTH];
  char title[MAXLINE];
+ char model[MAXLINE]; /**< The model line */
  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];
- Line 994  double dval;
+ Line 1064  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 1056  double ***cotvar; /* Time varying covari
+ Line 1127  double ***cotvar; /* Time varying covari
  double ***cotqvar; /* Time varying quantitative covariate itqv */
  double  idx;
  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
+ /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ /*k          1  2   3   4     5    6    7     8    9 */
+ /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
+ /* Tndvar[k]    1   2   3               4          5 */
+ /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
+ /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
+ /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
+ /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
+ /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
+ /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
+ /* Tprod[i]=k           4               7            */
+ /* Tage[i]=k                  5               8      */
+ /* */
+ /* Type                    */
+ /* V         1  2  3  4  5 */
+ /*           F  F  V  V  V */
+ /*           D  Q  D  D  Q */
+ /*                         */
+ int *TvarsD;
+ int *TvarsDind;
+ int *TvarsQ;
+ int *TvarsQind;
+ #define MAXRESULTLINES 10
+ int nresult=0;
+ int TKresult[MAXRESULTLINES];
+ int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
+ int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
+ double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
+ int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
+ /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
+ int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+ int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+ int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+ int *Tvarsel; /**< Selected covariates for output */
+ double *Tvalsel; /**< Selected modality value of covariate for output */
  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
  int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
  int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
+ int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
  int *Tage;
  int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
- int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
  int *Ndum; /** Freq of modality (tricode */
  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
  int **Tvard;
  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;
+ #define FD 1; /* Fixed dummy covariate */
+ #define FQ 2; /* Fixed quantitative covariate */
+ #define FP 3; /* Fixed product covariate */
+ #define FPDD 7; /* Fixed product dummy*dummy covariate */
+ #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
+ #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
+ #define VD 10; /* Varying dummy covariate */
+ #define VQ 11; /* Varying quantitative covariate */
+ #define VP 12; /* Varying product covariate */
+ #define VPDD 13; /* Varying product dummy*dummy covariate */
+ #define VPDQ 14; /* Varying product dummy*quantitative covariate */
+ #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
+ #define APFD 16; /* Age product * fixed dummy covariate */
+ #define APFQ 17; /* Age product * fixed quantitative covariate */
+ #define APVD 18; /* Age product * varying dummy covariate */
+ #define APVQ 19; /* Age product * varying quantitative covariate */
+ #define FTYPE 1; /* Fixed covariate */
+ #define VTYPE 2; /* Varying covariate (loop in wave) */
+ #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
+ struct kmodel{
+         int maintype; /* main type */
+         int subtype; /* subtype */
+ };
+ struct kmodel modell[NCOVMAX];
  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
  double ftolhess; /**< Tolerance for computing hessian */
- Line 1269  int nbocc(char *s, char occ)
+ Line 1421  int nbocc(char *s, char occ)
    i=0;
    lg=strlen(s);
    for(i=0; i<= lg; i++) {
-   if  (s[i] == occ ) j++;
+     if  (s[i] == occ ) j++;
    }
    return j;
  }
- Line 1942  void powell(double p[], double **xi, int
+ Line 2094  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 1977  void powell(double p[], double **xi, int
+ Line 2129  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 2055  void powell(double p[], double **xi, int
+ Line 2240  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 2101  void powell(double p[], double **xi, int
+ Line 2287  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 2160  void powell(double p[], double **xi, int
+ Line 2346  void powell(double p[], double **xi, int
        if (directest < 0.0) { /* Then we use it for new direction */
  #endif
  #ifdef DEBUGLINMIN
-                                 printf("Before linmin in direction P%d-P0\n",n);
+         printf("Before linmin in direction P%d-P0\n",n);
-                                 for (j=1;j<=n;j++) {
+         for (j=1;j<=n;j++) {
-                                         printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-                                         fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-                                         if(j % ncovmodel == 0){
+           if(j % ncovmodel == 0){
-                                                 printf("\n");
+             printf("\n");
-                                                 fprintf(ficlog,"\n");
+             fprintf(ficlog,"\n");
-                                         }
+           }
-                                 }
+         }
  #endif
  #ifdef LINMINORIGINAL
-                                 linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+         linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
  #else
-                                 linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
+         linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
-                                 flatdir[i]=flat; /* Function is vanishing in that direction i */
+         flatdir[i]=flat; /* Function is vanishing in that direction i */
  #endif
  #ifdef DEBUGLINMIN
-                                 for (j=1;j<=n;j++) {
+         for (j=1;j<=n;j++) {
-                                         printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-                                         fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
+           fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
-                                         if(j % ncovmodel == 0){
+           if(j % ncovmodel == 0){
-                                                 printf("\n");
+             printf("\n");
-                                                 fprintf(ficlog,"\n");
+             fprintf(ficlog,"\n");
-                                         }
+           }
-                                 }
+         }
  #endif
-                                 for (j=1;j<=n;j++) {
+         for (j=1;j<=n;j++) {
-                                         xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
+           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
-                                         xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
+           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
-                                 }
+         }
  #ifdef LINMINORIGINAL
  #else
-                                 for (j=1, flatd=0;j<=n;j++) {
+         for (j=1, flatd=0;j<=n;j++) {
-                                         if(flatdir[j]>0)
+           if(flatdir[j]>0)
-                                                 flatd++;
+             flatd++;
-                                 }
+         }
-                                 if(flatd >0){
+         if(flatd >0){
-                                         printf("%d flat directions\n",flatd);
+           printf("%d flat directions\n",flatd);
-                                         fprintf(ficlog,"%d flat directions\n",flatd);
+           fprintf(ficlog,"%d flat directions\n",flatd);
-                                         for (j=1;j<=n;j++) {
+           for (j=1;j<=n;j++) {
-                                                 if(flatdir[j]>0){
+             if(flatdir[j]>0){
-                                                         printf("%d ",j);
+               printf("%d ",j);
-                                                         fprintf(ficlog,"%d ",j);
+               fprintf(ficlog,"%d ",j);
-                                                 }
+             }
-                                         }
+           }
-                                         printf("\n");
+           printf("\n");
-                                         fprintf(ficlog,"\n");
+           fprintf(ficlog,"\n");
-                                 }
+         }
  #endif
-                                 printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
-                                 fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
+         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
  #ifdef DEBUG
-                                 printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-                                 fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
-                                 for(j=1;j<=n;j++){
+         for(j=1;j<=n;j++){
-                                         printf(" %lf",xit[j]);
+           printf(" %lf",xit[j]);
-                                         fprintf(ficlog," %lf",xit[j]);
+           fprintf(ficlog," %lf",xit[j]);
-                                 }
+         }
-                                 printf("\n");
+         printf("\n");
-                                 fprintf(ficlog,"\n");
+         fprintf(ficlog,"\n");
  #endif
        } /* end of t or directest negative */
  #ifdef POWELLNOF3INFF1TEST
  #else
-     } /* end if (fptt < fp)  */
+       } /* end if (fptt < fp)  */
  #endif
  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
-                 } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
+     } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
  #else
  #endif
-   } /* loop iteration */
+                 } /* loop iteration */
  }
  /**** Prevalence limit (stable or period prevalence)  ****************/
- double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
+   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
- {
+   {
-   /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
+     /* Computes the prevalence limit in each live state at age x and for covariate combination ij
-      matrix by transitions matrix until convergence is reached with precision ftolpl */
+        (and selected quantitative values in nres)
+        by left multiplying the unit
+        matrix by transitions matrix until convergence is reached with precision ftolpl */
    /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
    /* Wx is row vector: population in state 1, population in state 2, population dead */
    /* or prevalence in state 1, prevalence in state 2, 0 */
- Line 2258  double **prevalim(double **prlim, int nl
+ Line 2446  double **prevalim(double **prlim, int nl
    /* {0.51571254859325999, 0.4842874514067399, */
    /*  0.51326036147820708, 0.48673963852179264} */
    /* If we start from prlim again, prlim tends to a constant matrix */
    int i, ii,j,k;
    double *min, *max, *meandiff, maxmax,sumnew=0.;
    /* double **matprod2(); */ /* test */
- Line 2288  double **prevalim(double **prlim, int nl
+ Line 2476  double **prevalim(double **prlim, int nl
      cov[2]=agefin;
      if(nagesqr==1)
        cov[3]= agefin*agefin;;
-     for (k=1; k<=cptcovn;k++) {
+     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
-                         /* Here comes the value of the covariate 'ij' */
+       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+       /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
-       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
+     }
-     }
+     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
-     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
-     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
+       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
-     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
+       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
-     for (k=1; k<=cptcovprod;k++) /* Useless */
+     }
-       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+     for (k=1; k<=cptcovage;k++){  /* For product with age */
-       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+       if(Dummy[Tvar[Tage[k]]]){
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       } else{
+         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+       }
+       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
+     }
+     for (k=1; k<=cptcovprod;k++){ /* For product without age */
+       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
+       if(Dummy[Tvard[k][1]==0]){
+         if(Dummy[Tvard[k][2]==0]){
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
+         }
+       }else{
+         if(Dummy[Tvard[k][2]==0]){
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
+         }
+       }
+     }
      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
- Line 2358  Earliest age to start was %d-%d=%d, ncvl
+ Line 2567  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
       matrix by transitions matrix until convergence is reached with precision ftolpl */
- Line 2381  Earliest age to start was %d-%d=%d, ncvl
+ Line 2590  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 2417  Earliest age to start was %d-%d=%d, ncvl
+ Line 2627  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 combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
