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Diff for /imach/src/imach.c between versions 1.226 and 1.246

-version 1.226, 2016/07/12 18:42:34
+version 1.246, 2016/09/02 08:49:22
  Line 1
  /* $Id$
    $State$
    $Log$
+   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 639
+ Line 698
    Short summary of the programme:
-   This program computes Healthy Life Expectancies from
+   This program computes Healthy Life Expectancies or State-specific
-   cross-longitudinal data. Cross-longitudinal data consist in: -1- a
+   (if states aren't health statuses) Expectancies from
-   first survey ("cross") where individuals from different ages are
+   cross-longitudinal data. Cross-longitudinal data consist in:
-   interviewed on their health status or degree of disability (in the
-   case of a health survey which is our main interest) -2- at least a
+   -1- a first survey ("cross") where individuals from different ages
-   second wave of interviews ("longitudinal") which measure each change
+   are interviewed on their health status or degree of disability (in
-   (if any) in individual health status.  Health expectancies are
+   the case of a health survey which is our main interest)
-   computed from the time spent in each health state according to a
-   model. More health states you consider, more time is necessary to reach the
+   -2- at least a second wave of interviews ("longitudinal") which
-   Maximum Likelihood of the parameters involved in the model.  The
+   measure each change (if any) in individual health status.  Health
-   simplest model is the multinomial logistic model where pij is the
+   expectancies are computed from the time spent in each health state
-   probability to be observed in state j at the second wave
+   according to a model. More health states you consider, more time is
-   conditional to be observed in state i at the first wave. Therefore
+   necessary to reach the Maximum Likelihood of the parameters involved
-   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
+   in the model.  The simplest model is the multinomial logistic model
-   'age' is age and 'sex' is a covariate. If you want to have a more
+   where pij is the probability to be observed in state j at the second
-   complex model than "constant and age", you should modify the program
+   wave conditional to be observed in state i at the first
-   where the markup *Covariates have to be included here again* invites
+   wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
-   you to do it.  More covariates you add, slower the
+   etc , where 'age' is age and 'sex' is a covariate. If you want to
+   have a more complex model than "constant and age", you should modify
+   the program where the markup *Covariates have to be included here
+   again* invites you to do it.  More covariates you add, slower the
    convergence.
    The advantage of this computer programme, compared to a simple
- Line 678
+ Line 740
    of the life expectancies. It also computes the period (stable) prevalence.
  Back prevalence and projections:
-  - back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj)
-     Computes the back prevalence limit  for any combination     of covariate values k
+  - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
-     at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
+    double agemaxpar, double ftolpl, int *ncvyearp, double
-    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
+    dateprev1,double dateprev2, int firstpass, int lastpass, int
-  - hBijx Back Probability to be in state i at age x-h being in j at x
+    mobilavproj)
+     Computes the back prevalence limit for any combination of
+     covariate values k at any age between ageminpar and agemaxpar and
+     returns it in **bprlim. In the loops,
+    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
+        **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
+    - hBijx Back Probability to be in state i at age x-h being in j at x
     Computes for any combination of covariates k and any age between bage and fage
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                          oldm=oldms;savm=savms;
-          - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
       Computes the transition matrix starting at age 'age' over
       'nhstepm*hstepm*stepm' months (i.e. until
       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
-      nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling
+      nhstepm*hstepm matrices.
-      p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
-,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+      Returns p3mat[i][j][h] after calling
+      p3mat[i][j][h]=matprod2(newm,
+      bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
+      dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+      oldm);
  Important routines
- Line 882  int cptcovsnq=0; /**< cptcovsnq number o
+ Line 958  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 907  int **dh; /* dh[mi][i] is number of step
+ Line 988  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 937  char fileresv[FILENAMELENGTH];
+ Line 1020  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 974  double dval;
+ Line 1058  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 1036  double ***cotvar; /* Time varying covari
+ Line 1121  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[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
+ int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
- int *Dummy; /** Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
+ int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
+ int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
  int *Tage;
+ int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
+ int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1  */
  int *Ndum; /** Freq of modality (tricode */
  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
- int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
+ int **Tvard;
+ int *Tprod;/**< Gives the k position of the k1 product */
+ /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
+ int *Tposprod; /**< Gives the k1 product from the k position */
+    /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
+    /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
+ int cptcovprod, *Tvaraff, *invalidvarcomb;
  double *lsurv, *lpop, *tpop;
+ #define FD 1; /* Fixed dummy covariate */
+ #define FQ 2; /* Fixed quantitative covariate */
+ #define FP 3; /* Fixed product covariate */
+ #define FPDD 7; /* Fixed product dummy*dummy covariate */
+ #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
+ #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
+ #define VD 10; /* Varying dummy covariate */
+ #define VQ 11; /* Varying quantitative covariate */
+ #define VP 12; /* Varying product covariate */
+ #define VPDD 13; /* Varying product dummy*dummy covariate */
+ #define VPDQ 14; /* Varying product dummy*quantitative covariate */
+ #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
+ #define APFD 16; /* Age product * fixed dummy covariate */
+ #define APFQ 17; /* Age product * fixed quantitative covariate */
+ #define APVD 18; /* Age product * varying dummy covariate */
+ #define APVQ 19; /* Age product * varying quantitative covariate */
+ #define FTYPE 1; /* Fixed covariate */
+ #define VTYPE 2; /* Varying covariate (loop in wave) */
+ #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
+ struct kmodel{
+         int maintype; /* main type */
+         int subtype; /* subtype */
+ };
+ struct kmodel modell[NCOVMAX];
  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
  double ftolhess; /**< Tolerance for computing hessian */
- Line 1240  int nbocc(char *s, char occ)
+ Line 1415  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 1913  void powell(double p[], double **xi, int
+ Line 2088  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 1948  void powell(double p[], double **xi, int
+ Line 2123  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 2026  void powell(double p[], double **xi, int
+ Line 2234  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 2072  void powell(double p[], double **xi, int
+ Line 2281  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 2131  void powell(double p[], double **xi, int
+ Line 2340  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 2229  double **prevalim(double **prlim, int nl
+ Line 2440  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 2259  double **prevalim(double **prlim, int nl
+ Line 2470  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 2329  Earliest age to start was %d-%d=%d, ncvl
+ Line 2561  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 2388  Earliest age to start was %d-%d=%d, ncvl
+ Line 2620  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 2421  Earliest age to start was %d-%d=%d, ncvl
+ Line 2685  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 2578  double **pmij(double **ps, double *cov,
+ Line 2842  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 2619  double **bpmij(double **ps, double *cov,
+ Line 2884  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 2719  double **matprod2(double **out, double *
+ Line 2984  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 2754  double ***hpxij(double ***po, int nhstep
+ Line 3019  double ***hpxij(double ***po, int nhstep
        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
        cov[2]=agexact;
        if(nagesqr==1)
-                                 cov[3]= agexact*agexact;
+         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);*/
        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                          /* right multiplication of oldm by the current matrix */
- Line 2917  double func( double *x)
+ Line 3200  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 2944  double func( double *x)
+ Line 3226  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 2966  double func( double *x)
+ Line 3244  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 2988  double func( double *x)
+ Line 3260  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 3004  double func( double *x)
+ Line 3279  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 3246  double func( double *x)
+ Line 3521  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 3269  double funcone( double *x)
+ Line 3545  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 3302  double funcone( double *x)
+ Line 3604  double funcone( double *x)
          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 3347  double funcone( double *x)
+ Line 3652  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 3357  double funcone( double *x)
+ Line 3662  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 3705  double hessij( double x[], double **hess
+ Line 4010  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 3867  void  freqsummary(char fileres[], int ia
+ Line 4172  void  freqsummary(char fileres[], int ia
                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
  {  /* Some frequencies */
-   int i, m, jk, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, k, iv;
    int iind=0, iage=0;
    int mi; /* Effective wave */
    int first;
- Line 3894  void  freqsummary(char fileres[], int ia
+ Line 4199  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 3904  void  freqsummary(char fileres[], int ia
+ Line 4209  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;
+   /* 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 excluding varying and quantitatives */
+   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
      posproptt=0.;
      /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
        scanf("%d", i);*/
- Line 3948  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4253  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;
        posprop[i]=0;
        pospropt[i]=0;
      }
-     for (z1=1; z1<= nqfveff; z1++) {
+     /* for (z1=1; z1<= nqfveff; z1++) {   */
-       meanq[z1]+=0.;
+     /*   meanq[z1]+=0.; */
-       for(m=1;m<=lastpass;m++){
+     /*   for(m=1;m<=lastpass;m++){ */
-         meanqt[m][z1]=0.;
+     /*  meanqt[m][z1]=0.; */
-       }
+     /*   } */
-     }
+     /* } */
      dateintsum=0;
      k2cpt=0;
-     /* For that comination of covariate j1, we count and print the frequencies */
+     /* For that combination of covariate j1, we count and print the frequencies in one pass */
      for (iind=1; iind<=imx; iind++) { /* For each individual iind */
        bool=1;
-       if (nqfveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
-         for (z1=1; z1<= nqfveff; z1++) {
+         if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-           meanq[z1]+=coqvar[Tvar[z1]][iind];
+           /* for (z1=1; z1<= nqfveff; z1++) {   */
-         }
+           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
-         for (z1=1; z1<=ncoveff; z1++) {
+           /* } */
-           /* if(Tvaraff[z1] ==-20){ */
+           for (z1=1; z1<=cptcoveff; z1++) {
-           /*     /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
+             /* if(Tvaraff[z1] ==-20){ */
-           /* }else  if(Tvaraff[z1] ==-10){ */
+             /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-           /*     /\* sumnew+=coqvar[z1][iind]; *\/ */
+             /* }else  if(Tvaraff[z1] ==-10){ */
-           /* }else  */
+             /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
-           if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
+             /* }else  */
-             /* Tests if this individual i responded to j1 (V4=1 V3=0) */
+             if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
-             bool=0;
+               /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
-             /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
+               bool=0;
-                bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
+               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
-                j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-             /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-           }
+               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-         } /* end z1 */
+             } /* Onlyf fixed */
-       } /* cptcovn > 0 */
+           } /* end z1 */
+         } /* cptcovn > 0 */
-       if (bool==1){ /* We selected an individual iin satisfying combination j1 */
+       } /* end any */
+       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
          /* for(m=firstpass; m<=lastpass; m++){ */
-         for(mi=1; mi<wav[iind];mi++){
+         for(mi=1; mi<wav[iind];mi++){ /* For that wave */
            m=mw[mi][iind];
-           /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+           if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-              and mw[mi+1][iind]. dh depends on stepm. */
+             for (z1=1; z1<=cptcoveff; z1++) {
-           agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+               if( Fixed[Tmodelind[z1]]==1){
-           ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-           if(m >=firstpass && m <=lastpass){
+                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
-             k2=anint[m][iind]+(mint[m][iind]/12.);
+                   bool=0;
-             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+               }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-             if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-             if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+                   bool=0;
-             if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                 }
-               prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+               }
-             if (m<lastpass) {
-               /* if(s[m][iind]==4 && s[m+1][iind]==4) */
-               /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
-               if(s[m][iind]==-1)
-                 printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
-               freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
-               /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
-               freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
              }
-           }
+           }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
-           if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
+           /* bool =0 we keep that guy which corresponds to the combination of dummy values */
-             dateintsum=dateintsum+k2;
+           if(bool==1){
-             k2cpt++;
+             /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
-             /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
+                and mw[mi+1][iind]. dh depends on stepm. */
-           }
+             agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
-           /*}*/
+             ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
+             if(m >=firstpass && m <=lastpass){
+               k2=anint[m][iind]+(mint[m][iind]/12.);
+               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+               if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+               if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+               if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+               if (m<lastpass) {
+                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */
+                 /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
+                 if(s[m][iind]==-1)
+                   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
+                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+                 /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
+                 freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
+               }
+             } /* end if between passes */
+             if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
+               dateintsum=dateintsum+k2;
+               k2cpt++;
+               /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
+             }
+           } /* end bool 2 */
          } /* end m */
        } /* end bool */
      } /* end iind = 1 to imx */
      /* prop[s][age] is feeded for any initial and valid live state as well as
         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      pstamp(ficresp);
-     if  (ncoveff>0) {
+     if  (cptcoveff>0){
        fprintf(ficresp, "\n#********** Variable ");
        fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
        fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-       for (z1=1; z1<=ncoveff; z1++){
+       fprintf(ficlog, "\n#********** Variable ");
-         fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       for (z1=1; z1<=cptcoveff; z1++){
-         fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         if(DummyV[z1]){
-         fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresphtm, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficresphtmfr, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         }else{
+           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<=ncoveff; 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 4062  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4390  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 4101  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4429  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 4188  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4516  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 4203  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4531  Title=%s <br>Datafile=%s Firstpass=%d La
  }
  /************ Prevalence ********************/
-  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
+ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
-  {
+ {
-    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
+   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
-       in each health status at the date of interview (if between dateprev1 and dateprev2).
