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Diff for /imach/src/imach.c between versions 1.205 and 1.222

version 1.205, 2015/10/23 15:50:53 version 1.222, 2016/02/17 08:14:50
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.222  2016/02/17 08:14:50  brouard
     Summary: Probably last 0.98 stable version 0.98r6
   
     Revision 1.221  2016/02/15 23:35:36  brouard
     Summary: minor bug
   
     Revision 1.219  2016/02/15 00:48:12  brouard
     *** empty log message ***
   
     Revision 1.218  2016/02/12 11:29:23  brouard
     Summary: 0.99 Back projections
   
     Revision 1.217  2015/12/23 17:18:31  brouard
     Summary: Experimental backcast
   
     Revision 1.216  2015/12/18 17:32:11  brouard
     Summary: 0.98r4 Warning and status=-2
   
     Version 0.98r4 is now:
      - displaying an error when status is -1, date of interview unknown and date of death known;
      - permitting a status -2 when the vital status is unknown at a known date of right truncation.
     Older changes concerning s=-2, dating from 2005 have been supersed.
   
     Revision 1.215  2015/12/16 08:52:24  brouard
     Summary: 0.98r4 working
   
     Revision 1.214  2015/12/16 06:57:54  brouard
     Summary: temporary not working
   
     Revision 1.213  2015/12/11 18:22:17  brouard
     Summary: 0.98r4
   
     Revision 1.212  2015/11/21 12:47:24  brouard
     Summary: minor typo
   
     Revision 1.211  2015/11/21 12:41:11  brouard
     Summary: 0.98r3 with some graph of projected cross-sectional
   
     Author: Nicolas Brouard
   
     Revision 1.210  2015/11/18 17:41:20  brouard
     Summary: Start working on projected prevalences
   
     Revision 1.209  2015/11/17 22:12:03  brouard
     Summary: Adding ftolpl parameter
     Author: N Brouard
   
     We had difficulties to get smoothed confidence intervals. It was due
     to the period prevalence which wasn't computed accurately. The inner
     parameter ftolpl is now an outer parameter of the .imach parameter
     file after estepm. If ftolpl is small 1.e-4 and estepm too,
     computation are long.
   
     Revision 1.208  2015/11/17 14:31:57  brouard
     Summary: temporary
   
     Revision 1.207  2015/10/27 17:36:57  brouard
     *** empty log message ***
   
     Revision 1.206  2015/10/24 07:14:11  brouard
     *** empty log message ***
   
   Revision 1.205  2015/10/23 15:50:53  brouard    Revision 1.205  2015/10/23 15:50:53  brouard
   Summary: 0.98r3 some clarification for graphs on likelihood contributions    Summary: 0.98r3 some clarification for graphs on likelihood contributions
   
Line 601 Line 663
   hPijx.    hPijx.
   
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the period (stable) prevalence.     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
       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);
        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 
        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);
   
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
Line 663 Line 742
 /* #define DEBUGLINMIN */  /* #define DEBUGLINMIN */
 /* #define DEBUGHESS */  /* #define DEBUGHESS */
 #define DEBUGHESSIJ  #define DEBUGHESSIJ
 /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */  #define LINMINORIGINAL  /* Don't use loop on scale in linmin (accepting nan)*/
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
 #define POWELLF1F3 /* Skip test */  #define POWELLF1F3 /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
Line 735  typedef struct { Line 814  typedef struct {
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
   /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
   #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130  /* #define AGESUP 130 */
   #define AGESUP 150
   #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
 #define AGEBASE 40  #define AGEBASE 40
 #define AGEOVERFLOW 1.e20  #define AGEOVERFLOW 1.e20
 #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
Line 769  int cptcovage=0; /**< Number of covariat Line 852  int cptcovage=0; /**< Number of covariat
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
Line 791  double jmean=1; /* Mean space between 2 Line 875  double jmean=1; /* Mean space between 2
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double   **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
   