+     }
+     /* for (k=1; k<=cptcovn;k++) { */
+     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
+     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
+     /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
+     /* } */
+     for (k=1; k<=nsq;k++) { /* For single varying covariates only */
+                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
+       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
+       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
+     }
+     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
+     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
+     /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
+     /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
+     for (k=1; k<=cptcovage;k++){  /* For product with age */
+       if(Dummy[Tvar[Tage[k]]]){
+         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       } else{
+         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+       }
+       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
+     }
+     for (k=1; k<=cptcovprod;k++){ /* For product without age */
+       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
+       if(Dummy[Tvard[k][1]==0]){
+         if(Dummy[Tvard[k][2]==0]){
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
+         }
+       }else{
+         if(Dummy[Tvard[k][2]==0]){
+           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
+         }else{
+           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
+         }
+       }
      }
-     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
-     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
-     for (k=1; k<=cptcovprod;k++) /* Useless */
-       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
-       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- Line 2450  Earliest age to start was %d-%d=%d, ncvl
+ Line 2692  Earliest age to start was %d-%d=%d, ncvl
      }
      for(j=1; j<=nlstate; j++){
        for(i=1;i<=nlstate;i++){
-                                 /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
+         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
-                                 bprlim[i][j]= newm[i][j];
+         bprlim[i][j]= newm[i][j];
-                                 max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
+         max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
-                                 min[i]=FMIN(min[i],bprlim[i][j]);
+         min[i]=FMIN(min[i],bprlim[i][j]);
        }
      }
- Line 2474  Earliest age to start was %d-%d=%d, ncvl
+ Line 2716  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 2607  double **pmij(double **ps, double *cov,
+ Line 2854  double **pmij(double **ps, double *cov,
          /* }else */
          doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
        }else{
-         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
+         ;
+         /* 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)] */
- Line 2648  double **bpmij(double **ps, double *cov,
+ Line 2896  double **bpmij(double **ps, double *cov,
    /*double t34;*/
    int i,j, nc, ii, jj;
-         for(i=1; i<= nlstate; i++){
+   for(i=1; i<= nlstate; i++){
-                 for(j=1; j<i;j++){
+     for(j=1; j<i;j++){
-                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/
+         /*lnpijopii += param[i][j][nc]*cov[nc];*/
-                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
+         lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
-                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-                         }
+       }
-                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
+       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
-                 }
+     }
-                 for(j=i+1; j<=nlstate+ndeath;j++){
+     for(j=i+1; j<=nlstate+ndeath;j++){
-                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
-                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+         /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
-                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+         lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
-                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
+         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
-                         }
+       }
-                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
+       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
-                 }
+     }
-         }
+   }
-         for(i=1; i<= nlstate; i++){
+   for(i=1; i<= nlstate; i++){
-                 s1=0;
+     s1=0;
-                 for(j=1; j<i; j++){
+     for(j=1; j<i; j++){
-                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-                 }
+     }
-                 for(j=i+1; j<=nlstate+ndeath; j++){
+     for(j=i+1; j<=nlstate+ndeath; j++){
-                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
+       s1+=exp(ps[i][j]); /* In fact sums pij/pii */
-                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
+       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
-                 }
+     }
-                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
+     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
-                 ps[i][i]=1./(s1+1.);
+     ps[i][i]=1./(s1+1.);
-                 /* Computing other pijs */
+     /* Computing other pijs */
-                 for(j=1; j<i; j++)
+     for(j=1; j<i; j++)
-                         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-                 for(j=i+1; j<=nlstate+ndeath; j++)
+     for(j=i+1; j<=nlstate+ndeath; j++)
-                         ps[i][j]= exp(ps[i][j])*ps[i][i];
+       ps[i][j]= exp(ps[i][j])*ps[i][i];
-                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
-         } /* end i */
+   } /* end i */
-         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
-                 for(jj=1; jj<= nlstate+ndeath; jj++){
+     for(jj=1; jj<= nlstate+ndeath; jj++){
-                         ps[ii][jj]=0;
+       ps[ii][jj]=0;
-                         ps[ii][ii]=1;
+       ps[ii][ii]=1;
-                 }
+     }
-         }
+   }
-         /* Added for backcast */ /* Transposed matrix too */
+   /* Added for backcast */ /* Transposed matrix too */
-         for(jj=1; jj<= nlstate+ndeath; jj++){
+   for(jj=1; jj<= nlstate+ndeath; jj++){
-                 s1=0.;
+     s1=0.;
-                 for(ii=1; ii<= nlstate+ndeath; ii++){
+     for(ii=1; ii<= nlstate+ndeath; ii++){
-                         s1+=ps[ii][jj];
+       s1+=ps[ii][jj];
-                 }
+     }
-                 for(ii=1; ii<= nlstate; ii++){
+     for(ii=1; ii<= nlstate; ii++){
-                         ps[ii][jj]=ps[ii][jj]/s1;
+       ps[ii][jj]=ps[ii][jj]/s1;
-                 }
+     }
-         }
+   }
-         /* Transposition */
+   /* Transposition */
-         for(jj=1; jj<= nlstate+ndeath; jj++){
+   for(jj=1; jj<= nlstate+ndeath; jj++){
-                 for(ii=jj; ii<= nlstate+ndeath; ii++){
+     for(ii=jj; ii<= nlstate+ndeath; ii++){
-                         s1=ps[ii][jj];
+       s1=ps[ii][jj];
-                         ps[ii][jj]=ps[jj][ii];
+       ps[ii][jj]=ps[jj][ii];
-                         ps[jj][ii]=s1;
+       ps[jj][ii]=s1;
-                 }
+     }
-         }
+   }
-         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
+   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
+   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
-         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
+   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
-         /*   } */
+   /*   } */
-         /*   printf("\n "); */
+   /*   printf("\n "); */
-         /* } */
+   /* } */
-         /* printf("\n ");printf("%lf ",cov[2]);*/
+   /* printf("\n ");printf("%lf ",cov[2]);*/
-         /*
+   /*
-                 for(i=1; i<= npar; i++) printf("%f ",x[i]);
+     for(i=1; i<= npar; i++) printf("%f ",x[i]);
-                 goto end;*/
+     goto end;*/
-         return ps;
+   return ps;
  }
- Line 2748  double **matprod2(double **out, double *
+ Line 2996  double **matprod2(double **out, double *
  /************* Higher Matrix Product ***************/
- double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
  {
    /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
       'nhstepm*hstepm*stepm' months (i.e. until
- Line 2784  double ***hpxij(double ***po, int nhstep
+ Line 3032  double ***hpxij(double ***po, int nhstep
        cov[2]=agexact;
        if(nagesqr==1)
          cov[3]= agexact*agexact;
-       for (k=1; k<=cptcovn;k++)
+       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
-         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
+                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
-       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
+         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
-       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
+         /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
-         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+       }
-         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+       for (k=1; k<=nsq;k++) { /* For single varying covariates only */
-       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
+         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
-       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
+         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
-         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
+         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
-       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
+       }
+       for (k=1; k<=cptcovage;k++){
+         if(Dummy[Tvar[Tage[k]]]){
+           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
+         } else{
+           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
+         }
+         /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
+       }
+       for (k=1; k<=cptcovprod;k++){ /*  */
+         /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
+       }
+       /* for (k=1; k<=cptcovn;k++)  */
+       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
+       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
+       /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
+       /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
+       /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
- Line 2946  double func( double *x)
+ Line 3212  double func( double *x)
    int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
-   double sw; /* Sum of weights */
    double lli; /* Individual log likelihood */
    int s1, s2;
-   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
    double bbh, survp;
    long ipmx;
    double agexact;
- Line 2973  double func( double *x)
+ Line 3238  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 ;
-       /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
+    /* Fixed */
-       for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
+       for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
-         cov[++ioffset]=covar[Tvar[k]][i];
+         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)*/
        }
-       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
-         cov[++ioffset]=coqvar[iqv][i];
-       }
        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
           has been calculated etc */
- Line 2995  double func( double *x)
+ Line 3256  double func( double *x)
           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
        */
        for(mi=1; mi<= wav[i]-1; mi++){
-         for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
+         for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
-           cov[ioffset+itv]=cotvar[mw[mi][i]][itv][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(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
-           if(cotqvar[mw[mi][i]][iqtv][i] == -1){
-             printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
-           }
-           cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
-         }
-         /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
          for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 3017  double func( double *x)
+ Line 3272  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));
            savm=oldm;
            oldm=newm;
          } /* end mult */
          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          /* But now since version 0.9 we anticipate for bias at large stepm.
           * If stepm is larger than one month (smallest stepm) and if the exact delay
- Line 3033  double func( double *x)
+ Line 3291  double func( double *x)
           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           * probability in order to take into account the bias as a fraction of the way
-          * from savm to out if bh is negative or even beyond if bh is positive. bh varies
+                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies
-          * -stepm/2 to stepm/2 .
+                                  * -stepm/2 to stepm/2 .
-          * For stepm=1 the results are the same as for previous versions of Imach.
+                                  * For stepm=1 the results are the same as for previous versions of Imach.
-          * For stepm > 1 the results are less biased than in previous versions.
+                                  * For stepm > 1 the results are less biased than in previous versions.