+      in each health status at the date of interview (if between dateprev1 and dateprev2).
-       We still use firstpass and lastpass as another selection.
+      We still use firstpass and lastpass as another selection.
-    */
+   */
-    int i, m, jk, j1, bool, z1,j;
+   int i, m, jk, j1, bool, z1,j, iv;
-    int mi; /* Effective wave */
+   int mi; /* Effective wave */
-    int iage;
+   int iage;
-    double agebegin, ageend;
+   double agebegin, ageend;
-    double **prop;
+   double **prop;
-    double posprop;
+   double posprop;
-    double  y2; /* in fractional years */
+   double  y2; /* in fractional years */
-    int iagemin, iagemax;
+   int iagemin, iagemax;
-    int first; /** to stop verbosity which is redirected to log file */
+   int first; /** to stop verbosity which is redirected to log file */
-    iagemin= (int) agemin;
+   iagemin= (int) agemin;
-    iagemax= (int) agemax;
+   iagemax= (int) agemax;
-    /*pp=vector(1,nlstate);*/
+   /*pp=vector(1,nlstate);*/
-    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
+   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
-    j1=0;
+   j1=0;
-    /*j=cptcoveff;*/
+   /*j=cptcoveff;*/
-    if (cptcovn<1) {j=1;ncodemax[1]=1;}
+   if (cptcovn<1) {j=1;ncodemax[1]=1;}
-    first=1;
+   first=1;
-    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
+   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
-      for (i=1; i<=nlstate; i++)
+     for (i=1; i<=nlstate; i++)
-        for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
+       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
-          prop[i][iage]=0.0;
+         prop[i][iage]=0.0;
+     printf("Prevalence combination of varying and fixed dummies %d\n",j1);
-      for (i=1; i<=imx; i++) { /* Each individual */
+     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
-        bool=1;
+     fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
-        if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-          for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
+     for (i=1; i<=imx; i++) { /* Each individual */
-            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
+       bool=1;
-              bool=0;
+       /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
-        }
+       for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
-        if (bool==1) { /* For this combination of covariates values, this individual fits */
+         m=mw[mi][i];
-          /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
+         /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
-          for(mi=1; mi<wav[i];mi++){
+         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
-            m=mw[mi][i];
+         for (z1=1; z1<=cptcoveff; z1++){
-            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
+           if( Fixed[Tmodelind[z1]]==1){
-            /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
+             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-            if(m >=firstpass && m <=lastpass){
+             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
-              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
+               bool=0;
-              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
+           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
-                if(agev[m][i]==0) agev[m][i]=iagemax+1;
+             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-                if(agev[m][i]==1) agev[m][i]=iagemax+2;
+               bool=0;
-                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
+             }
-                  printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
+         }
-                  exit(1);
+         if(bool==1){ /* Otherwise we skip that wave/person */
-                }
+           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
-                if (s[m][i]>0 && s[m][i]<=nlstate) {
+           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
-                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
+           if(m >=firstpass && m <=lastpass){
-                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
+             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
-                  prop[s[m][i]][iagemax+3] += weight[i];
+             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
-                } /* end valid statuses */
+               if(agev[m][i]==0) agev[m][i]=iagemax+1;
-              } /* end selection of dates */
+               if(agev[m][i]==1) agev[m][i]=iagemax+2;
-            } /* end selection of waves */
+               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
-          } /* end effective waves */
+                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
-        } /* end bool */
+                 exit(1);
-      }
+               }
-      for(i=iagemin; i <= iagemax+3; i++){
+               if (s[m][i]>0 && s[m][i]<=nlstate) {
-        for(jk=1,posprop=0; jk <=nlstate ; jk++) {
+                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
-          posprop += prop[jk][i];
+                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
-        }
+                 prop[s[m][i]][iagemax+3] += weight[i];
+               } /* end valid statuses */
-        for(jk=1; jk <=nlstate ; jk++){
+             } /* end selection of dates */
-          if( i <=  iagemax){
+           } /* end selection of waves */
-            if(posprop>=1.e-5){
+         } /* end bool */
-              probs[i][jk][j1]= prop[jk][i]/posprop;
+       } /* end wave */
-            } else{
+     } /* end individual */
-              if(first==1){
+     for(i=iagemin; i <= iagemax+3; i++){
-                first=0;
+       for(jk=1,posprop=0; jk <=nlstate ; jk++) {
-                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
+         posprop += prop[jk][i];
-              }
+       }
-            }
-          }
+       for(jk=1; jk <=nlstate ; jk++){
-        }/* end jk */
+         if( i <=  iagemax){
-      }/* end i */
+           if(posprop>=1.e-5){
+             probs[i][jk][j1]= prop[jk][i]/posprop;
+           } else{
+             if(first==1){
+               first=0;
+               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
+             }
+           }
+         }
+       }/* end jk */
+     }/* end i */
       /*} *//* end i1 */
-    } /* end j1 */
+   } /* end j1 */
-    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
+   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
-    /*free_vector(pp,1,nlstate);*/
+   /*free_vector(pp,1,nlstate);*/
-    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
+   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
-  }  /* End of prevalence */
+ }  /* End of prevalence */
  /************* Waves Concatenation ***************/
- Line 4304  void  concatwav(int wav[], int **dh, int
+ Line 4642  void  concatwav(int wav[], int **dh, int
       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       and mw[mi+1][i]. dh depends on stepm.
-      */
+   */
    int i=0, mi=0, m=0, mli=0;
    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
- Line 4323  void  concatwav(int wav[], int **dh, int
+ Line 4661  void  concatwav(int wav[], int **dh, int
  /* Treating live states */
    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
      mi=0;  /* First valid wave */
-                 mli=0; /* Last valid wave */
+     mli=0; /* Last valid wave */
      m=firstpass;
      while(s[m][i] <= nlstate){  /* a live state */
-                         if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
+       if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
-                                 mli=m-1;/* mw[++mi][i]=m-1; */
+         mli=m-1;/* mw[++mi][i]=m-1; */
-                         }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
+       }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
-                                 mw[++mi][i]=m;
+         mw[++mi][i]=m;
-                                 mli=m;
+         mli=m;
        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
        if(m < lastpass){ /* m < lastpass, standard case */
-                                 m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
+         m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
        }
-                         else{ /* m >= lastpass, eventual special issue with warning */
+       else{ /* m >= lastpass, eventual special issue with warning */
  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
-                                 break;
+         break;
  #else
-                                 if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
+         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
-                                         if(firsthree == 0){
+           if(firsthree == 0){
-                                                 printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
-                                                 firsthree=1;
+             firsthree=1;
-                                         }
+           }
-                                         fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
+           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
-                                         mw[++mi][i]=m;
+           mw[++mi][i]=m;
-                                         mli=m;
+           mli=m;
-                                 }
+         }
-                                 if(s[m][i]==-2){ /* Vital status is really unknown */
+         if(s[m][i]==-2){ /* Vital status is really unknown */
-                                         nbwarn++;
+           nbwarn++;
-                                         if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
+           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
-                                                 printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
-                                                 fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
+             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
-                                         }
+           }
-                                         break;
+           break;
-                                 }
+         }
-                                 break;
+         break;
  #endif
-                         }/* End m >= lastpass */
+       }/* End m >= lastpass */
      }/* end while */
-         /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
+     /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
      /* After last pass */
  /* Treating death states */
      if (s[m][i] > nlstate){  /* In a death state */
-                         /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
+       /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
-                         /* } */
+       /* } */
        mi++;     /* Death is another wave */
        /* if(mi==0)  never been interviewed correctly before death */
-                         /* Only death is a correct wave */
+       /* Only death is a correct wave */
        mw[mi][i]=m;
      }
  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-                 else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
+     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
        /* m++; */
        /* mi++; */
        /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
        /* mw[mi][i]=m; */
        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
-                                 if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
+         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
-                                         nbwarn++;
+           nbwarn++;
-                                         if(firstfiv==0){
+           if(firstfiv==0){
-                                                 printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
-                                                 firstfiv=1;
+             firstfiv=1;
-                                         }else{
+           }else{
-                                                 fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
+             fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
-                                         }
+           }
-                                 }else{ /* Death occured afer last wave potential bias */
+         }else{ /* Death occured afer last wave potential bias */
-                                         nberr++;
+           nberr++;
-                                         if(firstwo==0){
+           if(firstwo==0){
-                                                 printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
-                                                 firstwo=1;
+             firstwo=1;
-                                         }
+           }
-                                         fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
-                                 }
+         }
        }else{ /* end date of interview is known */
-                                 /* death is known but not confirmed by death status at any wave */
+         /* death is known but not confirmed by death status at any wave */
-                                 if(firstfour==0){
+         if(firstfour==0){
-                                         printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
-                                         firstfour=1;
+           firstfour=1;
-                                 }
+         }
-                                 fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
        }
      } /* end if date of death is known */
  #endif
- Line 4410  void  concatwav(int wav[], int **dh, int
+ Line 4748  void  concatwav(int wav[], int **dh, int
      if(mi==0){
        nbwarn++;
        if(first==0){
-                                 printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
-                                 first=1;
+         first=1;
        }
        if(first==1){
-                                 fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
+         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
        }
      } /* end mi==0 */
    } /* End individuals */
- Line 4424  void  concatwav(int wav[], int **dh, int
+ Line 4762  void  concatwav(int wav[], int **dh, int
    for(i=1; i<=imx; i++){
      for(mi=1; mi<wav[i];mi++){
        if (stepm <=0)
-                                 dh[mi][i]=1;
+         dh[mi][i]=1;
        else{
-                                 if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
+         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
-                                         if (agedc[i] < 2*AGESUP) {
+           if (agedc[i] < 2*AGESUP) {
-                                                 j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
-                                                 if(j==0) j=1;  /* Survives at least one month after exam */
+             if(j==0) j=1;  /* Survives at least one month after exam */
-                                                 else if(j<0){
+             else if(j<0){
-                                                         nberr++;
+               nberr++;
-                                                         printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                                         j=1; /* Temporary Dangerous patch */
+               j=1; /* Temporary Dangerous patch */
-                                                         printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-                                                         fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                                         fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
+               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
-                                                 }
+             }
-                                                 k=k+1;
+             k=k+1;
-                                                 if (j >= jmax){
+             if (j >= jmax){
-                                                         jmax=j;
+               jmax=j;
-                                                         ijmax=i;
+               ijmax=i;
-                                                 }
+             }
-                                                 if (j <= jmin){
+             if (j <= jmin){
-                                                         jmin=j;
+               jmin=j;
-                                                         ijmin=i;
+               ijmin=i;
-                                                 }
+             }
-                                                 sum=sum+j;
+             sum=sum+j;
-                                                 /*if (j<0) printf("j=%d num=%d \n",j,i);*/
+             /*if (j<0) printf("j=%d num=%d \n",j,i);*/
-                                                 /*        printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
+             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
-                                         }
+           }
-                                 }
+         }
-                                 else{
+         else{
-                                         j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
-                                         k=k+1;
+           k=k+1;
-                                         if (j >= jmax) {
+           if (j >= jmax) {
-                                                 jmax=j;
+             jmax=j;
-                                                 ijmax=i;
+             ijmax=i;
-                                         }
+           }
-                                         else if (j <= jmin){
+           else if (j <= jmin){
-                                                 jmin=j;
+             jmin=j;
-                                                 ijmin=i;
+             ijmin=i;
-                                         }
+           }
-                                         /*          if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
-                                         /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
+           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
-                                         if(j<0){
+           if(j<0){
-                                                 nberr++;
+             nberr++;
-                                                 printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                                 fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
+             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
-                                         }
+           }
-                                         sum=sum+j;
+           sum=sum+j;
-                                 }
+         }
-                                 jk= j/stepm;
+         jk= j/stepm;
-                                 jl= j -jk*stepm;
+         jl= j -jk*stepm;
-                                 ju= j -(jk+1)*stepm;
+         ju= j -(jk+1)*stepm;
-                                 if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
+         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
-                                         if(jl==0){
+           if(jl==0){
-                                                 dh[mi][i]=jk;
+             dh[mi][i]=jk;
-                                                 bh[mi][i]=0;
+             bh[mi][i]=0;
-                                         }else{ /* We want a negative bias in order to only have interpolation ie
+           }else{ /* We want a negative bias in order to only have interpolation ie
-                                                                         * to avoid the price of an extra matrix product in likelihood */
+                   * to avoid the price of an extra matrix product in likelihood */
-                                                 dh[mi][i]=jk+1;
+             dh[mi][i]=jk+1;
-                                                 bh[mi][i]=ju;
+             bh[mi][i]=ju;
-                                         }
+           }
-                                 }else{
+         }else{
-                                         if(jl <= -ju){
+           if(jl <= -ju){
-                                                 dh[mi][i]=jk;
+             dh[mi][i]=jk;
-                                                 bh[mi][i]=jl;   /* bias is positive if real duration
+             bh[mi][i]=jl;       /* bias is positive if real duration
-                                                                                                          * is higher than the multiple of stepm and negative otherwise.