 /*FILE *fic ; */ /* Used in readdata only */  /*FILE *fic ; */ /* Used in readdata only */
 FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
 FILE *ficlog, *ficrespow;  FILE *ficlog, *ficrespow;
 int globpr=0; /* Global variable for printing or not */  int globpr=0; /* Global variable for printing or not */
 double fretone; /* Only one call to likelihood */  double fretone; /* Only one call to likelihood */
Line 815  char fileresv[FILENAMELENGTH]; Line 901  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvpl;
 char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
 char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 char command[FILENAMELENGTH];  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 char fileresu[FILENAMELENGTH]; /* fileres without r in front */  char fileresu[FILENAMELENGTH]; /* fileres without r in front */
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
Line 898  int *ncodemaxwundef;  /* ncodemax[j]= Nu Line 984  int *ncodemaxwundef;  /* ncodemax[j]= Nu
                              covariate for which somebody answered including                                covariate for which somebody answered including 
                              undefined. Usually 3: -1, 0 and 1. */                               undefined. Usually 3: -1, 0 and 1. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs; /* Global pointer */
   double ***mobaverage, ***mobaverages; /* New global variable */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   
Line 913  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1000  int **nbcode, *Tvar; /**< model=V2 => Tv
 int *Tage;  int *Tage;
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
 double ftol=FTOL; /**< Tolerance for computing Max Likelihood */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
Line 1354  char *subdirf3(char fileres[], char *pre Line 1441  char *subdirf3(char fileres[], char *pre
   strcat(tmpout,fileres);    strcat(tmpout,fileres);
   return tmpout;    return tmpout;
 }  }
    
   /*************** function subdirfext ***********/
   char *subdirfext(char fileres[], char *preop, char *postop)
   {
     
     strcpy(tmpout,preop);
     strcat(tmpout,fileres);
     strcat(tmpout,postop);
     return tmpout;
   }
   
   /*************** function subdirfext3 ***********/
   char *subdirfext3(char fileres[], char *preop, char *postop)
   {
     
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,fileres);
     strcat(tmpout,postop);
     return tmpout;
   }
    
 char *asc_diff_time(long time_sec, char ascdiff[])  char *asc_diff_time(long time_sec, char ascdiff[])
 {  {
   long sec_left, days, hours, minutes;    long sec_left, days, hours, minutes;
Line 1958  void powell(double p[], double **xi, int Line 2068  void powell(double p[], double **xi, int
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
      matrix by transitions matrix until convergence is reached with precision ftolpl */       matrix by transitions matrix until convergence is reached with precision ftolpl */
       /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
     /* Wx is row vector: population in state 1, population in state 2, population dead */
     /* or prevalence in state 1, prevalence in state 2, 0 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
     /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
     /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
     /*  0,                   0                  , 1} */
     /*
      * and after some iteration: */
     /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
     /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     /* {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;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
   double **newm;    double **newm;
   double agefin, delaymax=100 ; /* Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
       
     min=vector(1,nlstate);
     max=vector(1,nlstate);
     meandiff=vector(1,nlstate);
   
           /* Starting with matrix unity */
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 1987  double **prevalim(double **prlim, int nl Line 2119  double **prevalim(double **prlim, int nl
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;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,Tvar[k])]; */
                           /* Here comes the value of the covariate 'ij' */
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,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])]); */        /* 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])]); */
     }      }
Line 2002  double **prevalim(double **prlim, int nl Line 2135  double **prevalim(double **prlim, int nl
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
                   /* age and covariate values of ij are in 'cov' */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           
     savm=oldm;      savm=oldm;
     oldm=newm;      oldm=newm;
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){      for(j=1; j<=nlstate; j++){
       min=1.;        max[j]=0.;
       max=0.;        min[j]=1.;
       for(i=1; i<=nlstate; i++) {      }
         sumnew=0;      for(i=1;i<=nlstate;i++){
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        sumnew=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         for(j=1; j<=nlstate; j++){ 
         prlim[i][j]= newm[i][j]/(1-sumnew);          prlim[i][j]= newm[i][j]/(1-sumnew);
         max=FMAX(max,prlim[i][j]);          max[j]=FMAX(max[j],prlim[i][j]);
         min=FMIN(min,prlim[i][j]);          min[j]=FMIN(min[j],prlim[i][j]);
         /* printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min); */  
       }        }
       maxmin=(max-min)/(max+min)*2;      }
       maxmax=FMAX(maxmax,maxmin);  
       maxmax=0.;
       for(j=1; j<=nlstate; j++){
         meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
         maxmax=FMAX(maxmax,meandiff[j]);
         /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
     } /* j loop */      } /* j loop */
     *ncvyear= (int)age- (int)agefin;      *ncvyear= (int)age- (int)agefin;
     /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */      /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */        /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
         free_vector(max,1,nlstate);
         free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* age loop */
   printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\      /* After some age loop it doesn't converge */
 Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);    printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
 /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */  Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
     free_vector(min,1,nlstate);
     free_vector(max,1,nlstate);
     free_vector(meandiff,1,nlstate);
     
   return prlim; /* should not reach here */    return prlim; /* should not reach here */
 }  }
   