-          */
+                                  */
          s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm;
- Line 3275  double func( double *x)
+ Line 3533  double func( double *x)
  /*************** log-likelihood *************/
  double funcone( double *x)
  {
-   /* Same as likeli but slower because of a lot of printf and if */
+   /* Same as func but slower because of a lot of printf and if */
    int i, ii, j, k, mi, d, kk;
-         int ioffset=0;
+   int ioffset=0;
    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    double **out;
    double lli; /* Individual log likelihood */
    double llt;
    int s1, s2;
-         int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
+   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
    double bbh, survp;
    double agexact;
    double agebegin, ageend;
- Line 3298  double funcone( double *x)
+ Line 3557  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+nqfveff;k++){ /* Simple and product fixed covariates without age* products */
+     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
-       cov[++ioffset]=covar[Tvar[k]][i];
+     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)*/
-     for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
+ /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
-       cov[++ioffset]=coqvar[Tvar[iqv]][i];
+ /*    cov[2+6]=covar[Tvar[6]][i];  */
+ /*    cov[2+6]=covar[2][i]; V2  */
+ /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
+ /*    cov[2+7]=covar[Tvar[7]][i];  */
+ /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
+ /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
+ /*    cov[2+9]=covar[Tvar[9]][i];  */
+ /*    cov[2+9]=covar[1][i]; V1  */
      }
+     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
+     /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
+     /* } */
+     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
+     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
+     /* } */
      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
-       for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
+     /* Wave varying (but not age varying) */
-         cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
+       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]; */
-       for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
+         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
-         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
+       }
-       }
+       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
+       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
+       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
+       /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
+       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
+       /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+       /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
+       /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
+       /* } */
        for (ii=1;ii<=nlstate+ndeath;ii++)
          for (j=1;j<=nlstate+ndeath;j++){
            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- Line 3323  double funcone( double *x)
+ Line 3608  double funcone( double *x)
        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
+       /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
          /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
            and mw[mi+1][i]. dh depends on stepm.*/
          newm=savm;
-         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
          cov[2]=agexact;
          if(nagesqr==1)
            cov[3]= agexact*agexact;
          for (kk=1; kk<=cptcovage;kk++) {
-           cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           if(!FixedV[Tvar[Tage[kk]]])
+             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
+           else
+             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
          }
          /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
- Line 3376  double funcone( double *x)
+ Line 3665  double funcone( double *x)
        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
        if(globpr){
-         fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %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,
 *weight[i]*lli,out[s1][s2],savm[s1][s2]);
- Line 3386  double funcone( double *x)
+ Line 3675  double funcone( double *x)
          }
          fprintf(ficresilk," %10.6f\n", -llt);
        }
-     } /* end of wave */
+         } /* end of wave */
-   } /* end of individual */
+ } /* end of individual */
-   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
-   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
-   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-   if(globpr==0){ /* First time we count the contributions and weights */
+ if(globpr==0){ /* First time we count the contributions and weights */
-     gipmx=ipmx;
+         gipmx=ipmx;
-     gsw=sw;
+         gsw=sw;
-   }
+ }
-   return -l;
+ return -l;
  }
- Line 3734  double hessij( double x[], double **hess
+ Line 4023  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 3923  void  freqsummary(char fileres[], int ia
+ Line 4212  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 3933  void  freqsummary(char fileres[], int ia
+ Line 4222  void  freqsummary(char fileres[], int ia
    }
    else{
      fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
              fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
+   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
      printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
      fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
      fflush(ficlog);
      exit(70);
-   }
+   } else{
-   else{
      fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
- <hr size=\"2\" color=\"#EC5E5E\"> \n\
+ <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
              fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
    }
-   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
+   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
    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
    */
    for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
      posproptt=0.;
      /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
- Line 3978  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4266  Title=%s <br>Datafile=%s Firstpass=%d La
        for (jk=-5; jk<=nlstate+ndeath; jk++)
          for(m=iagemin; m <= iagemax+3; m++)
            freq[i][jk][m]=0;
      for (i=1; i<=nlstate; i++)  {
        for(m=iagemin; m <= iagemax+3; m++)
          prop[i][m]=0;
- Line 3991  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4279  Title=%s <br>Datafile=%s Firstpass=%d La
      /*  meanqt[m][z1]=0.; */
      /*   } */
      /* } */
      dateintsum=0;
      k2cpt=0;
      /* For that combination of covariate j1, we count and print the frequencies in one pass */
- Line 4070  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4358  Title=%s <br>Datafile=%s Firstpass=%d La
      } /* end iind = 1 to imx */
      /* prop[s][age] is feeded for any initial and valid live state as well as
         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      pstamp(ficresp);
-     /* if  (ncoveff>0) { */
+     if  (cptcoveff>0){
-     if  (cptcoveff>0) {
        fprintf(ficresp, "\n#********** Variable ");
        fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
        fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+       fprintf(ficlog, "\n#********** Variable ");
        for (z1=1; z1<=cptcoveff; z1++){
-         fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         if(DummyV[z1]){
-         fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         fprintf(ficresphtmfr, "V%d=%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{
+           fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         }
        }
        fprintf(ficresp, "**********\n#");
        fprintf(ficresphtm, "**********</h3>\n");
        fprintf(ficresphtmfr, "**********</h3>\n");
-       fprintf(ficlog, "\n#********** Variable ");
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(ficlog, "**********\n");
      }
      fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
      for(i=1; i<=nlstate;i++) {
-       fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+       fprintf(ficresp, " Age Prev(%d)  N(%d)  N  ",i,i);
        fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
      }
      fprintf(ficresp, "\n");
      fprintf(ficresphtm, "\n");
      /* Header of frequency table by age */
      fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
      fprintf(ficresphtmfr,"<th>Age</th> ");
- Line 4109  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4403  Title=%s <br>Datafile=%s Firstpass=%d La
        }
      }
      fprintf(ficresphtmfr, "\n");
      /* For each age */
      for(iage=iagemin; iage <= iagemax+3; iage++){
        fprintf(ficresphtm,"<tr>");
- Line 4148  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4442  Title=%s <br>Datafile=%s Firstpass=%d La
            fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
          }
        }
        for(jk=1; jk <=nlstate ; jk++){
          /* 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
- Line 4235  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4529  Title=%s <br>Datafile=%s Firstpass=%d La
      fprintf(ficresphtmfr,"</table>\n");
    } /* end selected combination of covariate j1 */
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
    fclose(ficresphtm);
    fclose(ficresphtmfr);
- Line 4570  void  concatwav(int wav[], int **dh, int
+ Line 4864  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 */
-         */
+          for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-         ij=0; /* ij is similar to i but can jump over null modalities */
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-         for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+              break;
-           if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+            }
-             break;
+            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*/
-           ij++;
+            cptcode = ij; /* New max modality for covar j */
-           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*/
+          } /* end of loop on modality i=-1 to 1 or more */
-           cptcode = ij; /* New max modality for covar j */
+          break;
-         } /* end of loop on modality i=-1 to 1 or more */
+        case 1: /* Testing on varying covariate, could be simple and
-         break;
+                 * should look at waves or product of fixed *
-       case 1: /* Testing on varying covariate, could be simple and
+                 * varying. No time to test -1, assuming 0 and 1 only */
-                * should look at waves or product of fixed *
+          ij=0;
-                * varying. No time to test -1, assuming 0 and 1 only */
+          for(i=0; i<=1;i++){
-         ij=0;
+            nbcode[Tvar[k]][++ij]=i;
-         for(i=0; i<=1;i++){
+          }
-           nbcode[Tvar[k]][++ij]=i;
+          break;
-         }
+        default:
-         break;
+          break;
-       default:
+        } /* end switch */
-         break;
+      } /* end dummy test */
-       } /* end switch */
-     } /* end dummy test */
+      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+      /*         /\*recode from 0 *\/ */
-     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+      /*                                      k is a modality. If we have model=V1+V1*sex  */
-     /*  /\*recode from 0 *\/ */
+      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-     /*                               k is a modality. If we have model=V1+V1*sex  */
+      /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
-     /*                               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 *\/ */
+      /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
-     /*  } */
+      /*         if (ij > ncodemax[j]) { */
-     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-     /*  if (ij > ncodemax[j]) { */
+      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+      /*           break; */
-     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+      /*         } */
-     /*    break; */
+      /*   }  /\* 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 modality k *\/ */
-   } /* 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;
+    /* Look at fixed dummy (single or product) covariates to check empty modalities */
-   for (k=-1; k< maxncov; k++) Ndum[k]=0;
+    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
-   /* Look at fixed dummy (single or product) covariates to check empty modalities */
+      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
-   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*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 */
-     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+      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 */
-     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 */
+      /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
-     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 */
+    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
-     /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
-   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+    ij=0;
+    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
-   ij=0;
+    for (k=1; k<=  cptcovt; k++) { /* 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) *\/ */
+      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
-   for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
-     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
-     /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
+        /* If product not in single variable we don't print results */
-     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
-       /* If product not in single variable we don't print results */
+        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
-       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        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*/
-       ++ij;
+        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
-       Tvaraff[ij]=Tvar[k]; /*For printing */
+        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 */
-       Tmodelind[ij]=k;
+        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++){
-   /* To be sorted */
+      TmodelInvind[j]=0;
-   ;
+    }
- }
+    /* To be sorted */
+    ;
+  }
  /*********** Health Expectancies ****************/
- void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
+  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
  {
    /* Health expectancies, no variances */
- Line 4749  void evsij(double ***eij, double x[], in
+ Line 5045  void evsij(double ***eij, double x[], in
    double ***p3mat;
    double eip;
-   pstamp(ficreseij);
+   /* pstamp(ficreseij); */
    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
    fprintf(ficreseij,"# Age");
    for(i=1; i<=nlstate;i++){
- Line 4812  void evsij(double ***eij, double x[], in
+ Line 5108  void evsij(double ***eij, double x[], in
      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
-     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
- Line 4847  void evsij(double ***eij, double x[], in
+ Line 5143  void evsij(double ***eij, double x[], in
  }
- void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
+  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
  {
    /* Covariances of health expectancies eij and of total life expectancies according
- Line 4960  void cvevsij(double ***eij, double x[],
+ Line 5256  void cvevsij(double ***eij, double x[],
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          xm[i] = x[i] - (i==theta ?delti[theta]:0);
        }
-       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
-       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
+       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
        for(j=1; j<= nlstate; j++){
          for(i=1; i<=nlstate; i++){
- Line 5002  void cvevsij(double ***eij, double x[],
+ Line 5298  void cvevsij(double ***eij, double x[],
      }
      /* Computing expectancies */
-     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- Line 5057  void cvevsij(double ***eij, double x[],
+ Line 5353  void cvevsij(double ***eij, double x[],
  }
  /************ Variance ******************/
-  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
+  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- Line 5114  void cvevsij(double ***eij, double x[],
+ Line 5410  void cvevsij(double ***eij, double x[],
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
+    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
+    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+    }
+    for(j=1;j<=cptcoveff;j++)
+      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
+    fprintf(ficresprobmorprev,"\n");
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
- Line 5183  void cvevsij(double ***eij, double x[],
+ Line 5487  void cvevsij(double ***eij, double x[],
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
-        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
         if (popbased==1) {
           if(mobilav ==0){
- Line 5195  void cvevsij(double ***eij, double x[],
+ Line 5499  void cvevsij(double ***eij, double x[],
           }
         }
-        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
- Line 5215  void cvevsij(double ***eij, double x[],
+ Line 5519  void cvevsij(double ***eij, double x[],
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
-        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
+        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
         if (popbased==1) {
           if(mobilav ==0){
- Line 5227  void cvevsij(double ***eij, double x[],
+ Line 5531  void cvevsij(double ***eij, double x[],
           }
         }
-        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
- Line 5292  void cvevsij(double ***eij, double x[],
+ Line 5596  void cvevsij(double ***eij, double x[],
       /* end ppptj */
       /*  x centered again */
-      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
+      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
       if (popbased==1) {
         if(mobilav ==0){
- Line 5308  void cvevsij(double ***eij, double x[],
+ Line 5612  void cvevsij(double ***eij, double x[],
          computed over hstepm (estepm) matrices product = hstepm*stepm months)
          as a weighted average of prlim.