+                                  * is higher than the multiple of stepm and negative otherwise.
-                                                                                                          */
+                                  */
-                                         }
+           }
-                                         else{
+           else{
-                                                 dh[mi][i]=jk+1;
+             dh[mi][i]=jk+1;
-                                                 bh[mi][i]=ju;
+             bh[mi][i]=ju;
-                                         }
+           }
-                                         if(dh[mi][i]==0){
+           if(dh[mi][i]==0){
-                                                 dh[mi][i]=1; /* At least one step */
+             dh[mi][i]=1; /* At least one step */
-                                                 bh[mi][i]=ju; /* At least one step */
+             bh[mi][i]=ju; /* At least one step */
-                                                 /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
+             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
-                                         }
+           }
-                                 } /* end if mle */
+         } /* end if mle */
        }
      } /* end wave */
    }
    jmean=sum/k;
    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
-  }
+ }
  /*********** Tricode ****************************/
   void tricode(int *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 */
-   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
-   for (j=1; j<=cptcovsnq; j++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-     for (k=-1; k < maxncov; k++) Ndum[k]=0;
-     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
-                                 modality of this covariate Vj*/
-       switch(Typevar[j]) {
-       case 1: /* A real fixed dummy covariate */
-         ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-                                       * If product of Vn*Vm, still boolean *:
-                                       * 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   */
-         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-            modality of the nth covariate of individual i. */
-         if (ij > modmaxcovj)
-           modmaxcovj=ij;
-         else if (ij < modmincovj)
-           modmincovj=ij;
-         if ((ij < -1) && (ij > NCOVMAX)){
-           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-           exit(1);
-         }else
-           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 */
-         /*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
-            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-            female ies 1, then modmaxcovj=1.*/
-         break;
-       case 2:
-         break;
-       }
+    /* Loop on covariates without age and products and no quantitative variable */
-     } /* end for loop on individuals i */
+    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
-     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
-     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
+      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
-     cptcode=modmaxcovj;
+      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
-     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
+        switch(Fixed[k]) {
-     /*for (i=0; i<=cptcode; i++) {*/
+        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
-     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
+          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*/
-       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+            ij=(int)(covar[Tvar[k]][i]);
-       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
+            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
-       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
+             * If product of Vn*Vm, still boolean *:
-         if( k != -1){
+             * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
-           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
+             * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
-                              covariate for which somebody answered excluding
+            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
-                              undefined. Usually 2: 0 and 1. */
+               modality of the nth covariate of individual i. */
-         }
+            if (ij > modmaxcovj)
-         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
+              modmaxcovj=ij;
-                                 covariate for which somebody answered including
+            else if (ij < modmincovj)
-                                 undefined. Usually 3: -1, 0 and 1. */
+              modmincovj=ij;
-       }
+            if ((ij < -1) && (ij > NCOVMAX)){
-       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
+              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
-        * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
+              exit(1);
-     } /* Ndum[-1] number of undefined modalities */
+            }else
+              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
-     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
+            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
-     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
+            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
-        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
+            /* getting the maximum value of the modality of the covariate
-        modmincovj=3; modmaxcovj = 7;
+               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
-        There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
+               female ies 1, then modmaxcovj=1.
-        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.
+          } /* end for loop on individuals i */
-        nbcode[Tvar[j]][ij]=k;
+          printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-        nbcode[Tvar[j]][1]=0;
+          fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
-        nbcode[Tvar[j]][2]=1;
+          cptcode=modmaxcovj;
-        nbcode[Tvar[j]][3]=2;
+          /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
-        To be continued (not working yet).
+          /*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 */
-     ij=0; /* ij is similar to i but can jump over null modalities */
+            printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-     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*/
+            fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
-       if (Ndum[i] == 0) { /* If nobody responded to this modality k */
+            if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
-         break;
+              if( j != -1){
-       }
+                ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
-       ij++;
+                                   covariate for which somebody answered excluding
-       nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
+                                   undefined. Usually 2: 0 and 1. */
-       cptcode = ij; /* New max modality for covar j */
+              }
-     } /* end of loop on modality i=-1 to 1 or more */
+              ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
+                                      covariate for which somebody answered including
-     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
+                                      undefined. Usually 3: -1, 0 and 1. */
-     /*  /\*recode from 0 *\/ */
+            }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
-     /*                               k is a modality. If we have model=V1+V1*sex  */
+                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
-     /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+          } /* Ndum[-1] number of undefined modalities */
-     /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
-     /*  } */
+          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
-     /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
+          /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
-     /*  if (ij > ncodemax[j]) { */
+          /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
-     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+          /* modmincovj=3; modmaxcovj = 7; */
-     /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+          /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
-     /*    break; */
+          /* 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.*/
-     /*   }  /\* end of loop on modality k *\/ */
+          /* nbcode[Tvar[j]][ij]=k; */
-   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+          /* nbcode[Tvar[j]][1]=0; */
+          /* nbcode[Tvar[j]][2]=1; */
-   for (k=-1; k< maxncov; k++) Ndum[k]=0;
+          /* nbcode[Tvar[j]][3]=2; */
+          /* To be continued (not working yet). */
-   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
+          ij=0; /* ij is similar to i but can jump over null 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=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
-     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
+            if (Ndum[i] == 0) { /* If nobody responded to this modality k */
-     Ndum[ij]++; /* Might be supersed V1 + V1*age */
+              break;
-   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+            }
+            ij++;
-   ij=0;
+            nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
-   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+            cptcode = ij; /* New max modality for covar j */
-     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+          } /* end of loop on modality i=-1 to 1 or more */
-     if((Ndum[i]!=0) && (i<=ncovcol)){
+          break;
-       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        case 1: /* Testing on varying covariate, could be simple and
-       Tvaraff[++ij]=i; /*For printing (unclear) */
+                 * should look at waves or product of fixed *
-     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){
+                 * varying. No time to test -1, assuming 0 and 1 only */
-       Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */
+          ij=0;
-     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){
+          for(i=0; i<=1;i++){
-       Tvaraff[++ij]=i; /*For printing (unclear) */
+            nbcode[Tvar[k]][++ij]=i;
-     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){
+          }
-       Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */
+          break;
-     }
+        default:
-   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+          break;
-   /* ij--; */
+        } /* end switch */
-   /* cptcoveff=ij; /\*Number of total covariates*\/ */
+      } /* end dummy test */
-   *cptcov=ij; /*Number of total real effective covariates: effective
-                * because they can be excluded from the model and real
+      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-                * if in the model but excluded because missing values*/
+      /*         /\*recode from 0 *\/ */
- }
+      /*                                      k is a modality. If we have model=V1+V1*sex  */
+      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
+      /*                                   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]) { */
+      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
+      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
+      /*           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*/
+    for (k=-1; k< maxncov; k++) Ndum[k]=0;
+    /* Look at fixed dummy (single or product) covariates to check empty modalities */
+    for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
+      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
+      ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
+      Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
+      /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
+    } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
+    ij=0;
+    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
+    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
+      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
+      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
+      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
+        /* If product not in single variable we don't print results */
+        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
+        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
+        Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
+        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
+        TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
+        if(Fixed[k]!=0)
+          anyvaryingduminmodel=1;
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
+        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
+        /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
+        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
+        /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
+      }
+    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
+    /* ij--; */
+    /* cptcoveff=ij; /\*Number of total covariates*\/ */
+    *cptcov=ij; /*Number of total real effective covariates: effective
+                 * because they can be excluded from the model and real
+                 * if in the model but excluded because missing values, but how to get k from ij?*/
+    for(j=ij+1; j<= cptcovt; j++){
+      Tvaraff[j]=0;
+      Tmodelind[j]=0;
+    }
+    for(j=ntveff+1; j<= cptcovt; j++){
+      TmodelInvind[j]=0;
+    }
+    /* To be sorted */
+    ;
+  }
  /*********** 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 4668  void evsij(double ***eij, double x[], in
+ Line 5032  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 4731  void evsij(double ***eij, double x[], in
+ Line 5095  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 4766  void evsij(double ***eij, double x[], in
+ Line 5130  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 4879  void cvevsij(double ***eij, double x[],
+ Line 5243  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 4921  void cvevsij(double ***eij, double x[],
+ Line 5285  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 4976  void cvevsij(double ***eij, double x[],
+ Line 5340  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 5033  void cvevsij(double ***eij, double x[],
+ Line 5397  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 5102  void cvevsij(double ***eij, double x[],
+ Line 5474  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 5114  void cvevsij(double ***eij, double x[],
+ Line 5486  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 5134  void cvevsij(double ***eij, double x[],
+ Line 5506  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 5146  void cvevsij(double ***eij, double x[],
+ Line 5518  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 5211  void cvevsij(double ***eij, double x[],
+ Line 5583  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 5227  void cvevsij(double ***eij, double x[],
+ Line 5599  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 5290  void cvevsij(double ***eij, double x[],
+ Line 5662  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 5306  void cvevsij(double ***eij, double x[],
+ Line 5678  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 5333  void cvevsij(double ***eij, double x[],
+ Line 5707  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 5343  void cvevsij(double ***eij, double x[],
+ Line 5717  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 5392  void cvevsij(double ***eij, double x[],
+ Line 5766  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 5753  void printinghtml(char fileresu[], char
+ Line 6129  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 5792  void printinghtml(char fileresu[], char
+ Line 6170  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 5810  void printinghtml(char fileresu[], char
+ Line 6200  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 5912  See page 'Matrix of variance-covariance
+ Line 6302  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 5928  See page 'Matrix of variance-covariance
+ Line 6327  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 5948  void printinggnuplot(char fileresu[], ch
+ Line 6348  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 5996  void printinggnuplot(char fileresu[], ch
+ Line 6397  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)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-+(cpt-1),  cpt );
+               vlv= nbcode[Tvaraff[k]][lv];
-             }else{
-               fprintf(ficgp,"$%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 */