   
    /**** Back Prevalence limit (stable or period prevalence)  ****************/
   
    /* 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)
   {
     /* 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 */
     /* 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 */
     /* newm is the matrix after multiplications, its rows are identical at a factor */
     /* Initial matrix pimij */
     /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
     /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
     /*  0,                   0                  , 1} */
     /*
      * and after some iteration: */
     /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
     /*  0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
     /*  0,                   0                  , 1} */
     /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
     /* {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 */
     double **out, cov[NCOVMAX+1], **bmij();
     double **newm;
     double         **dnewm, **doldm, **dsavm;  /* for use */
     double         **oldm, **savm;  /* for use */
   
     double agefin, delaymax=200. ; /* 100 Max number of years to converge */
     int ncvloop=0;
     
     min=vector(1,nlstate);
     max=vector(1,nlstate);
     meandiff=vector(1,nlstate);
   
           dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
           oldm=oldms; savm=savms;
   
           /* Starting with matrix unity */
           for (ii=1;ii<=nlstate+ndeath;ii++)
                   for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
     
     cov[1]=1.;
     
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
     /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
     for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
       ncvloop++;
       newm=savm; /* oldm should be kept from previous iteration or unity at start */
                   /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
       /* Covariates have to be included here again */
       cov[2]=agefin;
       if(nagesqr==1)
         cov[3]= agefin*agefin;;
       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])]); */
       }
       /*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]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
                   /* ij should be linked to the correct index of cov */
                   /* age and covariate values ij are in 'cov', but we need to pass
                    * ij for the observed prevalence at age and status and covariate
                    * number:  prevacurrent[(int)agefin][ii][ij]
                    */
       /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
       /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
       savm=oldm;
       oldm=newm;
       for(j=1; j<=nlstate; j++){
         max[j]=0.;
         min[j]=1.;
       }
       for(j=1; j<=nlstate; j++){ 
         for(i=1;i<=nlstate;i++){
                                   /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                                   bprlim[i][j]= newm[i][j];
                                   max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                                   min[i]=FMIN(min[i],bprlim[i][j]);
         }
       }
                   
       maxmax=0.;
       for(i=1; i<=nlstate; i++){
         meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
         maxmax=FMAX(maxmax,meandiff[i]);
         /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
       } /* j loop */
       *ncvyear= -( (int)age- (int)agefin);
       /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
       if(maxmax < ftolpl){
         /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
         free_vector(min,1,nlstate);
         free_vector(max,1,nlstate);
         free_vector(meandiff,1,nlstate);
         return bprlim;
       }
     } /* age loop */
       /* After some age loop it doesn't converge */
     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
   Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
     free_vector(min,1,nlstate);
     free_vector(max,1,nlstate);
     free_vector(meandiff,1,nlstate);
     
     return bprlim; /* should not reach here */
   }
   
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
Line 2055  double **pmij(double **ps, double *cov, Line 2334  double **pmij(double **ps, double *cov,
   /*double t34;*/    /*double t34;*/
   int i,j, nc, ii, jj;    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) */
                           /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   }
                   for(j=i+1; j<=nlstate+ndeath;j++){
                           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[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); */
                           }
                           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); */          for(i=1; i<= nlstate; i++){
       }                  s1=0;
       for(j=i+1; j<=nlstate+ndeath;j++){                  for(j=1; j<i; j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){                          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/                          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           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); */                  for(j=i+1; j<=nlstate+ndeath; j++){
                           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); */
                   }
                   /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   ps[i][i]=1./(s1+1.);
                   /* Computing other pijs */
                   for(j=1; j<i; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   for(j=i+1; j<=nlstate+ndeath; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           } /* end i */
     
           for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   for(jj=1; jj<= nlstate+ndeath; jj++){
                           ps[ii][jj]=0;
                           ps[ii][ii]=1;
                   }
         }          }
         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */    
       }    
     }          /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
               /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     for(i=1; i<= nlstate; i++){          /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       s1=0;          /*   } */
       for(j=1; j<i; j++){          /*   printf("\n "); */
         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("\n ");printf("%lf ",cov[2]);*/
       }          /*
       for(j=i+1; j<=nlstate+ndeath; j++){                  for(i=1; i<= npar; i++) printf("%f ",x[i]);
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */                  goto end;*/
         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */          return ps;
       }  }
       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */  
       ps[i][i]=1./(s1+1.);  /*************** backward transition probabilities ***************/ 
       /* Computing other pijs */  
       for(j=1; j<i; j++)   /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
         ps[i][j]= exp(ps[i][j])*ps[i][i];  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
       for(j=i+1; j<=nlstate+ndeath; j++)   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
         ps[i][j]= exp(ps[i][j])*ps[i][i];  {
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    /* Computes the backward probability at age agefin and covariate ij
     } /* end i */     * and returns in **ps as well as **bmij.
          */
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    int i, ii, j,k;
       for(jj=1; jj<= nlstate+ndeath; jj++){    
         ps[ii][jj]=0;    double **out, **pmij();
         ps[ii][ii]=1;    double sumnew=0.;
     double agefin;
     