       */
-      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++)
           gmp[j] += prlim[i][i]*p3mat[i][j][1];
- Line 5371  void cvevsij(double ***eij, double x[],
+ Line 5675  void cvevsij(double ***eij, double x[],
   }  /* end varevsij */
  /************ Variance of prevlim ******************/
-  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
+  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
  {
    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- Line 5387  void cvevsij(double ***eij, double x[],
+ Line 5691  void cvevsij(double ***eij, double x[],
    pstamp(ficresvpl);
    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
-   fprintf(ficresvpl,"# Age");
+   fprintf(ficresvpl,"# Age ");
+   if(nresult >=1)
+     fprintf(ficresvpl," Result# ");
    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %1d-%1d",i,i);
    fprintf(ficresvpl,"\n");
- Line 5414  void cvevsij(double ***eij, double x[],
+ Line 5720  void cvevsij(double ***eij, double x[],
          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }
        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        else
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gp[i] = prlim[i][i];
          mgp[theta][i] = prlim[i][i];
- Line 5424  void cvevsij(double ***eij, double x[],
+ Line 5730  void cvevsij(double ***eij, double x[],
        for(i=1; i<=npar; i++) /* Computes gradient */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        else
-         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
+         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
        for(i=1;i<=nlstate;i++){
          gm[i] = prlim[i][i];
          mgm[theta][i] = prlim[i][i];
- Line 5473  void cvevsij(double ***eij, double x[],
+ Line 5779  void cvevsij(double ***eij, double x[],
        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      fprintf(ficresvpl,"%.0f ",age );
+     if(nresult >=1)
+       fprintf(ficresvpl,"%d ",nres );
      for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      fprintf(ficresvpl,"\n");
- Line 5834  void printinghtml(char fileresu[], char
+ Line 6142  void printinghtml(char fileresu[], char
                    int popforecast, int prevfcast, int backcast, int estepm , \
                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                    double jprev2, double mprev2,double anprev2, double dateprev2){
-   int jj1, k1, i1, cpt;
+   int jj1, k1, i1, cpt, k4, nres;
     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  </ul>");
+    fprintf(fichtm,"<ul><li> model=1+age+%s\n \
+ </ul>", model);
     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
- Line 5873  void printinghtml(char fileresu[], char
+ Line 6183  void printinghtml(char fileresu[], char
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     jj1=0;
-    for(k1=1; k1<=m;k1++){
+    for(nres=1; nres <= nresult; nres++) /* For each resultline */
+    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
+      if(TKresult[nres]!= k1)
+        continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         for (cpt=1; cpt<=cptcoveff;cpt++){
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
-          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
+          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+          /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
         }
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
+       }
+        /* if(nqfveff+nqtveff 0) */ /* Test to be done */
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         if(invalidvarcomb[k1]){
           fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
- Line 5891  void printinghtml(char fileresu[], char
+ Line 6213  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: 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-%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 to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
       }
       if(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 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-%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) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <img src=\"%s_%d-%d.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, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
         }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
+        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
- <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
+ <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
       }
       /* } /\* end i1 *\/ */
     }/* End k1 */
- Line 5993  See page 'Matrix of variance-covariance
+ Line 6315  See page 'Matrix of variance-covariance
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     jj1=0;
+    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k1=1; k1<=m;k1++){
+      if(TKresult[nres]!= k1)
+        continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
       if (cptcovn > 0) {
         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
-          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
+          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
+        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         if(invalidvarcomb[k1]){
- Line 6009  See page 'Matrix of variance-covariance
+ Line 6340  See page 'Matrix of variance-covariance
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Observed (cross-sectional) 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\">",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);
  }
- Line 6029  void printinggnuplot(char fileresu[], ch
+ Line 6361  void printinggnuplot(char fileresu[], ch
    char dirfileres[132],optfileres[132];
    char gplotcondition[132];
-   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
    int lv=0, vlv=0, kl=0;
    int ng=0;
    int vpopbased;
    int ioffset; /* variable offset for columns */
+   int nres=0; /* Index of resultline */
  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
  /*     printf("Problem with file %s",optionfilegnuplot); */
- Line 6077  void printinggnuplot(char fileresu[], ch
+ Line 6410  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 */
-       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
+         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
+         if(TKresult[nres]!= k1)
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
+           continue;
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+         /* We are interested in selected combination by the resultline */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
-         vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
-         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           /* 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 */
-       fprintf(ficgp,"\n#\n");
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       if(invalidvarcomb[k1]){
+           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
-         continue;
+           /* printf(" V%d=%d ",Tvaraff[k],vlv); */
-       }
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
+           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
-       fprintf(ficgp,"set xlabel \"Age\" \n\
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
- set ylabel \"Probability\" \n   \
+         }
- set ter svg size 640, 480\n     \
+         /* printf("\n#\n"); */
- plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
-       for (i=1; i<= nlstate ; i ++) {
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+           continue;
-         else        fprintf(ficgp," %%*lf (%%*lf)");
+         }
-       }
-       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
-       for (i=1; i<= nlstate ; i ++) {
+         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         fprintf(ficgp,"set 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);
-         else fprintf(ficgp," %%*lf (%%*lf)");
-       }
+         for (i=1; i<= nlstate ; i ++) {
-       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);
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-       for (i=1; i<= nlstate ; i ++) {
+           else        fprintf(ficgp," %%*lf (%%*lf)");
-         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+         }
-         else fprintf(ficgp," %%*lf (%%*lf)");
+         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
-       }
+         for (i=1; i<= nlstate ; i ++) {
-       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
+           else fprintf(ficgp," %%*lf (%%*lf)");
-         /* 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 */
+         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
-         if(cptcoveff ==0){
+         for (i=1; i<= nlstate ; i ++) {
-           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
+           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
-         }else{
+           else fprintf(ficgp," %%*lf (%%*lf)");
-           kl=0;
+         }
-           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
+         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
-             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
-             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
-             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
-             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           if(cptcoveff ==0){
-             vlv= nbcode[Tvaraff[k]][lv];
+             fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
-             kl++;
+           }else{
-             /* 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 *\/ */
+             kl=0;
-             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
-             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-             if(k==cptcoveff){
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-+(cpt-1),  cpt );  /* 4 or 6 ?*/
+               vlv= nbcode[Tvaraff[k]][lv];
-             }else{
-               fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,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 *\/ */
-           } /* end covariate */
+               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
-         } /* end if no covariate */
+               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
-       } /* end if backcast */
+               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
-       fprintf(ficgp,"\nset out \n");
+               if(k==cptcoveff){
+                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
++cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
+               }else{
+                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
+                 kl++;
+               }
+             } /* end covariate */
+           } /* end if no covariate */
+         } /* end if backcast */
+         fprintf(ficgp,"\nset out \n");
+       } /* nres */
      } /* k1 */
    } /* cpt */
-   /*2 eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-     for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+   /*2 eme*/
-       lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+   for (k1=1; k1<= m ; k1 ++){
-       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+       if(TKresult[nres]!= k1)
-       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+         continue;
-       vlv= nbcode[Tvaraff[k]][lv];
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
-       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-     }
-     fprintf(ficgp,"\n#\n");
-     if(invalidvarcomb[k1]){
-       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       continue;
-     }
-     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
-     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-       if(vpopbased==0)
-         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
-       else
-         fprintf(ficgp,"\nreplot ");
-       for (i=1; i<= nlstate+1 ; i ++) {
-         k=2*i;
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
-         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         fprintf(ficgp,"\" t\"\" w l lt 0,");
-         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
-         for (j=1; j<= nlstate+1 ; j ++) {
-           if (j==i) fprintf(ficgp," %%lf (%%lf)");
-           else fprintf(ficgp," %%*lf (%%*lf)");
-         }
-         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
-         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
-       } /* state */
-     } /* vpopbased */
-     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
-   } /* k1 */
-   /*3eme*/
-   for (k1=1; k1<= m ; k1 ++) {
-     for (cpt=1; cpt<= nlstate ; cpt ++) {
-       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6214  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 6507  plot [%.f:%.f] \"%s\" every :::%d::%d u
          vlv= nbcode[Tvaraff[k]][lv];
          fprintf(ficgp," 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]);
+       }
        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);
+         if(vpopbased==0)
-       fprintf(ficgp,"set ter svg size 640, 480\n\
+           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-%d.svg\"; replot; set out; \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(TKresult[nres]!= k1)
+         continue;
+       for (cpt=1; cpt<= nlstate ; cpt ++) {
+         fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         /*       k=2+nlstate*(2*cpt-2); */
+         k=2+(nlstate+1)*(cpt-1);
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+         fprintf(ficgp,"set ter svg size 640, 480\n\
  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
-       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
-         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
-         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+           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_"),k1-1,k1-1,k+i,cpt,i+1);
-         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
+           /*    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_"),k1-1,k1-1,k+nlstate,cpt);
-     }
+       }
-   }
+     } /* end nres */
+   } /* end kl 3eme */
    /* 4eme */
    /* Survival functions (period) from state i in state j by initial state i */
-   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       if(TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
+         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
- set ter svg size 640, 480\n                                                                                                                                                                                     \
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- unset log y\n                                                                                                                                                                                                                                           \
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-       k=3;
+           vlv= nbcode[Tvaraff[k]][lv];
-       for (i=1; i<= nlstate ; i ++){
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-         if(i==1){
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-         }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/($%d",k1,k+l+(cpt-1),k+l);
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-         for (j=2; j<= nlstate+ndeath ; j ++)
+         }
-           fprintf(ficgp,"+$%d",k+l+j-1);
+         fprintf(ficgp,"\n#\n");
-         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         if(invalidvarcomb[k1]){
-       } /* nlstate */
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-       fprintf(ficgp,"\nset out\n");
+           continue;
-     } /* end cpt state*/
+         }
-   } /* end covariate */
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
+         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\n");
+       } /* end cpt state*/
+     } /* end nres */
+   } /* end covariate k1 */
  /* 5eme */
    /* Survival functions (period) from state i in state j by final state j */
-   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
+   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(TKresult[nres]!= k1)
-       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
-       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
-         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
-         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-         vlv= nbcode[Tvaraff[k]][lv];
-         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-       }
-       fprintf(ficgp,"\n#\n");
-       if(invalidvarcomb[k1]){
-         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
-       }
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
+         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;
+         }
-       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 xlabel \"Age\" \nset ylabel \"Probability to be alive\" \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                                                           \
+         k=3;
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       k=3;
+           if(j==1)
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-         if(j==1)
+           else
-           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+             fprintf(ficgp,", '' ");
-         else
+           l=(nlstate+ndeath)*(cpt-1) +j;
-           fprintf(ficgp,", '' ");
+           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-         l=(nlstate+ndeath)*(cpt-1) +j;
+           /* for (i=2; i<= nlstate+ndeath ; i ++) */
-         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-         /* for (i=2; i<= nlstate+ndeath ; i ++) */