-       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;
-     }
-     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);
+   /*2 eme*/
+   for (k1=1; k1<= m ; k1 ++){
+     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+       if(TKresult[nres]!= k1)
+         continue;
+       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6133  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 6494  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 */
+       if(TKresult[nres]!= 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);
+         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           vlv= nbcode[Tvaraff[k]][lv];
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+         }
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+         }
+         fprintf(ficgp,"\n#\n");
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+           continue;
+         }
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"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 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 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-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),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 (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           if(j==1)
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
+           else
+             fprintf(ficgp,", '' ");
+           l=(nlstate+ndeath)*(cpt-1) +j;
+           fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
+           /* for (i=2; i<= nlstate+ndeath ; i ++) */
+           /*   fprintf(ficgp,"+$%d",k+l+i-1); */
+           fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
+         } /* nlstate */
+         fprintf(ficgp,", '' ");
+         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
+         for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
+           l=(nlstate+ndeath)*(cpt-1) +j;
+           if(j < nlstate)
+             fprintf(ficgp,"$%d +",k+l);
+           else
+             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
+         }
+         fprintf(ficgp,"\nset out\n");
+       } /* end cpt state*/
+     } /* end covariate */
+   } /* end nres */
+ /* 6eme */
+   /* CV preval stable (period) for each covariate */
+   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination 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# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
+       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6175  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 6705  plot [%.f:%.f] \"%s\" every :::%d::%d u
          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,"LIJ_"),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 to be alive\" \n\
+       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                                                                                                                                                                                                                                           \
+       k=3; /* Offset */
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
-       k=3;
        for (i=1; i<= nlstate ; i ++){
-         if(i==1){
+         if(i==1)
            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-         }else{
+         else
            fprintf(ficgp,", '' ");
-         }
          l=(nlstate+ndeath)*(i-1)+1;
          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
-         for (j=2; j<= nlstate+ndeath ; j ++)
+         for (j=2; j<= nlstate ; j ++)
            fprintf(ficgp,"+$%d",k+l+j-1);
-         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
+         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-       } /* nlstate */
-       fprintf(ficgp,"\nset out\n");
-     } /* end cpt state*/
-   } /* end covariate */
- /* 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 (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);
-       }
-       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,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
- set ter svg size 640, 480\n                                                                                                                                                                                     \
- unset log y\n                                                                                                                                                                                                                                           \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
-       k=3;
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-                                 if(j==1)
-                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
-                                 else
-                                         fprintf(ficgp,", '' ");
-                                 l=(nlstate+ndeath)*(cpt-1) +j;
-                                 fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
-                                 /* for (i=2; i<= nlstate+ndeath ; i ++) */
-                                 /*   fprintf(ficgp,"+$%d",k+l+i-1); */
-                                 fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
        } /* nlstate */
-       fprintf(ficgp,", '' ");
-       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
-       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
-                                 l=(nlstate+ndeath)*(cpt-1) +j;
-                                 if(j < nlstate)
-                                         fprintf(ficgp,"$%d +",k+l);
-                                 else
-                                         fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
-       }
        fprintf(ficgp,"\nset out\n");
      } /* end cpt state*/
    } /* end covariate */
- /* 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 (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);
-       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;
-       }
-       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
-       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
- set ter svg size 640, 480\n                                                                                                                                                                              \
- unset log y\n                                                                                                                                                                                                                                    \
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
-       k=3; /* Offset */
-       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/($%d",k1,k+l+(cpt-1),k+l);
-                                 for (j=2; j<= nlstate ; j ++)
-                                         fprintf(ficgp,"+$%d",k+l+j-1);
-                                 fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
-       } /* nlstate */
-       fprintf(ficgp,"\nset out\n");
-     } /* end cpt state*/
-   } /* end covariate */
  /* 7eme */
    if(backcast == 1){
      /* CV back preval stable (period) for each covariate */
-     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (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);
+         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 */
+         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 */
+           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(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-                                         vlv= nbcode[Tvaraff[k]][lv];
+           vlv= nbcode[Tvaraff[k]][lv];
-                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-                                 }
+         }
-                                 fprintf(ficgp,"\n#\n");
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-                                 if(invalidvarcomb[k1]){
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         }
-                                         continue;
+         fprintf(ficgp,"\n#\n");
-                                 }
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
+           continue;
-                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
+         }
- set ter svg size 640, 480\n                                                                                                                                                                                     \
- unset log y\n                                                                                                                                                                                                                                           \
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-                                 k=3; /* Offset */
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
-                                 for (i=1; i<= nlstate ; i ++){
+         k=3; /* Offset */
-                                         if(i==1)
+         for (i=1; i<= nlstate ; i ++){
-                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
+           if(i==1)
-                                         else
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
-                                                 fprintf(ficgp,", '' ");
+           else
-                                         /* l=(nlstate+ndeath)*(i-1)+1; */
+             fprintf(ficgp,", '' ");
-                                         l=(nlstate+ndeath)*(cpt-1)+1;
+           /* l=(nlstate+ndeath)*(i-1)+1; */
-                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
+           l=(nlstate+ndeath)*(cpt-1)+1;
-                                         /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
-                                         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
-                                         /* for (j=2; j<= nlstate ; j ++) */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
-                                         /*      fprintf(ficgp,"+$%d",k+l+j-1); */
+           /* for (j=2; j<= nlstate ; j ++) */
-                                         /*      /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
+           /*    fprintf(ficgp,"+$%d",k+l+j-1); */
-                                         fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
-                                 } /* nlstate */
+           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
-                                 fprintf(ficgp,"\nset out\n");
+         } /* nlstate */
+         fprintf(ficgp,"\nset out\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if backcast */
- Line 6345  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6788  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);
+         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  */
+         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
-                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
-                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-                                         vlv= nbcode[Tvaraff[k]][lv];
+           vlv= nbcode[Tvaraff[k]][lv];
-                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
-                                 }
+         }
-                                 fprintf(ficgp,"\n#\n");
+         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-                                 if(invalidvarcomb[k1]){
+           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+         }
-                                         continue;
+         fprintf(ficgp,"\n#\n");
-                                 }
+         if(invalidvarcomb[k1]){
+           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
-                                 fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
+           continue;
-                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
+         }
-                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
- set ter svg size 640, 480\n                                                                                                                                                                                     \
+         fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
- unset log y\n                                                                                                                                                                                                                                           \
+         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
- plot [%.f:%.f]  ", ageminpar, agemaxpar);
+         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
-                                 for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
+ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
-                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
-                                         /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-                                         /*# 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 */
-                                         /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-                                         if(i==1){
+           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
+           if(i==1){
-                                         }else{
+             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
-                                                 fprintf(ficgp,",\\\n '' ");
+           }else{
-                                         }
+             fprintf(ficgp,",\\\n '' ");
-                                         if(cptcoveff ==0){ /* No covariate */
+           }
-                                                 ioffset=2; /* Age is in 2 */
+           if(cptcoveff ==0){ /* No covariate */
-                                                 /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             ioffset=2; /* Age is in 2 */
-                                                 /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
-                                                 /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
-                                                 /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
+             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
-                                                 fprintf(ficgp," u %d:(", ioffset);
+             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
-                                                 if(i==nlstate+1)
+             fprintf(ficgp," u %d:(", ioffset);
-                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",                    \
+             if(i==nlstate+1)
-                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+               fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \
-                                                 else
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-                                                         fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
+             else
-                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
-                                         }else{ /* more than 2 covariates */
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-                                                 if(cptcoveff ==1){
+           }else{ /* more than 2 covariates */
-                                                         ioffset=4; /* Age is in 4 */
+             if(cptcoveff ==1){
-                                                 }else{
+               ioffset=4; /* Age is in 4 */
-                                                         ioffset=6; /* Age is in 6 */
+             }else{
-                                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+               ioffset=6; /* Age is in 6 */
-                                                         /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
+               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
-                                                 }
+               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
-                                                 fprintf(ficgp," u %d:(",ioffset);
+             }
-                                                 kl=0;
+             fprintf(ficgp," u %d:(",ioffset);
-                                                 strcpy(gplotcondition,"(");
+             kl=0;
-                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
+             strcpy(gplotcondition,"(");
-                                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
-                                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
+               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