+           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
-         /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+         } /* nlstate */
-         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+         fprintf(ficgp,", '' ");
-       } /* nlstate */
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-       fprintf(ficgp,", '' ");
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+           l=(nlstate+ndeath)*(cpt-1) +j;
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           if(j < nlstate)
-         l=(nlstate+ndeath)*(cpt-1) +j;
+             fprintf(ficgp,"$%d +",k+l);
-         if(j < nlstate)
+           else
-           fprintf(ficgp,"$%d +",k+l);
+             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-         else
+         }
-           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         fprintf(ficgp,"\nset out\n");
-       }
+       } /* end cpt state*/
-       fprintf(ficgp,"\nset out\n");
+     } /* end covariate */
-     } /* end cpt state*/
+   } /* end nres */
-   } /* end covariate */
  /* 6eme */
    /* CV preval stable (period) for each covariate */
-   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+     if(TKresult[nres]!= k1)
+       continue;
      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
- Line 6348  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6718  plot [%.f:%.f]  ", ageminpar, agemaxpar)
          vlv= nbcode[Tvaraff[k]][lv];
          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
        }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
        fprintf(ficgp,"\n#\n");
        if(invalidvarcomb[k1]){
          fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
          continue;
        }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.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 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 ++){
          if(i==1)
- Line 6379  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6750  plot [%.f:%.f]  ", ageminpar, agemaxpar)
  /* 7eme */
    if(backcast == 1){
      /* CV back preval stable (period) for each covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(TKresult[nres]!= k1)
+         continue;
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
          fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
- Line 6390  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6764  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            vlv= nbcode[Tvaraff[k]][lv];
            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
          }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
          fprintf(ficgp,"\n#\n");
          if(invalidvarcomb[k1]){
            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
            continue;
          }
-         fprintf(ficgp,"\nset out \"%s_%d-%d.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 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 ++){
            if(i==1)
- Line 6426  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6801  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    if(prevfcast==1){
      /* Projection from cross-sectional to stable (period) for each covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
+     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(TKresult[nres]!= k1)
+         continue;
        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
- Line 6437  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6815  plot [%.f:%.f]  ", ageminpar, agemaxpar)
            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);
- Line 6444  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6825  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 xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
- set ter svg size 640, 480\n                                             \
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
- unset log y\n                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
          for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
            /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
- Line 6515  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6894  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    } /* End if prevfcast */
-   /* proba elementaires */
+   /* 9eme writing MLE parameters */
-   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
+   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
    for(i=1,jk=1; i <=nlstate; i++){
      fprintf(ficgp,"# initial state %d\n",i);
      for(k=1; k <=(nlstate+ndeath); k++){
- Line 6533  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6912  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 6548  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6928  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
    fprintf(ficgp,"#\n");
    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
-     fprintf(ficgp,"# ng=%d\n",ng);
+     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
-     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
+     fprintf(ficgp,"#model=%s \n",model);
-     for(jk=1; jk <=m; jk++) {
+     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
-       fprintf(ficgp,"#    jk=%d\n",jk);
+     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
+     for(jk=1; jk <=m; jk++)  /* For each combination of covariate */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(TKresult[nres]!= jk)
+         continue;
+       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
+       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");
+       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);
        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 6592  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6981  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                break;
              }
              ij=1;/* To be checked else nbcode[0][0] wrong */
-             for(j=3; j <=ncovmodel-nagesqr; j++) {
+             ijp=1; /* product no age */
+             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
+             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
-               if(ij <=cptcovage) { /* Bug valgrind */
+               if(j==Tage[ij]) { /* Product by age */
-                 if((j-2)==Tage[ij]) { /* Bug valgrind */
+                 if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
-                   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
+                   if(DummyV[j]==0){
-                   /* 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+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+                   }else{ /* quantitative */
+                     fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
+                   }
                    ij++;
                  }
-               }
+               }else if(j==Tprod[ijp]) { /* */
-               else
+                 /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
-                 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
+                 if(ijp <=cptcovprod) { /* Product */
-             }
+                   if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
+                     if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+                       /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
+                       fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+                     }else{ /* Vn is dummy and Vm is quanti */
+                       /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+                     }
+                   }else{ /* Vn*Vm Vn is quanti */
+                     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++;
+                 }
+               } else{  /* simple covariate */
+                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,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])]); */
+                 }
+               } /* end simple */
+             } /* end j */
            }else{
              i=i-ncovmodel;
              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
- Line 6621  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7042  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                ij=1;
                for(j=3; j <=ncovmodel-nagesqr; j++){
-                 if(ij <=cptcovage) { /* Bug valgrind */
+                 if((j-2)==Tage[ij]) { /* Bug valgrind */
-                   if((j-2)==Tage[ij]) { /* Bug valgrind */
+                   if(ij <=cptcovage) { /* Bug valgrind */
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                      /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                      ij++;
- Line 6774  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7195  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       } /* end bad */
       for (age=bage; age<=fage; age++){
-        printf("%d %d ", cptcod, (int)age);
+        /* printf("%d %d ", cptcod, (int)age); */
         sumnewp[cptcod]=0.;
         sumnewm[cptcod]=0.;
         for (i=1; i<=nlstate;i++){
- Line 6813  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7234  plot [%.f:%.f]  ", ageminpar, agemaxpar)
  /************** Forecasting ******************/
- void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
+  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
    /* proj1, year, month, day of starting projection
       agemin, agemax range of age
       dateprev1 dateprev2 range of dates during which prevalence is computed
       anproj2 year of en of projection (same day and month as proj1).
    */
-   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
+    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
    double agec; /* generic age */
    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
    double *popeffectif,*popcount;
- Line 6841  void prevforecast(char fileres[], double
+ Line 7262  void prevforecast(char fileres[], double
      printf("Problem with forecast resultfile: %s\n", fileresf);
      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
    }
-   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
+   printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
-   fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
+   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
    if (cptcoveff==0) ncodemax[cptcoveff]=1;
- Line 6873  void prevforecast(char fileres[], double
+ Line 7294  void prevforecast(char fileres[], double
    fprintf(ficresf,"#****** Routine prevforecast **\n");
  /*            if (h==(int)(YEARM*yearp)){ */
-   for(k=1;k<=i1;k++){
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
+   for(k=1; k<=i1;k++){
+     if(TKresult[nres]!= k)
+       continue;
      if(invalidvarcomb[k]){
        printf("\nCombination (%d) projection ignored because no cases \n",k);
        continue;
- Line 6882  void prevforecast(char fileres[], double
+ Line 7306  void prevforecast(char fileres[], double
      for(j=1;j<=cptcoveff;j++) {
        fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
      }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+     }
      fprintf(ficresf," yearproj age");
      for(j=1; j<=nlstate+ndeath;j++){
        for(i=1; i<=nlstate;i++)
- Line 6896  void prevforecast(char fileres[], double
+ Line 7323  void prevforecast(char fileres[], double
          nhstepm = nhstepm/hstepm;
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
          for (h=0; h<=nhstepm; h++){
            if (h*hstepm/YEARM*stepm ==yearp) {
- Line 7489  int readdata(char datafile[], int firsto
+ Line 7916  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 7530  int readdata(char datafile[], int firsto
+ Line 7979  int readdata(char datafile[], int firsto
          if(strb[0]=='.') { /* Missing value */
            lval=-1;
            cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
+           cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
            if(isalpha(strb[1])) { /* .m or .d Really Missing value */
              printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
              fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
- Line 7549  int readdata(char datafile[], int firsto
+ Line 7999  int readdata(char datafile[], int firsto
              return 1;
            }
            cotqvar[j][iv][i]=dval;
+           cotvar[j][ntv+iv][i]=dval;
          }
          strcpy(line,stra);
        }/* end loop ntqv */
- Line 7762  int readdata(char datafile[], int firsto
+ Line 8213  int readdata(char datafile[], int firsto
    return (1);
  }
- void removespace(char *str) {
+ void removefirstspace(char **stri){/*, char stro[]) {*/
-   char *p1 = str, *p2 = str;
+   char *p1 = *stri, *p2 = *stri;
-   do
+   while (*p2 == ' ')
-     while (*p2 == ' ')
+     p2++;
-       p2++;
+   /* while ((*p1++ = *p2++) !=0) */
-   while (*p1++ == *p2++);
+   /*   ; */
+   /* do */
+   /*   while (*p2 == ' ') */
+   /*     p2++; */
+   /* while (*p1++ == *p2++); */
+   *stri=p2;
+ }
+ int decoderesult ( char resultline[], int nres)
+ /**< This routine decode one result line and returns the combination # of dummy covariates only **/
+ {
+   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
+   char resultsav[MAXLINE];
+   int resultmodel[MAXLINE];
+   int modelresult[MAXLINE];
+   char stra[80], strb[80], strc[80], strd[80],stre[80];
+   removefirstspace(&resultline);
+   printf("decoderesult:%s\n",resultline);
+   if (strstr(resultline,"v") !=0){
+     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
+     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
+     return 1;
+   }
+   trimbb(resultsav, resultline);
+   if (strlen(resultsav) >1){
+     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
+   }
+   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
+     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
+   }
+   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
+     if(nbocc(resultsav,'=') >1){
+        cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
+                                       resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
+        cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
+     }else
+       cutl(strc,strd,resultsav,'=');
+     Tvalsel[k]=atof(strc); /* 1 */
+     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
+     Tvarsel[k]=atoi(strc);
+     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
+     /* cptcovsel++;     */
+     if (nbocc(stra,'=') >0)
+       strcpy(resultsav,stra); /* and analyzes it */
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     if(Typevar[k1]==0){ /* Single covariate in model */
+       match=0;
+       for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
+           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
+           match=1;
+           break;
+         }
+       }
+       if(match == 0){
+         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+       }
+     }
+   }
+   /* Checking for missing or useless values in comparison of current model needs */
+   for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+     match=0;
+     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       if(Typevar[k1]==0){ /* Single */
+         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
+           resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
+           ++match;
+         }
+       }
+     }
+     if(match == 0){
+       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
+     }else if(match > 1){
+       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
+     }
+   }
+   /* We need to deduce which combination number is chosen and save quantitative values */
+   /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+   /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
+   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
+   /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
+   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
+   /*    1 0 0 0 */
+   /*    2 1 0 0 */
+   /*    3 0 1 0 */
+   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
+   /*    5 0 0 1 */
+   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
+   /*    7 0 1 1 */
+   /*    8 1 1 1 */
+   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
+   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
+   /* V5*age V5 known which value for nres?  */
+   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
+   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
+     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
+       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
+       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
+       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
+       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
+       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
+       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
+       k4++;;
+     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
+       k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
+       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
+       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
+       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
+       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
+       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
+       k4q++;;
+     }
+   }
+   TKresult[nres]=++k; /* Combination for the nresult and the model */
+   return (0);
  }
- int decodemodel ( char model[], int lastobs)
+ int decodemodel( char model[], int lastobs)
-  /**< This routine decode the model and returns:
+  /**< This routine decodes the model and returns:
          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
          * - nagesqr = 1 if age*age in the model, otherwise 0.
          * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
- Line 7786  int decodemodel ( char model[], int last
+ Line 8360  int decodemodel ( char model[], int last
          * - 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 7922  int decodemodel ( char model[], int last
+ Line 8496  int decodemodel ( char model[], int last
              cptcovprodnoage++;k1++;
              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
              Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
-                                    because this model-covariate is a construction we invent a new column
+                                                 because this model-covariate is a construction we invent a new column
-                                    which is after existing variables ncovcol+nqv+ntv+nqtv + k1
+                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1
-                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+                                                 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
-                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+                                                 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
              Typevar[k]=2;  /* 2 for double fixed dummy covariates */
              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
- Line 7969  int decodemodel ( char model[], int last
+ Line 8543  int decodemodel ( char model[], int last
       scanf("%d ",i);*/
- /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
+ /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
-    of variable (dummy vs quantitative, fixed vs time varying) is behind */
+    of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
  /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
     model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
     k =           1    2   3     4       5       6      7      8        9
- Line 7992  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 8566  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, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
+   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
-     if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
+     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       nsd++;
+       modell[k].maintype= FTYPE;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
        Fixed[k]= 0;
        Dummy[k]= 0;
        ncoveff++;
-     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
+       ncovf++;
+       modell[k].maintype= FTYPE;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
        Fixed[k]= 0;
        Dummy[k]= 1;
-       nqfveff++;  /* Only simple fixed quantitative variable */
+       nqfveff++;
-     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
+       modell[k].maintype= FTYPE;
+       modell[k].subtype= FQ;
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
+       ncovf++;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+       TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
        Fixed[k]= 1;
        Dummy[k]= 0;
        ntveff++; /* Only simple time varying dummy variable */
-     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){
+       modell[k].maintype= VTYPE;
-         Fixed[k]= 1;
+       modell[k].subtype= VD;
-         Dummy[k]= 1;
+       nsd++;
-         nqtveff++;/* Only simple time varying quantitative variable */
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       ncovv++; /* Only simple time varying variables */
+       TvarV[ncovv]=Tvar[k];
+       TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
+       TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
+       TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
+       printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
+       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
+     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
+       Fixed[k]= 1;
+       Dummy[k]= 1;
+       nqtveff++;
+       modell[k].maintype= VTYPE;
+       modell[k].subtype= VQ;
+       ncovv++; /* Only simple time varying variables */
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
+       TvarV[ncovv]=Tvar[k];
+       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
+       TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+       TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
+       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
+       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
+       printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
+       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
      }else if (Typevar[k] == 1) {  /* product with age */
-       if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
+       ncova++;
-         Fixed[k]= 2;
+       TvarA[ncova]=Tvar[k];
-         Dummy[k]= 2;
+       TvarAind[ncova]=k;
-         /* ncoveff++; */
+       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;
-         /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
+         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;
-         /* ntveff++; /\* Only simple time varying dummy variable *\/ */
+         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;
-         /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
+         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;
-         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           modell[k].maintype= FTYPE;
-           Fixed[k]= 0;  /* or 2 ?*/
+           modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
-           Dummy[k]= 1;
+           ncovf++; /* Fixed variables without age */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           TvarF[ncovf]=Tvar[k];
-           Fixed[k]= 1;
+           TvarFind[ncovf]=k;
-           Dummy[k]= 0;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 0;  /* or 2 ?*/
-           Fixed[k]= 1;
+           Dummy[k]= 1;
-           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;
-         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           modell[k].maintype= FTYPE;
-           Fixed[k]= 0; /* or 2 ?*/
+           modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
-           Dummy[k]= 1;
+           ncovf++; /* Fixed variables without age */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           TvarF[ncovf]=Tvar[k];
-           Fixed[k]= 1;
+           TvarFind[ncovf]=k;
-           Dummy[k]= 1;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
-           Fixed[k]= 1;
+           Dummy[k]= 1;
-           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
-         }
+           modell[k].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;
-         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           modell[k].maintype= VTYPE;
-           Fixed[k]= 1;
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
-           Dummy[k]= 1;
+           ncovv++; /* Varying variables without age */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           TvarV[ncovv]=Tvar[k];
-           Fixed[k]= 1;
+           TvarVind[ncovv]=k;
-           Dummy[k]= 0;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
-           Fixed[k]= 1;
+           Dummy[k]= 1;
-           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
-         }
+           modell[k].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;
-         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           modell[k].maintype= VTYPE;
-           Fixed[k]= 1;
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
-           Dummy[k]= 1;
+           ncovv++; /* Varying variables without age */
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           TvarV[ncovv]=Tvar[k];
-           Fixed[k]= 1;
+           TvarVind[ncovv]=k;
-           Dummy[k]= 1;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
-         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
-           Fixed[k]= 1;
+           Dummy[k]= 1;
-           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
-         }
+           modell[k].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]);
      }
      printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
      fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
    }
    /* Searching for doublons in the model */
- Line 8121  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 8837  Dummy[k] 0=dummy (0 1), 1 quantitative (
    }
    printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
    fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
+   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
+   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
    return (0); /* with covar[new additional covariate if product] and Tage if age */
    /*endread:*/
    printf("Exiting decodemodel: ");
- Line 8128  Dummy[k] 0=dummy (0 1), 1 quantitative (
+ Line 8846  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 8435  void syscompilerinfo(int logged)
+ Line 9153  void syscompilerinfo(int logged)
  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
    /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
-   int i, j, k, i1 ;
+   int i, j, k, i1, k4=0, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
    double tot;
- Line 8460  int prevalence_limit(double *p, double *
+ Line 9178  int prevalence_limit(double *p, double *
    agelim=agemaxpar;
    /* i1=pow(2,ncoveff); */
-   i1=pow(2,cptcoveff); /* Number of dummy covariates */
+   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
    if (cptcovn < 1){i1=1;}
-   for(k=1; k<=i1;k++){
+   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
-   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       if(TKresult[nres]!= k)
-     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         continue;
-     /* k=k+1; */
-     /* to clean */
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     fprintf(ficrespl,"#******");
-     printf("#******");
-     fprintf(ficlog,"#******");
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
-     fprintf(ficrespl,"******\n");
-     printf("******\n");
-     fprintf(ficlog,"******\n");
-     if(invalidvarcomb[k]){
-       printf("\nCombination (%d) ignored because no case \n",k);
-       fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
-       fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
-                                                 continue;
-     }
-     fprintf(ficrespl,"#Age ");
+       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-     for(j=1;j<=cptcoveff;j++) {
+       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
-       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     }
+       /* k=k+1; */
-     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       /* to clean */
-     fprintf(ficrespl,"Total Years_to_converge\n");
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       fprintf(ficrespl,"#******");
+       printf("#******");
+       fprintf(ficlog,"#******");
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
+       fprintf(ficrespl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       if(invalidvarcomb[k]){
+         printf("\nCombination (%d) ignored because no case \n",k);
+         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
+         continue;
+       }
+       fprintf(ficrespl,"#Age ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
+       fprintf(ficrespl,"Total Years_to_converge\n");
-     for (age=agebase; age<=agelim; age++){
+       for (age=agebase; age<=agelim; age++){
-       /* for (age=agebase; age<=agebase; age++){ */
+         /* for (age=agebase; age<=agebase; age++){ */
-       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
-       fprintf(ficrespl,"%.0f ",age );
+         fprintf(ficrespl,"%.0f ",age );
-       for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcoveff;j++)
-         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       tot=0.;
+         tot=0.;
-       for(i=1; i<=nlstate;i++){
+         for(i=1; i<=nlstate;i++){
-         tot +=  prlim[i][i];
+           tot +=  prlim[i][i];
-         fprintf(ficrespl," %.5f", prlim[i][i]);
+           fprintf(ficrespl," %.5f", prlim[i][i]);
-       }
+         }
-       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
-     } /* Age */