-                                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
+               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
-                                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
+               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
-                                                         vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
+               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
-                                                         kl++;
+               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
-                                                         sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+               kl++;
-                                                         kl++;
+               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
-                                                         if(k <cptcoveff && cptcoveff>1)
+               kl++;
-                                                                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
+               if(k <cptcoveff && cptcoveff>1)
-                                                 }
+                 sprintf(gplotcondition+strlen(gplotcondition)," && ");
-                                                 strcpy(gplotcondition+strlen(gplotcondition),")");
+             }
-                                                 /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+             strcpy(gplotcondition+strlen(gplotcondition),")");
-                                                 /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
-                                                 /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+             /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
-                                                 /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
-                                                 if(i==nlstate+1){
+             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
-                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
+             if(i==nlstate+1){
-                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
-                                                 }else{
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
-                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
+             }else{
-                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
+               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
-                                                 }
+                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
-                                         } /* end if covariate */
+             }
-                                 } /* nlstate */
+           } /* end if covariate */
-                                 fprintf(ficgp,"\nset out\n");
+         } /* nlstate */
+         fprintf(ficgp,"\nset out\n");
        } /* end cpt state*/
      } /* end covariate */
    } /* End if prevfcast */
-   /* proba elementaires */
+   /* 9eme writing MLE parameters */
-   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
+   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
    for(i=1,jk=1; i <=nlstate; i++){
      fprintf(ficgp,"# initial state %d\n",i);
      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i) {
-                                 fprintf(ficgp,"#   current state %d\n",k);
+         fprintf(ficgp,"#   current state %d\n",k);
-                                 for(j=1; j <=ncovmodel; j++){
+         for(j=1; j <=ncovmodel; j++){
-                                         fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
+           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
-                                         jk++;
+           jk++;
-                                 }
+         }
-                                 fprintf(ficgp,"\n");
+         fprintf(ficgp,"\n");
        }
      }
    }
    fprintf(ficgp,"##############\n#\n");
    /*goto avoid;*/
-   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
+   /* 10eme Graphics of probabilities or incidences using written MLE parameters */
+   fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
- Line 6467  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6915  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 6511  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 6968  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 */
                fprintf(ficgp," (1.");
            }
            if(ng != 1){
              fprintf(ficgp,")/(1");
              for(k1=1; k1 <=nlstate; k1++){
                if(nagesqr==0)
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
- Line 6540  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7029  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 6693  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7182  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 6732  plot [%.f:%.f]  ", ageminpar, agemaxpar)
+ Line 7221  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 6760  void prevforecast(char fileres[], double
+ Line 7249  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 6784  void prevforecast(char fileres[], double
+ Line 7273  void prevforecast(char fileres[], double
    if(jprojmean==0) jprojmean=1;
    if(mprojmean==0) jprojmean=1;
-   i1=cptcoveff;
+   i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
    fprintf(ficresf,"#****** Routine prevforecast **\n");
  /*            if (h==(int)(YEARM*yearp)){ */
-   for(cptcov=1, k=0;cptcov<=i1;cptcov++){
+   for(nres=1; nres <= nresult; nres++) /* For each resultline */
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+   for(k=1; k<=i1;k++){
-       k=k+1;
+     if(TKresult[nres]!= k)
-       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
+       continue;
-       for(j=1;j<=cptcoveff;j++) {
+     if(invalidvarcomb[k]){
-                                 fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       printf("\nCombination (%d) projection ignored because no cases \n",k);
-       }
+       continue;
-       fprintf(ficresf," yearproj age");
+     }
-       for(j=1; j<=nlstate+ndeath;j++){
+     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
-                                 for(i=1; i<=nlstate;i++)
+     for(j=1;j<=cptcoveff;j++) {
-           fprintf(ficresf," p%d%d",i,j);
+       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                                 fprintf(ficresf," wp.%d",j);
+     }
-       }
+     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-                                 fprintf(ficresf,"\n");
+     }
-                                 fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
+     fprintf(ficresf," yearproj age");
-                                 for (agec=fage; agec>=(ageminpar-1); agec--){
+     for(j=1; j<=nlstate+ndeath;j++){
-                                         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+       for(i=1; i<=nlstate;i++)
-                                         nhstepm = nhstepm/hstepm;
+         fprintf(ficresf," p%d%d",i,j);
-                                         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       fprintf(ficresf," wp.%d",j);
-                                         oldm=oldms;savm=savms;
+     }
-                                         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
+     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
+       fprintf(ficresf,"\n");
-                                         for (h=0; h<=nhstepm; h++){
+       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-                                                 if (h*hstepm/YEARM*stepm ==yearp) {
+       for (agec=fage; agec>=(ageminpar-1); agec--){
-               fprintf(ficresf,"\n");
+         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
-               for(j=1;j<=cptcoveff;j++)
+         nhstepm = nhstepm/hstepm;
-                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-                                                         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+         oldm=oldms;savm=savms;
-                                                 }
+         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
-                                                 for(j=1; j<=nlstate+ndeath;j++) {
-                                                         ppij=0.;
+         for (h=0; h<=nhstepm; h++){
-                                                         for(i=1; i<=nlstate;i++) {
+           if (h*hstepm/YEARM*stepm ==yearp) {
-                                                                 if (mobilav==1)
+             fprintf(ficresf,"\n");
-                                                                         ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
+             for(j=1;j<=cptcoveff;j++)
-                                                                 else {
+               fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                                                                         ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
+             fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
-                                                                 }
+           }
-                                                                 if (h*hstepm/YEARM*stepm== yearp) {
+           for(j=1; j<=nlstate+ndeath;j++) {
-                                                                         fprintf(ficresf," %.3f", p3mat[i][j][h]);
+             ppij=0.;
-                                                                 }
+             for(i=1; i<=nlstate;i++) {
-                                                         } /* end i */
+               if (mobilav==1)
-                                                         if (h*hstepm/YEARM*stepm==yearp) {
+                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
-                                                                 fprintf(ficresf," %.3f", ppij);
+               else {
-                                                         }
+                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
-                                                 }/* end j */
+               }
-                                         } /* end h */
+               if (h*hstepm/YEARM*stepm== yearp) {
-                                         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+                 fprintf(ficresf," %.3f", p3mat[i][j][h]);
-                                 } /* end agec */
+               }
-       } /* end yearp */
+             } /* end i */
-     } /* end cptcod */
+             if (h*hstepm/YEARM*stepm==yearp) {
-   } /* end  cptcov */
+               fprintf(ficresf," %.3f", ppij);
+             }
+           }/* end j */
+         } /* end h */
+         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+       } /* end agec */
+     } /* end yearp */
+   } /* end  k */
    fclose(ficresf);
    printf("End of Computing forecasting \n");
- Line 6982  void prevforecast(char fileres[], double
+ Line 7478  void prevforecast(char fileres[], double
  /* } */
  /************** Forecasting *****not tested NB*************/
- void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+ /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
-   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+ /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
-   int *popage;
+ /*   int *popage; */
-   double calagedatem, agelim, kk1, kk2;
+ /*   double calagedatem, agelim, kk1, kk2; */
-   double *popeffectif,*popcount;
+ /*   double *popeffectif,*popcount; */
-   double ***p3mat,***tabpop,***tabpopprev;
+ /*   double ***p3mat,***tabpop,***tabpopprev; */
-   /* double ***mobaverage; */
+ /*   /\* double ***mobaverage; *\/ */
-   char filerespop[FILENAMELENGTH];
+ /*   char filerespop[FILENAMELENGTH]; */
-   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   agelim=AGESUP;
+ /*   agelim=AGESUP; */
-   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+ /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
-   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
-   strcpy(filerespop,"POP_");
+ /*   strcpy(filerespop,"POP_");  */
-   strcat(filerespop,fileresu);
+ /*   strcat(filerespop,fileresu); */
-   if((ficrespop=fopen(filerespop,"w"))==NULL) {
+ /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
-     printf("Problem with forecast resultfile: %s\n", filerespop);
+ /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
-     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
-   }
+ /*   } */
-   printf("Computing forecasting: result on file '%s' \n", filerespop);
+ /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
-   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+ /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
-   if (cptcoveff==0) ncodemax[cptcoveff]=1;
+ /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
-   /* if (mobilav!=0) { */
+ /*   /\* if (mobilav!=0) { *\/ */
-   /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
-   /*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
+ /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
-   /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
+ /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-   /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
+ /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
-   /*   } */
+ /*   /\*   } *\/ */
-   /* } */
+ /*   /\* } *\/ */
-   stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
-   if (stepm<=12) stepsize=1;
+ /*   if (stepm<=12) stepsize=1; */
-   agelim=AGESUP;
+ /*   agelim=AGESUP; */
-   hstepm=1;
+ /*   hstepm=1; */
-   hstepm=hstepm/stepm;
+ /*   hstepm=hstepm/stepm;  */
-   if (popforecast==1) {
+ /*   if (popforecast==1) { */
-     if((ficpop=fopen(popfile,"r"))==NULL) {
+ /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
-       printf("Problem with population file : %s\n",popfile);exit(0);
+ /*       printf("Problem with population file : %s\n",popfile);exit(0); */
-       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
-     }
+ /*     }  */
-     popage=ivector(0,AGESUP);
+ /*     popage=ivector(0,AGESUP); */
-     popeffectif=vector(0,AGESUP);
+ /*     popeffectif=vector(0,AGESUP); */
-     popcount=vector(0,AGESUP);
+ /*     popcount=vector(0,AGESUP); */
-     i=1;
+ /*     i=1;    */
-     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+ /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
-     imx=i;
+ /*     imx=i; */
-     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
-   }
+ /*   } */
-   for(cptcov=1,k=0;cptcov<=i2;cptcov++){
+ /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
-     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
-       k=k+1;
+ /*       k=k+1; */
-       fprintf(ficrespop,"\n#******");
+ /*       fprintf(ficrespop,"\n#******"); */
-       for(j=1;j<=cptcoveff;j++) {
+ /*       for(j=1;j<=cptcoveff;j++) { */
-         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
-       }
+ /*       } */
-       fprintf(ficrespop,"******\n");
+ /*       fprintf(ficrespop,"******\n"); */
-       fprintf(ficrespop,"# Age");
+ /*       fprintf(ficrespop,"# Age"); */
-       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+ /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
-       if (popforecast==1)  fprintf(ficrespop," [Population]");
+ /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
-       for (cpt=0; cpt<=0;cpt++) {
+ /*       for (cpt=0; cpt<=0;cpt++) {  */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
-           nhstepm = nhstepm/hstepm;
+ /*        nhstepm = nhstepm/hstepm;  */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-           oldm=oldms;savm=savms;
+ /*        oldm=oldms;savm=savms; */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-           for (h=0; h<=nhstepm; h++){
+ /*        for (h=0; h<=nhstepm; h++){ */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
-               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
-             }
+ /*          }  */
-             for(j=1; j<=nlstate+ndeath;j++) {
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
-               kk1=0.;kk2=0;
+ /*            kk1=0.;kk2=0; */
-               for(i=1; i<=nlstate;i++) {
+ /*            for(i=1; i<=nlstate;i++) {               */
-                 if (mobilav==1)
+ /*              if (mobilav==1)  */
-                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+ /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
-                 else {
+ /*              else { */
-                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+ /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
-                 }
+ /*              } */
-               }
+ /*            } */
-               if (h==(int)(calagedatem+12*cpt)){