+       } /* Age */
-     /* was end of cptcod */
+       /* was end of cptcod */
-   } /* cptcov */
+     } /* cptcov */
+   } /* nres */
    return 0;
  }
- Line 8519  int back_prevalence_limit(double *p, dou
+ Line 9247  int back_prevalence_limit(double *p, dou
          /* Computes the back prevalence limit  for any combination      of covariate values
     * at any age between ageminpar and agemaxpar
           */
-   int i, j, k, i1 ;
+   int i, j, k, i1, nres=0 ;
    /* double ftolpl = 1.e-10; */
    double age, agebase, agelim;
    double tot;
- Line 8550  int back_prevalence_limit(double *p, dou
+ Line 9278  int back_prevalence_limit(double *p, dou
    i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-   for(k=1; k<=i1;k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-     fprintf(ficresplb,"#******");
+       if(TKresult[nres]!= k)
-     printf("#******");
+         continue;
-     fprintf(ficlog,"#******");
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     for(j=1;j<=cptcoveff ;j++) {/* all covariates */
+       fprintf(ficresplb,"#******");
-       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       printf("#******");
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       fprintf(ficlog,"#******");
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-     }
+         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     fprintf(ficresplb,"******\n");
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     printf("******\n");
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     fprintf(ficlog,"******\n");
+       }
-     if(invalidvarcomb[k]){
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-       printf("\nCombination (%d) ignored because no cases \n",k);
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-       continue;
+       }
-     }
+       fprintf(ficresplb,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       if(invalidvarcomb[k]){
+         printf("\nCombination (%d) ignored because no cases \n",k);
+         fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+         fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+         continue;
+       }
-     fprintf(ficresplb,"#Age ");
+       fprintf(ficresplb,"#Age ");
-     for(j=1;j<=cptcoveff;j++) {
+       for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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);
-       }
+         }
-       fprintf(ficresplb,"%.0f ",age );
+         fprintf(ficresplb,"%.0f ",age );
-       for(j=1;j<=cptcoveff;j++)
+         for(j=1;j<=cptcoveff;j++)
-         fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+           fprintf(ficresplb,"%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 +=  bprlim[i][i];
+           tot +=  bprlim[i][i];
-         fprintf(ficresplb," %.5f", bprlim[i][i]);
+           fprintf(ficresplb," %.5f", bprlim[i][i]);
-       }
+         }
-       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
-     } /* Age */
+       } /* Age */
-     /* was end of cptcod */
+       /* was end of cptcod */
-   } /* cptcov */
+     } /* end of any combination */
+   } /* end of nres */
    /* hBijx(p, bage, fage); */
    /* fclose(ficrespijb); */
- Line 8618  int hPijx(double *p, int bage, int fage)
+ Line 9354  int hPijx(double *p, int bage, int fage)
    int agelim;
    int hstepm;
    int nhstepm;
-   int h, i, i1, j, k;
+   int h, i, i1, j, k, k4, nres=0;
    double agedeb;
    double ***p3mat;
- Line 8645  int hPijx(double *p, int bage, int fage)
+ Line 9381  int hPijx(double *p, int bage, int fage)
                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                  /*      k=k+1;  */
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       if(TKresult[nres]!= k)
+         continue;
        fprintf(ficrespij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+       }
        fprintf(ficrespij,"******\n");
        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
- Line 8659  int hPijx(double *p, int bage, int fage)
+ Line 9402  int hPijx(double *p, int bage, int fage)
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          oldm=oldms;savm=savms;
-         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
          fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
- Line 8689  int hPijx(double *p, int bage, int fage)
+ Line 9432  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 8717  int hPijx(double *p, int bage, int fage)
+ Line 9460  int hPijx(double *p, int bage, int fage)
    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*    k=k+1;  */
-   for (k=1; k <= (int) pow(2,cptcoveff); k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     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(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]){
-       /* 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);
-         for(j=1; j<=nlstate+ndeath;j++)
+         /* oldm=oldms;savm=savms; */
-           fprintf(ficrespijb," %1d-%1d",i,j);
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-       fprintf(ficrespijb,"\n");
+         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
-       for (h=0; h<=nhstepm; h++){
+         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
+         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
-         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," %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 8785  int main(int argc, char *argv[])
+ Line 9534  int main(int argc, char *argv[])
    int itimes;
    int NDIM=2;
    int vpopbased=0;
+   int nres=0;
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
- Line 8803  int main(int argc, char *argv[])
+ Line 9553  int main(int argc, char *argv[])
    char line[MAXLINE];
    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
-   char model[MAXLINE], modeltemp[MAXLINE];
+   char  modeltemp[MAXLINE];
+   char resultline[MAXLINE];
    char pathr[MAXLINE], pathimach[MAXLINE];
    char *tok, *val; /* pathtot */
    int firstobs=1, lastobs=10;
- Line 9115  int main(int argc, char *argv[])
+ Line 9867  int main(int argc, char *argv[])
    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
    coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
-   cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< Time varying covariate */
+   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
    cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
- Line 9138  int main(int argc, char *argv[])
+ Line 9890  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 9146  int main(int argc, char *argv[])
+ Line 9904  int main(int argc, char *argv[])
      fclose (ficlog);
      goto end;
      exit(0);
+   } else if(mle==-2) { /* Guessing from means */
+     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
+     printf(" You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso);
+     fprintf(ficlog," You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso);
    }  else if(mle==-5) { /* Main Wizard */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
- Line 9168  int main(int argc, char *argv[])
+ Line 9931  int main(int argc, char *argv[])
      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
      for(i=1; i <=nlstate; i++){
-                         j=0;
+       j=0;
        for(jj=1; jj <=nlstate+ndeath; jj++){
-                                 if(jj==i) continue;
+         if(jj==i) continue;
-                                 j++;
+         j++;
-                                 fscanf(ficpar,"%1d%1d",&i1,&j1);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-                                 if ((i1 != i) || (j1 != jj)){
+         if ((i1 != i) || (j1 != jj)){
-                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
  It might be a problem of design; if ncovcol and the model are correct\n \
  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
-                                         exit(1);
+           exit(1);
-                                 }
+         }
-                                 fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-                                 if(mle==1)
+         if(mle==1)
-                                         printf("%1d%1d",i,jj);
+           printf("%1d%1d",i,jj);
-                                 fprintf(ficlog,"%1d%1d",i,jj);
+         fprintf(ficlog,"%1d%1d",i,jj);
-                                 for(k=1; k<=ncovmodel;k++){
+         for(k=1; k<=ncovmodel;k++){
-                                         fscanf(ficpar," %lf",&param[i][j][k]);
+           fscanf(ficpar," %lf",&param[i][j][k]);
-                                         if(mle==1){
+           if(mle==1){
-                                                 printf(" %lf",param[i][j][k]);
+             printf(" %lf",param[i][j][k]);
-                                                 fprintf(ficlog," %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
-                                         }
+           }
-                                         else
+           else
-                                                 fprintf(ficlog," %lf",param[i][j][k]);
+             fprintf(ficlog," %lf",param[i][j][k]);
-                                         fprintf(ficparo," %lf",param[i][j][k]);
+           fprintf(ficparo," %lf",param[i][j][k]);
-                                 }
+         }
-                                 fscanf(ficpar,"\n");
+         fscanf(ficpar,"\n");
-                                 numlinepar++;
+         numlinepar++;
-                                 if(mle==1)
+         if(mle==1)
-                                         printf("\n");
+           printf("\n");
-                                 fprintf(ficlog,"\n");
+         fprintf(ficlog,"\n");
-                                 fprintf(ficparo,"\n");
+         fprintf(ficparo,"\n");
        }
      }
      fflush(ficlog);
      /* Reads scales values */
      p=param[1][1];
- Line 9219  run imach with mle=-1 to get a correct t
+ Line 9982  run imach with mle=-1 to get a correct t
      for(i=1; i <=nlstate; i++){
        for(j=1; j <=nlstate+ndeath-1; j++){
-                                 fscanf(ficpar,"%1d%1d",&i1,&j1);
+         fscanf(ficpar,"%1d%1d",&i1,&j1);
-                                 if ( (i1-i) * (j1-j) != 0){
+         if ( (i1-i) * (j1-j) != 0){
-                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
+           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
-                                         exit(1);
+           exit(1);
-                                 }
+         }
-                                 printf("%1d%1d",i,j);
+         printf("%1d%1d",i,j);
-                                 fprintf(ficparo,"%1d%1d",i1,j1);
+         fprintf(ficparo,"%1d%1d",i1,j1);
-                                 fprintf(ficlog,"%1d%1d",i1,j1);
+         fprintf(ficlog,"%1d%1d",i1,j1);
-                                 for(k=1; k<=ncovmodel;k++){
+         for(k=1; k<=ncovmodel;k++){
-                                         fscanf(ficpar,"%le",&delti3[i][j][k]);
+           fscanf(ficpar,"%le",&delti3[i][j][k]);
-                                         printf(" %le",delti3[i][j][k]);
+           printf(" %le",delti3[i][j][k]);
-                                         fprintf(ficparo," %le",delti3[i][j][k]);
+           fprintf(ficparo," %le",delti3[i][j][k]);
-                                         fprintf(ficlog," %le",delti3[i][j][k]);
+           fprintf(ficlog," %le",delti3[i][j][k]);
-                                 }
+         }
-                                 fscanf(ficpar,"\n");
+         fscanf(ficpar,"\n");
-                                 numlinepar++;
+         numlinepar++;
-                                 printf("\n");
+         printf("\n");
-                                 fprintf(ficparo,"\n");
+         fprintf(ficparo,"\n");
-                                 fprintf(ficlog,"\n");
+         fprintf(ficlog,"\n");
        }
      }
      fflush(ficlog);
      /* Reads covariance matrix */
      delti=delti3[1][1];
- Line 9331  Please run with mle=-1 to get a correct
+ Line 10094  Please run with mle=-1 to get a correct
    agedc=vector(1,n);
    cod=ivector(1,n);
    for(i=1;i<=n;i++){
-                 num[i]=0;
+     num[i]=0;
-                 moisnais[i]=0;
+     moisnais[i]=0;
-                 annais[i]=0;