+ /*            if (h==(int)(calagedatem+12*cpt)){ */
-                 tabpop[(int)(agedeb)][j][cptcod]=kk1;
+ /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
-                 /*fprintf(ficrespop," %.3f", kk1);
+ /*              /\*fprintf(ficrespop," %.3f", kk1); */
-                   if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+ /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
-               }
+ /*            } */
-             }
+ /*          } */
-             for(i=1; i<=nlstate;i++){
+ /*          for(i=1; i<=nlstate;i++){ */
-               kk1=0.;
+ /*            kk1=0.; */
-               for(j=1; j<=nlstate;j++){
+ /*            for(j=1; j<=nlstate;j++){ */
-                 kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+ /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
-               }
+ /*            } */
-               tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
+ /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
-             }
+ /*          } */
-             if (h==(int)(calagedatem+12*cpt))
+ /*          if (h==(int)(calagedatem+12*cpt)) */
-               for(j=1; j<=nlstate;j++)
+ /*            for(j=1; j<=nlstate;j++)  */
-                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+ /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
-           }
+ /*        } */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-         }
+ /*      } */
-       }
+ /*       } */
-       /******/
+ /*       /\******\/ */
-       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+ /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
-         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+ /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
-         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
+ /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
-           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ /*        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  */
-           nhstepm = nhstepm/hstepm;
+ /*        nhstepm = nhstepm/hstepm;  */
-           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-           oldm=oldms;savm=savms;
+ /*        oldm=oldms;savm=savms; */
-           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
-           for (h=0; h<=nhstepm; h++){
+ /*        for (h=0; h<=nhstepm; h++){ */
-             if (h==(int) (calagedatem+YEARM*cpt)) {
+ /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
-               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
-             }
+ /*          }  */
-             for(j=1; j<=nlstate+ndeath;j++) {
+ /*          for(j=1; j<=nlstate+ndeath;j++) { */
-               kk1=0.;kk2=0;
+ /*            kk1=0.;kk2=0; */
-               for(i=1; i<=nlstate;i++) {
+ /*            for(i=1; i<=nlstate;i++) {               */
-                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
-               }
+ /*            } */
-               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+ /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
-             }
+ /*          } */
-           }
+ /*        } */
-           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
-         }
+ /*      } */
-       }
+ /*       } */
-     }
+ /*     }  */
-   }
+ /*   } */
-   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
+ /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
-   if (popforecast==1) {
+ /*   if (popforecast==1) { */
-     free_ivector(popage,0,AGESUP);
+ /*     free_ivector(popage,0,AGESUP); */
-     free_vector(popeffectif,0,AGESUP);
+ /*     free_vector(popeffectif,0,AGESUP); */
-     free_vector(popcount,0,AGESUP);
+ /*     free_vector(popcount,0,AGESUP); */
-   }
+ /*   } */
-   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
-   fclose(ficrespop);
+ /*   fclose(ficrespop); */
- } /* End of popforecast */
+ /* } /\* End of popforecast *\/ */
  int fileappend(FILE *fichier, char *optionfich)
  {
- Line 7407  int readdata(char datafile[], int firsto
+ Line 7903  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 7448  int readdata(char datafile[], int firsto
+ Line 7966  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 7467  int readdata(char datafile[], int firsto
+ Line 7986  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 7680  int readdata(char datafile[], int firsto
+ Line 8200  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 7704  int decodemodel ( char model[], int last
+ Line 8347  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;
+   int  j1, k1, k2, k3, k4;
    char modelsav[80];
    char stra[80], strb[80], strc[80], strd[80],stre[80];
    char *strpt;
- Line 7806  int decodemodel ( char model[], int last
+ Line 8449  int decodemodel ( char model[], int last
        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
        /*
         * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
-       for(k=cptcovt; k>=1;k--) /**< Number of covariates not including constant and age, neither age*age*/
+       for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
-         Tvar[k]=0;
+         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
+       }
        cptcovage=0;
        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
          cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
- Line 7839  int decodemodel ( char model[], int last
+ Line 8483  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  */
+             Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
- Line 7864  int decodemodel ( char model[], int last
+ Line 8509  int decodemodel ( char model[], int last
            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
            /*  scanf("%d",i);*/
            cutl(strd,strc,strb,'V');
-           ks++; /**< Number of simple covariates*/
+           ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
            cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
            Tvar[k]=atoi(strd);
            Typevar[k]=0;  /* 0 for simple covariates */
- Line 7885  int decodemodel ( char model[], int last
+ Line 8530  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
     Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
     Typevar[k]=   0    0   0     2       1       0      2      1        1
-    Fixed[Tvar[k]]1    1   1     1       2       0      1      2        3
+    Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
-    Dummy[Tvar[k]]1    0   0     0       2       1      1      2        3
+    Dummy[k]      1    0   0     0       3       1      1      2        3
+           Tmodelind[combination of covar]=k;
  */
  /* Dispatching between quantitative and time varying covariates */
    /* If Tvar[k] >ncovcol it is a product */
    /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
          /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
-   for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
+   printf("Model=%s\n\
-     if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
-       Fixed[Tvar[k]]= 0;
+ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
-       Dummy[Tvar[k]]= 0;
+ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   fprintf(ficlog,"Model=%s\n\
+ Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
+ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
+ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
+   for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
+   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
+     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
+       ncoveff++;
+       ncovf++;
+       nsd++;
+       modell[k].maintype= FTYPE;
+       TvarsD[nsd]=Tvar[k];
+       TvarsDind[nsd]=k;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
+     }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
+       Fixed[k]= 0;
+       Dummy[k]= 0;
        ncoveff++;
-     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
+       ncovf++;
-       Fixed[Tvar[k]]= 0;
+       modell[k].maintype= FTYPE;
-       Dummy[Tvar[k]]= 1;
+       TvarF[ncovf]=Tvar[k];
-       nqfveff++;  /* Only simple fixed quantitative variable */
+       TvarFind[ncovf]=k;
-     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
+       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-       Fixed[Tvar[k]]= 1;
+       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
-       Dummy[Tvar[k]]= 0;
+     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
+       Fixed[k]= 0;
+       Dummy[k]= 1;
+       nqfveff++;
+       modell[k].maintype= FTYPE;
+       modell[k].subtype= FQ;
+       nsq++;
+       TvarsQ[nsq]=Tvar[k];
+       TvarsQind[nsq]=k;
+       ncovf++;
+       TvarF[ncovf]=Tvar[k];
+       TvarFind[ncovf]=k;
+       TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+       TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
+     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
+       Fixed[k]= 1;
+       Dummy[k]= 0;
        ntveff++; /* Only simple time varying dummy variable */
-     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
+       modell[k].maintype= VTYPE;
-       if( Typevar[k]==0){
+       modell[k].subtype= VD;
-         Fixed[Tvar[k]]= 1;
+       nsd++;
-         Dummy[Tvar[k]]= 1;
+       TvarsD[nsd]=Tvar[k];
-         nqtveff++;/* Only simple time varying quantitative variable */
+       TvarsDind[nsd]=k;
-       }
+       ncovv++; /* Only simple time varying variables */
-     }else if (Typevar[k] == 2) {
+       TvarV[ncovv]=Tvar[k];
-       for(k1=1; k1 <= cptcovprodnoage; k1++){
+       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 */
-         if(Tvard[k1][1] <=ncovcol){
+       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 */
-           if(Tvard[k1][2] <=ncovcol){
+       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 */
-             Fixed[Tvar[k]]= 1;
+       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);
-             Dummy[Tvar[k]]= 0;
+       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
-           }else if(Tvard[k1][2] <=ncovcol+nqv){
+     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
-             Fixed[Tvar[k]]= 0;
+       Fixed[k]= 1;
-             Dummy[Tvar[k]]= 1;
+       Dummy[k]= 1;
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+       nqtveff++;
-             Fixed[Tvar[k]]= 1;
+       modell[k].maintype= VTYPE;
-             Dummy[Tvar[k]]= 0;
+       modell[k].subtype= VQ;
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+       ncovv++; /* Only simple time varying variables */
-             Fixed[Tvar[k]]= 1;
+       nsq++;
-             Dummy[Tvar[k]]= 1;
+       TvarsQ[nsq]=Tvar[k];
-           }
+       TvarsQind[nsq]=k;
-         }else if(Tvard[k1][1] <=ncovcol+nqv){
+       TvarV[ncovv]=Tvar[k];
-           if(Tvard[k1][2] <=ncovcol){
+       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
-             Fixed[Tvar[k]]= 0;
+       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 */
-             Dummy[Tvar[k]]= 1;
+       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 */
-           }else if(Tvard[k1][2] <=ncovcol+nqv){
+       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
-             Fixed[Tvar[k]]= 0;
+       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
-             Dummy[Tvar[k]]= 1;
+       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);
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
-             Fixed[Tvar[k]]= 1;
+     }else if (Typevar[k] == 1) {  /* product with age */
-             Dummy[Tvar[k]]= 1;
+       ncova++;
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+       TvarA[ncova]=Tvar[k];
-             Fixed[Tvar[k]]= 1;
+       TvarAind[ncova]=k;
-             Dummy[Tvar[k]]= 1;
+       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
-           }
+         Fixed[k]= 2;
-         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
+         Dummy[k]= 2;
-           if(Tvard[k1][2] <=ncovcol){
+         modell[k].maintype= ATYPE;
-             Fixed[Tvar[k]]= 1;
+         modell[k].subtype= APFD;
-             Dummy[Tvar[k]]= 1;
+         /* ncoveff++; */
-           }else if(Tvard[k1][2] <=ncovcol+nqv){
+       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
-             Fixed[Tvar[k]]= 1;
+         Fixed[k]= 2;
-             Dummy[Tvar[k]]= 1;
+         Dummy[k]= 3;
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+         modell[k].maintype= ATYPE;
-             Fixed[Tvar[k]]= 1;
+         modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
-             Dummy[Tvar[k]]= 0;
+         /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+       }else if( Tvar[k] <=ncovcol+nqv+ntv ){
-             Fixed[Tvar[k]]= 1;
+         Fixed[k]= 3;
-             Dummy[Tvar[k]]= 1;
+         Dummy[k]= 2;
-           }
+         modell[k].maintype= ATYPE;
-         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
+         modell[k].subtype= APVD;                /*      Product age * varying dummy */
-           if(Tvard[k1][2] <=ncovcol){
+         /* ntveff++; /\* Only simple time varying dummy variable *\/ */
-             Fixed[Tvar[k]]= 1;
+       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
-             Dummy[Tvar[k]]= 1;
+         Fixed[k]= 3;
-           }else if(Tvard[k1][2] <=ncovcol+nqv){
+         Dummy[k]= 3;
-             Fixed[Tvar[k]]= 1;
+         modell[k].maintype= ATYPE;
-             Dummy[Tvar[k]]= 1;
+         modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+         /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
-             Fixed[Tvar[k]]= 1;
+       }
-             Dummy[Tvar[k]]= 1;
+     }else if (Typevar[k] == 2) {  /* product without age */
-           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+       k1=Tposprod[k];
-             Fixed[Tvar[k]]= 1;
+       if(Tvard[k1][1] <=ncovcol){
-             Dummy[Tvar[k]]= 1;
+         if(Tvard[k1][2] <=ncovcol){
-           }
+           Fixed[k]= 1;
-         }else{
+           Dummy[k]= 0;
-           printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+           modell[k].maintype= FTYPE;
-           fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+           modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
-         }
+           ncovf++; /* Fixed variables without age */
-       } /* end k1 */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 0;  /* or 2 ?*/
+           Dummy[k]= 1;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
+           ncovf++; /* Varying variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 0;  /* or 2 ?*/
+           Dummy[k]= 1;
+           modell[k].maintype= FTYPE;
+           modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
+           ncovf++; /* Fixed variables without age */
+           TvarF[ncovf]=Tvar[k];
+           TvarFind[ncovf]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 0;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
+         if(Tvard[k1][2] <=ncovcol){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
+           Fixed[k]= 1;
+           Dummy[k]= 1;
+           modell[k].maintype= VTYPE;
+           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
+           ncovv++; /* Varying variables without age */
+           TvarV[ncovv]=Tvar[k];
+           TvarVind[ncovv]=k;
+         }
+       }else{
+         printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+         fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
+       } /*end k1*/
      }else{
        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
      }
-     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[Tvar[k]],Dummy[Tvar[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]);
-     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[Tvar[k]],Dummy[Tvar[k]]);
+     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
+     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
+   }
+   /* Searching for doublons in the model */
+   for(k1=1; k1<= cptcovt;k1++){
+     for(k2=1; k2 <k1;k2++){
+       if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
+         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
+           if(Tvar[k1]==Tvar[k2]){
+             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             return(1);
+           }
+         }else if (Typevar[k1] ==2){
+           k3=Tposprod[k1];
+           k4=Tposprod[k2];
+           if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
+             printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
+             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
+             return(1);
+           }
+         }
+       }
+     }
    }
-   printf("Model=%s\n\
- Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
- Fixed[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product \n\
- Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
    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 8309  void syscompilerinfo(int logged)
+ Line 9140  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 8320  int prevalence_limit(double *p, double *