+     annais[i]=0;
-                 moisdc[i]=0;
+     moisdc[i]=0;
-                 andc[i]=0;
+     andc[i]=0;
-                 agedc[i]=0;
+     agedc[i]=0;
-                 cod[i]=0;
+     cod[i]=0;
-                 weight[i]=1.0; /* Equal weights, 1 by default */
+     weight[i]=1.0; /* Equal weights, 1 by default */
-         }
+   }
    mint=matrix(1,maxwav,1,n);
    anint=matrix(1,maxwav,1,n);
    s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
- Line 9352  Please run with mle=-1 to get a correct
+ Line 10115  Please run with mle=-1 to get a correct
      goto end;
    /* Calculation of the number of parameters from char model */
-     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
+   /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
          k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
          k=3 V4 Tvar[k=3]= 4 (from V4)
          k=2 V1 Tvar[k=2]= 1 (from V1)
          k=1 Tvar[1]=2 (from V2)
-     */
+   */
    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
+   TvarsDind=ivector(1,NCOVMAX); /*  */
+   TvarsD=ivector(1,NCOVMAX); /*  */
+   TvarsQind=ivector(1,NCOVMAX); /*  */
+   TvarsQ=ivector(1,NCOVMAX); /*  */
+   TvarF=ivector(1,NCOVMAX); /*  */
+   TvarFind=ivector(1,NCOVMAX); /*  */
+   TvarV=ivector(1,NCOVMAX); /*  */
+   TvarVind=ivector(1,NCOVMAX); /*  */
+   TvarA=ivector(1,NCOVMAX); /*  */
+   TvarAind=ivector(1,NCOVMAX); /*  */
+   TvarFD=ivector(1,NCOVMAX); /*  */
+   TvarFDind=ivector(1,NCOVMAX); /*  */
+   TvarFQ=ivector(1,NCOVMAX); /*  */
+   TvarFQind=ivector(1,NCOVMAX); /*  */
+   TvarVD=ivector(1,NCOVMAX); /*  */
+   TvarVDind=ivector(1,NCOVMAX); /*  */
+   TvarVQ=ivector(1,NCOVMAX); /*  */
+   TvarVQind=ivector(1,NCOVMAX); /*  */
+   Tvalsel=vector(1,NCOVMAX); /*  */
+   Tvarsel=ivector(1,NCOVMAX); /*  */
    Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
    Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
    Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
- Line 9385  Please run with mle=-1 to get a correct
+ Line 10170  Please run with mle=-1 to get a correct
 covariates (3 plus signs)
                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                        */
-   Tmodelind=ivector(1,NCOVMAX);/** five the k model position of an
+   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                  * individual dummy, fixed or varying:
                                  * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
                                  * 3, 1, 0, 0, 0, 0, 0, 0},
+                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
+                                 * V1 df, V2 qf, V3 & V4 dv, V5 qv
+                                 * Tmodelind[1]@9={9,0,3,2,}*/
+   TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
+   TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual quantitative, fixed or varying:
+                                 * Tmodelqind[1]=1,Tvaraff[1]@9={4,
+                                 * 3, 1, 0, 0, 0, 0, 0, 0},
                                  * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
  /* Main decodemodel */
- Line 9439  Please run with mle=-1 to get a correct
+ Line 10232  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 9642  Interval (in months) between two waves:
+ Line 10435  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 9880  Please run with mle=-1 to get a correct
+ Line 10673  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 10130  Please run with mle=-1 to get a correct
+ Line 10927  Please run with mle=-1 to get a correct
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        fputs(line,stdout);
+       fputs(line,ficres);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
- Line 10146  Please run with mle=-1 to get a correct
+ Line 10944  Please run with mle=-1 to get a correct
        fgets(line, MAXLINE, ficpar);
        fputs(line,stdout);
        fputs(line,ficparo);
+       fputs(line,ficres);
      }
      ungetc(c,ficpar);
- Line 10155  Please run with mle=-1 to get a correct
+ Line 10954  Please run with mle=-1 to get a correct
      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] == '#') {
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+         fputs(line,ficres);
+         continue;
+       }else
+         break;
+     }
+     if (!feof(ficpar))
+     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+       if (num_filled == 0){
+         resultline[0]='\0';
+       break;
+       } else if (num_filled != 1){
+         printf("ERROR %d: result line should be at minimum '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);
+       while(fgets(line, MAXLINE, ficpar)) {
+         /* If line starts with a # it is a comment */
+         if (line[0] == '#') {
+           numlinepar++;
+           fputs(line,stdout);
+           fputs(line,ficparo);
+           fputs(line,ficres);
+           fputs(line,ficlog);
+           continue;
+         }else
+           break;
+       }
+       if (feof(ficpar))
+         break;
+       else{ /* Processess output results for this combination of covariate values */
+       }
+     } /* end while */
-                 /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
+     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
-                         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+       printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
-                         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
+       fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
      }else{
- Line 10223  Please run with mle=-1 to get a correct
+ Line 11074  Please run with mle=-1 to get a correct
              mobaverages[i][j][k]=0.;
        mobaverage=mobaverages;
        if (mobilav!=0) {
+         printf("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);
- Line 10231  Please run with mle=-1 to get a correct
+ Line 11083  Please run with mle=-1 to get a correct
        /* /\* 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");
          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 10285  Please run with mle=-1 to get a correct
+ Line 11138  Please run with mle=-1 to get a correct
      }
      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
+     pstamp(ficreseij);
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+       if(TKresult[nres]!= k)
+         continue;
        fprintf(ficreseij,"\n#****** ");
+       printf("\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
        }
        fprintf(ficreseij,"******\n");
+       printf("******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
+       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
      }
- Line 10346  Please run with mle=-1 to get a correct
+ Line 11214  Please run with mle=-1 to get a correct
      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-       printf("\n#****** ");
+     if (cptcovn < 1){i1=1;}
-       fprintf(ficrest,"\n#****** ");
-       fprintf(ficlog,"\n#****** ");
+     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)
+         continue;
+       printf("\n#****** Result for:");
+       fprintf(ficrest,"\n#****** Result for:");
+       fprintf(ficlog,"\n#****** Result for:");
        for(j=1;j<=cptcoveff;j++){
          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficrest,"******\n");
        fprintf(ficlog,"******\n");
        printf("******\n");
- Line 10365  Please run with mle=-1 to get a correct
+ Line 11244  Please run with mle=-1 to get a correct
          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficresstdeij,"******\n");
        fprintf(ficrescveij,"******\n");
        fprintf(ficresvij,"\n#****** ");
+       /* pstamp(ficresvij); */
        for(j=1;j<=cptcoveff;j++)
          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficresvij,"******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       printf(" cvevsij combination#=%d, ",k);
+       printf(" cvevsij ");
-       fprintf(ficlog, " cvevsij combination#=%d, ",k);
+       fprintf(ficlog, " cvevsij ");
-       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
        printf(" end cvevsij \n ");
        fprintf(ficlog, " end cvevsij \n ");
- Line 10394  Please run with mle=-1 to get a correct
+ Line 11281  Please run with mle=-1 to get a correct
          cptcod= 0; /* To be deleted */
          printf("varevsij vpopbased=%d \n",vpopbased);
          fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
-         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
          if(vpopbased==1)
            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
- Line 10408  Please run with mle=-1 to get a correct
+ Line 11295  Please run with mle=-1 to get a correct
          printf("Computing age specific period (stable) prevalences in each health state \n");
          fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
          for(age=bage; age <=fage ;age++){
-           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
+           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
            if (vpopbased==1) {
              if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
- Line 10445  Please run with mle=-1 to get a correct
+ Line 11332  Please run with mle=-1 to get a correct
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_vector(epj,1,nlstate+1);
-       printf("done \n");fflush(stdout);
+       printf("done selection\n");fflush(stdout);
-       fprintf(ficlog,"done\n");fflush(ficlog);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
        /*}*/
-     } /* End k */
+     } /* End k selection */
      printf("done State-specific expectancies\n");fflush(stdout);
      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
- Line 10468  Please run with mle=-1 to get a correct
+ Line 11355  Please run with mle=-1 to get a correct
      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     i1=pow(2,cptcoveff);
+     if (cptcovn < 1){i1=1;}
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){
+       if(TKresult[nres]!= k)
+         continue;
        fprintf(ficresvpl,"\n#****** ");
        printf("\n#****** ");
        fprintf(ficlog,"\n#****** ");
- Line 10477  Please run with mle=-1 to get a correct
+ Line 11370  Please run with mle=-1 to get a correct
          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficresvpl,"******\n");
        printf("******\n");
        fprintf(ficlog,"******\n");
        varpl=matrix(1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
+       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
        free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
        /*}*/
      }
- Line 10518  Please run with mle=-1 to get a correct
+ Line 11416  Please run with mle=-1 to get a correct
    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);
-   free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
+   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
    free_matrix(coqvar,1,maxwav,1,n);
    free_matrix(covar,0,NCOVMAX,1,n);
    free_matrix(matcov,1,npar,1,npar);
- Line 10532  Please run with mle=-1 to get a correct
+ Line 11430  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);
+   free_ivector(TvarsQind,1,NCOVMAX);
+   free_ivector(TvarsD,1,NCOVMAX);
+   free_ivector(TvarsDind,1,NCOVMAX);
+   free_ivector(TvarFD,1,NCOVMAX);
+   free_ivector(TvarFDind,1,NCOVMAX);
+   free_ivector(TvarF,1,NCOVMAX);
+   free_ivector(TvarFind,1,NCOVMAX);
+   free_ivector(TvarV,1,NCOVMAX);
+   free_ivector(TvarVind,1,NCOVMAX);
+   free_ivector(TvarA,1,NCOVMAX);
+   free_ivector(TvarAind,1,NCOVMAX);
+   free_ivector(TvarFQ,1,NCOVMAX);
+   free_ivector(TvarFQind,1,NCOVMAX);
+   free_ivector(TvarVD,1,NCOVMAX);
+   free_ivector(TvarVDind,1,NCOVMAX);
+   free_ivector(TvarVQ,1,NCOVMAX);
+   free_ivector(TvarVQind,1,NCOVMAX);
+   free_ivector(Tvarsel,1,NCOVMAX);
+   free_vector(Tvalsel,1,NCOVMAX);
    free_ivector(Tposprod,1,NCOVMAX);
    free_ivector(Tprod,1,NCOVMAX);
    free_ivector(Tvaraff,1,NCOVMAX);
    free_ivector(invalidvarcomb,1,ncovcombmax);
    free_ivector(Tage,1,NCOVMAX);
    free_ivector(Tmodelind,1,NCOVMAX);
+   free_ivector(TmodelInvind,1,NCOVMAX);
+   free_ivector(TmodelInvQind,1,NCOVMAX);
    free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
    /* free_imatrix(codtab,1,100,1,10); */

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