+ Line 9151  int prevalence_limit(double *p, double *
      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
    }
-   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
-   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
    pstamp(ficrespl);
    fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
    fprintf(ficrespl,"#Age ");
- Line 8333  int prevalence_limit(double *p, double *
+ Line 9164  int prevalence_limit(double *p, double *
    agebase=ageminpar;
    agelim=agemaxpar;
-   i1=pow(2,ncoveff);
+   /* i1=pow(2,ncoveff); */
+   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<=nqfveff;j++) {
-       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     }
-     fprintf(ficrespl,"******\n");
-     printf("******\n");
-     fprintf(ficlog,"******\n");
-                 if(invalidvarcomb[k]){
-                                                 printf("\nCombination (%d) ignored because no cases \n",k);
-                                                 fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
-                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
-                                                 continue;
-                 }
-     fprintf(ficrespl,"#Age ");
+       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
-     for(j=1;j<=nqfveff;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,"#******");
-     for (age=agebase; age<=agelim; age++){
+       printf("#******");
-       /* for (age=agebase; age<=agebase; age++){ */
+       fprintf(ficlog,"#******");
-       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-       fprintf(ficrespl,"%.0f ",age );
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
-       for(j=1;j<=nqfveff;j++)
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-                                                         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       tot=0.;
+       }
-       for(i=1; i<=nlstate;i++){
+       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
-                                                         tot +=  prlim[i][i];
+         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-                                                         fprintf(ficrespl," %.5f", prlim[i][i]);
+         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       }
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
-       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+       }
-     } /* Age */
+       fprintf(ficrespl,"******\n");
-     /* was end of cptcod */
+       printf("******\n");
-   } /* cptcov */
+       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<=agebase; age++){ */
+         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
+         fprintf(ficrespl,"%.0f ",age );
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         tot=0.;
+         for(i=1; i<=nlstate;i++){
+           tot +=  prlim[i][i];
+           fprintf(ficrespl," %.5f", prlim[i][i]);
+         }
+         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
+       } /* Age */
+       /* was end of cptcod */
+     } /* cptcov */
+   } /* nres */
    return 0;
  }
- Line 8392  int back_prevalence_limit(double *p, dou
+ Line 9234  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 8420  int back_prevalence_limit(double *p, dou
+ Line 9262  int back_prevalence_limit(double *p, dou
    agelim=agemaxpar;
-   i1=pow(2,nqfveff);
+   i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}
-         for(k=1; k<=i1;k++){
+   for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
-     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
+       if(TKresult[nres]!= k)
-     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+         continue;
-     /* k=k+1; */
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
-     /* to clean */
+       fprintf(ficresplb,"#******");
-     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
+       printf("#******");
-     fprintf(ficresplb,"#******");
+       fprintf(ficlog,"#******");
-     printf("#******");
+       for(j=1;j<=cptcoveff ;j++) {/* all covariates */
-     fprintf(ficlog,"#******");
+         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-     for(j=1;j<=nqfveff;j++) {
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
-       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
-     }
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-     fprintf(ficresplb,"******\n");
+         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-     printf("******\n");
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
-     fprintf(ficlog,"******\n");
+       }
-                 if(invalidvarcomb[k]){
+       fprintf(ficresplb,"******\n");
-                                                 printf("\nCombination (%d) ignored because no cases \n",k);
+       printf("******\n");
-                                                 fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
+       fprintf(ficlog,"******\n");
-                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
+       if(invalidvarcomb[k]){
-                                                 continue;
+         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<=nqfveff;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);
-     fprintf(ficresplb,"Total Years_to_converge\n");
-     for (age=agebase; age<=agelim; age++){
-       /* for (age=agebase; age<=agebase; age++){ */
-       if(mobilavproj > 0){
-         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
-         /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-                                 bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
-       }else if (mobilavproj == 0){
-                                 printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
-                                 fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
-                                 exit(1);
-       }else{
-                                 /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-                                 bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
        }
-       fprintf(ficresplb,"%.0f ",age );
+       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
-       for(j=1;j<=nqfveff;j++)
+       fprintf(ficresplb,"Total Years_to_converge\n");
-                                 fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
-       tot=0.;
-       for(i=1; i<=nlstate;i++){
+       for (age=agebase; age<=agelim; age++){
-                                 tot +=  bprlim[i][i];
+         /* for (age=agebase; age<=agebase; age++){ */
-                                 fprintf(ficresplb," %.5f", bprlim[i][i]);
+         if(mobilavproj > 0){
-       }
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
-       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+           /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
-     } /* Age */
+           bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
-     /* was end of cptcod */
+         }else if (mobilavproj == 0){
-   } /* cptcov */
+           printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
+           exit(1);
+         }else{
+           /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
+           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
+         }
+         fprintf(ficresplb,"%.0f ",age );
+         for(j=1;j<=cptcoveff;j++)
+           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         tot=0.;
+         for(i=1; i<=nlstate;i++){
+           tot +=  bprlim[i][i];
+           fprintf(ficresplb," %.5f", bprlim[i][i]);
+         }
+         fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
+       } /* Age */
+       /* was end of cptcod */
+     } /* end of any combination */
+   } /* end of nres */
    /* hBijx(p, bage, fage); */
    /* fclose(ficrespijb); */
- Line 8496  int hPijx(double *p, int bage, int fage)
+ Line 9341  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 8519  int hPijx(double *p, int bage, int fage)
+ Line 9364  int hPijx(double *p, int bage, int fage)
      /* hstepm=1;   aff par mois*/
      pstamp(ficrespij);
      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
-     i1= pow(2,nqfveff);
+     i1= pow(2,cptcoveff);
                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                  /*      k=k+1;  */
-     for (k=1; k <= (int) pow(2,nqfveff); 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<=nqfveff;j++)
+       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 8537  int hPijx(double *p, int bage, int fage)
+ Line 9389  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 8567  int hPijx(double *p, int bage, int fage)
+ Line 9419  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 8591  int hPijx(double *p, int bage, int fage)
+ Line 9443  int hPijx(double *p, int bage, int fage)
    /* hstepm=1;   aff par mois*/
    pstamp(ficrespijb);
    fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
-   i1= pow(2,nqfveff);
+   i1= pow(2,cptcoveff);
    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*    k=k+1;  */
-   for (k=1; k <= (int) pow(2,nqfveff); 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<=nqfveff;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 8663  int main(int argc, char *argv[])
+ Line 9521  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 8681  int main(int argc, char *argv[])
+ Line 9540  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 8993  int main(int argc, char *argv[])
+ Line 9854  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 9046  int main(int argc, char *argv[])
+ Line 9907  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 9097  run imach with mle=-1 to get a correct t
+ Line 9958  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 9209  Please run with mle=-1 to get a correct
+ Line 10070  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 9230  Please run with mle=-1 to get a correct
+ Line 10091  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 9249  Please run with mle=-1 to get a correct
+ Line 10132  Please run with mle=-1 to get a correct
      ncovcol + k1
      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
      Tvar[3=V1*V4]=4+1 etc */
-   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
+   Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
+   Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
    /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
       if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
+      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
    */
    Tvaraff=ivector(1,NCOVMAX); /* Unclear */
    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
- Line 9261  Please run with mle=-1 to get a correct
+ Line 10146  Please run with mle=-1 to get a correct
 covariates (3 plus signs)
                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                        */
+   Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual dummy, fixed or varying:
+                                 * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
+                                 * 3, 1, 0, 0, 0, 0, 0, 0},
+                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
+                                 * V1 df, V2 qf, V3 & V4 dv, V5 qv
+                                 * Tmodelind[1]@9={9,0,3,2,}*/
+   TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
+   TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
+                                 * individual quantitative, fixed or varying:
+                                 * Tmodelqind[1]=1,Tvaraff[1]@9={4,
+                                 * 3, 1, 0, 0, 0, 0, 0, 0},
+                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
  /* Main decodemodel */
- Line 9323  Please run with mle=-1 to get a correct
+ Line 10220  Please run with mle=-1 to get a correct
    cptcoveff=0;
    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
      tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
-         }
+   }
-         ncovcombmax=pow(2,cptcoveff);
+   ncovcombmax=pow(2,cptcoveff);
-         invalidvarcomb=ivector(1, ncovcombmax);
+   invalidvarcomb=ivector(1, ncovcombmax);
-         for(i=1;i<ncovcombmax;i++)
+   for(i=1;i<ncovcombmax;i++)
-                 invalidvarcomb[i]=0;
+     invalidvarcomb[i]=0;
    /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
    /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
    /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
    /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
- Line 9492  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 10389  Title=%s <br>Datafile=%s Firstpass=%d La
    /* Calculates basic frequencies. Computes observed prevalence at single age
                   and for any valid combination of covariates
       and prints on file fileres'p'. */
-   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \
+   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
-                                                         firstpass, lastpass,  stepm,  weightopt, model);
+               firstpass, lastpass,  stepm,  weightopt, model);
    fprintf(fichtm,"\n");
    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
- Line 10002  Please run with mle=-1 to get a correct
+ Line 10899  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 10018  Please run with mle=-1 to get a correct
+ Line 10916  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 10027  Please run with mle=-1 to get a correct
+ Line 10926  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 10074  Please run with mle=-1 to get a correct
+ Line 11025  Please run with mle=-1 to get a correct
      /*#include "hpijx.h"*/
      hPijx(p, bage, fage);
      fclose(ficrespij);
      /* ncovcombmax=  pow(2,cptcoveff); */
      /*-------------- Variance of one-step probabilities---*/
      k=1;
      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
      /* Prevalence for each covariates in probs[age][status][cov] */
      probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
      for(i=1;i<=AGESUP;i++)
- Line 10089  Please run with mle=-1 to get a correct
+ Line 11040  Please run with mle=-1 to get a correct
      prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
      if (mobilav!=0 ||mobilavproj !=0 ) {
        mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
-                         for(i=1;i<=AGESUP;i++)
+       for(i=1;i<=AGESUP;i++)
-                                 for(j=1;j<=nlstate;j++)
+         for(j=1;j<=nlstate;j++)
-                                         for(k=1;k<=ncovcombmax;k++)
+           for(k=1;k<=ncovcombmax;k++)
-                                                 mobaverages[i][j][k]=0.;
+             mobaverages[i][j][k]=0.;
        mobaverage=mobaverages;
        if (mobilav!=0) {
-                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
+         printf("Movingaveraging observed prevalence\n");
-                                         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
+         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
-                                         printf(" Error in movingaverage mobilav=%d\n",mobilav);
+           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
-                                 }
+           printf(" Error in movingaverage mobilav=%d\n",mobilav);
+         }
        }
        /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
        /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
        else if (mobilavproj !=0) {
-                                 if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
+         printf("Movingaveraging projected observed prevalence\n");
-                                         fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
+         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
-                                         printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
+           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
-                                 }
+           printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
+         }
        }
      }/* end if moving average */
      /*---------- Forecasting ------------------*/
      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
      if(prevfcast==1){
- Line 10157  Please run with mle=-1 to get a correct
+ Line 11110  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++){
+     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)]);
+         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 10175  Please run with mle=-1 to get a correct
+ Line 11143  Please run with mle=-1 to get a correct
      printf("done evsij\n");fflush(stdout);
      fprintf(ficlog,"done evsij\n");fflush(ficlog);
-     /*---------- Health expectancies and variances ------------*/
+     /*---------- State-specific expectancies and variances ------------*/
      strcpy(filerest,"T_");
- Line 10191  Please run with mle=-1 to get a correct
+ Line 11159  Please run with mle=-1 to get a correct
      strcpy(fileresstde,"STDE_");
      strcat(fileresstde,fileresu);
      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
-       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
-       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+       fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
      }
-     printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
-     fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+     fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
      strcpy(filerescve,"CVE_");
      strcat(filerescve,fileresu);
      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
-       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
-       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+       fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
      }
-     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
-     fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+     fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
      strcpy(fileresv,"V_");
      strcat(fileresv,fileresu);
- Line 10212  Please run with mle=-1 to get a correct
+ Line 11180  Please run with mle=-1 to get a correct
        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
      }
-     printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
+     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
-     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
+     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
-       fprintf(ficrest,"\n#****** ");
+     if (cptcovn < 1){i1=1;}
-       for(j=1;j<=cptcoveff;j++)
-                                 fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
+     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
+       if(TKresult[nres]!= k)
+         continue;
+       printf("\n#****** Result for:");
+       fprintf(ficrest,"\n#****** Result for:");
+       fprintf(ficlog,"\n#****** Result for:");
+       for(j=1;j<=cptcoveff;j++){
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficrest,"******\n");
+       fprintf(ficlog,"******\n");
+       printf("******\n");
        fprintf(ficresstdeij,"\n#****** ");
        fprintf(ficrescveij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++) {
-                                 fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         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)]);
+         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)]);
+         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
        fprintf(ficresvij,"******\n");
        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
        oldm=oldms;savm=savms;
-       printf(" cvevsij %d, ",k);
+       printf(" cvevsij ");
-       fprintf(ficlog, " cvevsij %d, ",k);
+       fprintf(ficlog, " cvevsij ");
-       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
        printf(" end cvevsij \n ");
        fprintf(ficlog, " end cvevsij \n ");
- Line 10255  Please run with mle=-1 to get a correct
+ Line 11249  Please run with mle=-1 to get a correct
        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
-                                 oldm=oldms;savm=savms; /* ZZ Segmentation fault */
+         oldm=oldms;savm=savms; /* ZZ Segmentation fault */
-                                 cptcod= 0; /* To be deleted */
+         cptcod= 0; /* To be deleted */
-                                 printf("varevsij %d \n",vpopbased);
+         printf("varevsij vpopbased=%d \n",vpopbased);
-                                 fprintf(ficlog, "varevsij %d \n",vpopbased);
+         fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
-                                 varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
+         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
-                                 fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
+         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)
+         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);
+           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
-                                 else
+         else
-                                         fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
+           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
-                                 fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
+         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
-                                 for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
-                                 fprintf(ficrest,"\n");
+         fprintf(ficrest,"\n");
-                                 /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
+         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
-                                 epj=vector(1,nlstate+1);
+         epj=vector(1,nlstate+1);
-                                 printf("Computing age specific period (stable) prevalences in each health state \n");
+         printf("Computing age specific period (stable) prevalences in each health state \n");
-                                 fprintf(ficlog,"Computing age specific 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++){
+         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 (vpopbased==1) {
-                                                 if(mobilav ==0){
+             if(mobilav ==0){
-                                                         for(i=1; i<=nlstate;i++)
+               for(i=1; i<=nlstate;i++)
-                                                                 prlim[i][i]=probs[(int)age][i][k];
+                 prlim[i][i]=probs[(int)age][i][k];
-                                                 }else{ /* mobilav */
+             }else{ /* mobilav */
-                                                         for(i=1; i<=nlstate;i++)
+               for(i=1; i<=nlstate;i++)
-                                                                 prlim[i][i]=mobaverage[(int)age][i][k];
+                 prlim[i][i]=mobaverage[(int)age][i][k];
-                                                 }
+             }
-                                         }
+           }
-                                         fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
+           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
-                                         /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
+           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
-                                         /* printf(" age %4.0f ",age); */
+           /* printf(" age %4.0f ",age); */
-                                         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
-                                                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
+             for(i=1, epj[j]=0.;i <=nlstate;i++) {
-                                                         epj[j] += prlim[i][i]*eij[i][j][(int)age];
+               epj[j] += prlim[i][i]*eij[i][j][(int)age];
-                                                         /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
-                                                         /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
+               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
-                                                 }
+             }
-                                                 epj[nlstate+1] +=epj[j];
+             epj[nlstate+1] +=epj[j];
-                                         }
+           }
-                                         /* printf(" age %4.0f \n",age); */
+           /* printf(" age %4.0f \n",age); */
-                                         for(i=1, vepp=0.;i <=nlstate;i++)
+           for(i=1, vepp=0.;i <=nlstate;i++)
-                                                 for(j=1;j <=nlstate;j++)
+             for(j=1;j <=nlstate;j++)
-                                                         vepp += vareij[i][j][(int)age];
+               vepp += vareij[i][j][(int)age];
-                                         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
-                                         for(j=1;j <=nlstate;j++){
+           for(j=1;j <=nlstate;j++){
-                                                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
-                                         }
+           }
-                                         fprintf(ficrest,"\n");
+           fprintf(ficrest,"\n");
-                                 }
+         }
        } /* End vpopbased */
        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
        free_vector(epj,1,nlstate+1);
-       printf("done \n");fflush(stdout);
+       printf("done selection\n");fflush(stdout);
-       fprintf(ficlog,"done\n");fflush(ficlog);
+       fprintf(ficlog,"done selection\n");fflush(ficlog);
        /*}*/
-     } /* End k */
+     } /* End k selection */
-     free_vector(weight,1,n);
-     free_imatrix(Tvard,1,NCOVMAX,1,2);
-     free_imatrix(s,1,maxwav+1,1,n);
-     free_matrix(anint,1,maxwav,1,n);
-     free_matrix(mint,1,maxwav,1,n);
-     free_ivector(cod,1,n);
-     free_ivector(tab,1,NCOVMAX);
-     fclose(ficresstdeij);
-     fclose(ficrescveij);
-     fclose(ficresvij);
-     fclose(ficrest);
-     printf("done Health expectancies\n");fflush(stdout);
-     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
-     fclose(ficpar);
-     /*------- Variance of period (stable) prevalence------*/
+     printf("done State-specific expectancies\n");fflush(stdout);
+     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
+     /*------- Variance of period (stable) prevalence------*/
      strcpy(fileresvpl,"VPL_");
      strcat(fileresvpl,fileresu);
      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
- Line 10340  Please run with mle=-1 to get a correct
+ Line 11323  Please run with mle=-1 to get a correct
      }
      printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
      fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-     for (k=1; k <= (int) pow(2,cptcoveff); k++){
+     i1=pow(2,cptcoveff);
-         fprintf(ficresvpl,"\n#****** ");
+     if (cptcovn < 1){i1=1;}
-                         for(j=1;j<=cptcoveff;j++)
-                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+     for(nres=1; nres <= nresult; nres++) /* For each resultline */
-                         fprintf(ficresvpl,"******\n");
+     for(k=1; k<=i1;k++){
+       if(TKresult[nres]!= k)
-                         varpl=matrix(1,nlstate,(int) bage, (int) fage);
+         continue;
-                         oldm=oldms;savm=savms;
+       fprintf(ficresvpl,"\n#****** ");
-                         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
+       printf("\n#****** ");
-                         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+       fprintf(ficlog,"\n#****** ");
+       for(j=1;j<=cptcoveff;j++) {
+         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+       }
+       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+       }
+       fprintf(ficresvpl,"******\n");
+       printf("******\n");
+       fprintf(ficlog,"******\n");
+       varpl=matrix(1,nlstate,(int) bage, (int) fage);
+       oldm=oldms;savm=savms;
+       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
+       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
        /*}*/
      }
      fclose(ficresvpl);
      printf("done variance-covariance of period prevalence\n");fflush(stdout);
      fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
+     free_vector(weight,1,n);
+     free_imatrix(Tvard,1,NCOVMAX,1,2);
+     free_imatrix(s,1,maxwav+1,1,n);
+     free_matrix(anint,1,maxwav,1,n);
+     free_matrix(mint,1,maxwav,1,n);
+     free_ivector(cod,1,n);
+     free_ivector(tab,1,NCOVMAX);
+     fclose(ficresstdeij);
+     fclose(ficrescveij);
+     fclose(ficresvij);
+     fclose(ficrest);
+     fclose(ficpar);
      /*---------- End : free ----------------*/
      if (mobilav!=0 ||mobilavproj !=0)
        free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
- Line 10368  Please run with mle=-1 to get a correct
+ Line 11383  Please run with mle=-1 to get a correct
      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
    }  /* mle==-3 arrives here for freeing */
-  /* endfree:*/
+   /* endfree:*/
-     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-     free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
+   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(coqvar,1,maxwav,1,n);
-     free_matrix(covar,0,NCOVMAX,1,n);
+   free_matrix(covar,0,NCOVMAX,1,n);
-     free_matrix(matcov,1,npar,1,npar);
+   free_matrix(matcov,1,npar,1,npar);
-     free_matrix(hess,1,npar,1,npar);
+   free_matrix(hess,1,npar,1,npar);
-     /*free_vector(delti,1,npar);*/
+   /*free_vector(delti,1,npar);*/
-     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_matrix(agev,1,maxwav,1,imx);
+   free_matrix(agev,1,maxwav,1,imx);
-     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-     free_ivector(ncodemax,1,NCOVMAX);
+   free_ivector(ncodemax,1,NCOVMAX);
-     free_ivector(ncodemaxwundef,1,NCOVMAX);
+   free_ivector(ncodemaxwundef,1,NCOVMAX);
-     free_ivector(Dummy,-1,NCOVMAX);
+   free_ivector(Dummy,-1,NCOVMAX);
-     free_ivector(Fixed,-1,NCOVMAX);
+   free_ivector(Fixed,-1,NCOVMAX);
-     free_ivector(Typevar,-1,NCOVMAX);
+   free_ivector(DummyV,1,NCOVMAX);
-     free_ivector(Tvar,1,NCOVMAX);
+   free_ivector(FixedV,1,NCOVMAX);
-     free_ivector(Tprod,1,NCOVMAX);
+   free_ivector(Typevar,-1,NCOVMAX);
-     free_ivector(Tvaraff,1,NCOVMAX);
+   free_ivector(Tvar,1,NCOVMAX);
-     free_ivector(invalidvarcomb,1,ncovcombmax);
+   free_ivector(TvarsQ,1,NCOVMAX);
-     free_ivector(Tage,1,NCOVMAX);
+   free_ivector(TvarsQind,1,NCOVMAX);
+   free_ivector(TvarsD,1,NCOVMAX);
-     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   free_ivector(TvarsDind,1,NCOVMAX);
-     /* free_imatrix(codtab,1,100,1,10); */
+   free_ivector(TvarFD,1,NCOVMAX);
+   free_ivector(TvarFDind,1,NCOVMAX);
+   free_ivector(TvarF,1,NCOVMAX);
+   free_ivector(TvarFind,1,NCOVMAX);
+   free_ivector(TvarV,1,NCOVMAX);
+   free_ivector(TvarVind,1,NCOVMAX);
+   free_ivector(TvarA,1,NCOVMAX);
+   free_ivector(TvarAind,1,NCOVMAX);
+   free_ivector(TvarFQ,1,NCOVMAX);
+   free_ivector(TvarFQind,1,NCOVMAX);
+   free_ivector(TvarVD,1,NCOVMAX);
+   free_ivector(TvarVDind,1,NCOVMAX);
+   free_ivector(TvarVQ,1,NCOVMAX);
+   free_ivector(TvarVQind,1,NCOVMAX);
+   free_ivector(Tvarsel,1,NCOVMAX);
+   free_vector(Tvalsel,1,NCOVMAX);
+   free_ivector(Tposprod,1,NCOVMAX);
+   free_ivector(Tprod,1,NCOVMAX);
+   free_ivector(Tvaraff,1,NCOVMAX);
+   free_ivector(invalidvarcomb,1,ncovcombmax);
+   free_ivector(Tage,1,NCOVMAX);
+   free_ivector(Tmodelind,1,NCOVMAX);
+   free_ivector(TmodelInvind,1,NCOVMAX);
+   free_ivector(TmodelInvQind,1,NCOVMAX);
+   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+   /* free_imatrix(codtab,1,100,1,10); */
    fflush(fichtm);
    fflush(ficgp);
    if((nberr >0) || (nbwarn>0)){
      printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
- Line 10417  Please run with mle=-1 to get a correct
+ Line 11458  Please run with mle=-1 to get a correct
    printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);
    fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);
    printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
- Line 10430  Please run with mle=-1 to get a correct
+ Line 11471  Please run with mle=-1 to get a correct
    fclose(ficgp);
    fclose(ficlog);
    /*------ End -----------*/
-    printf("Before Current directory %s!\n",pathcd);
+   printf("Before Current directory %s!\n",pathcd);
  #ifdef WIN32
-    if (_chdir(pathcd) != 0)
+   if (_chdir(pathcd) != 0)
-            printf("Can't move to directory %s!\n",path);
+     printf("Can't move to directory %s!\n",path);
-    if(_getcwd(pathcd,MAXLINE) > 0)
+   if(_getcwd(pathcd,MAXLINE) > 0)
  #else
-    if(chdir(pathcd) != 0)
+     if(chdir(pathcd) != 0)
-            printf("Can't move to directory %s!\n", path);
+       printf("Can't move to directory %s!\n", path);
-    if (getcwd(pathcd, MAXLINE) > 0)
+   if (getcwd(pathcd, MAXLINE) > 0)
  #endif
      printf("Current directory %s!\n",pathcd);
    /*strcat(plotcmd,CHARSEPARATOR);*/
- Line 10466  Please run with mle=-1 to get a correct
+ Line 11507  Please run with mle=-1 to get a correct
    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
    if((outcmd=system(plotcmd)) != 0){
      printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
- Line 10494  Please run with mle=-1 to get a correct
+ Line 11535  Please run with mle=-1 to get a correct
      else if (z[0] == 'g') system(plotcmd);
      else if (z[0] == 'q') exit(0);
    }
-   end:
+ end:
    while (z[0] != 'q') {
      printf("\nType  q for exiting: "); fflush(stdout);
      scanf("%s",z);

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