     double **dnewm, **dsavm, **doldm;
     double **bbmij;
     
     doldm=ddoldms; /* global pointers */
     dnewm=ddnewms;
     dsavm=ddsavms;
     
     agefin=cov[2];
     /* bmij *//* age is cov[2], ij is included in cov, but we need for
        the observed prevalence (with this covariate ij) */
     dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
     /* We do have the matrix Px in savm  and we need pij */
     for (j=1;j<=nlstate+ndeath;j++){
       sumnew=0.; /* w1 p11 + w2 p21 only on live states */
       for (ii=1;ii<=nlstate;ii++){
         sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
       } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
       for (ii=1;ii<=nlstate+ndeath;ii++){
         if(sumnew >= 1.e-10){
           /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
           /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
           /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
           /* }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);
       }        }
     }      } /*End ii */
         } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
         /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
     /*   } */    /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
     /*   printf("\n "); */    /* left Product of this matrix by diag matrix of prevalences (savm) */
     /* } */    for (j=1;j<=nlstate+ndeath;j++){
     /* printf("\n ");printf("%lf ",cov[2]);*/      for (ii=1;ii<=nlstate+ndeath;ii++){
     /*        dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
       for(i=1; i<= npar; i++) printf("%f ",x[i]);      }
       goto end;*/    } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
     return ps;    ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
     /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
     /* end bmij */
     return ps; 
   }
   /*************** transition probabilities ***************/ 
   
   double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
     /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
        lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
        Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     */
     double s1, lnpijopii;
     /*double t34;*/
     int i,j, nc, ii, jj;
   
           for(i=1; i<= nlstate; i++){
                   for(j=1; j<i;j++){
                           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                   /*lnpijopii += param[i][j][nc]*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); */
                           }
                           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                           /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                   }
                   for(j=i+1; j<=nlstate+ndeath;j++){
                           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[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); */
                           }
                           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                   }
           }
           
           for(i=1; i<= nlstate; i++){
                   s1=0;
                   for(j=1; j<i; j++){
                           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); */
                   }
                   for(j=i+1; j<=nlstate+ndeath; j++){
                           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); */
                   }
                   /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                   ps[i][i]=1./(s1+1.);
                   /* Computing other pijs */
                   for(j=1; j<i; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   for(j=i+1; j<=nlstate+ndeath; j++)
                           ps[i][j]= exp(ps[i][j])*ps[i][i];
                   /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           } /* end i */
           
           for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                   for(jj=1; jj<= nlstate+ndeath; jj++){
                           ps[ii][jj]=0;
                           ps[ii][ii]=1;
                   }
           }
           /* Added for backcast */ /* Transposed matrix too */
           for(jj=1; jj<= nlstate+ndeath; jj++){
                   s1=0.;
                   for(ii=1; ii<= nlstate+ndeath; ii++){
                           s1+=ps[ii][jj];
                   }
                   for(ii=1; ii<= nlstate; ii++){
                           ps[ii][jj]=ps[ii][jj]/s1;
                   }
           }
           /* Transposition */
           for(jj=1; jj<= nlstate+ndeath; jj++){
                   for(ii=jj; ii<= nlstate+ndeath; ii++){
                           s1=ps[ii][jj];
                           ps[ii][jj]=ps[jj][ii];
                           ps[jj][ii]=s1;
                   }
           }
           /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
           /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
           /*   } */
           /*   printf("\n "); */
           /* } */
           /* printf("\n ");printf("%lf ",cov[2]);*/
           /*
                   for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   goto end;*/
           return ps;
 }  }
   
   
 /**************** Product of 2 matrices ******************/  /**************** Product of 2 matrices ******************/
   
 double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
Line 2140  double **matprod2(double **out, double * Line 2579  double **matprod2(double **out, double *
   
 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 )
 {  {
   /* Computes the transition matrix starting at age 'age' over     /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      nhstepm*hstepm matrices.        nhstepm*hstepm matrices. 
Line 2156  double ***hpxij(double ***po, int nhstep Line 2595  double ***hpxij(double ***po, int nhstep
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
   double agexact;    double agexact;
     double agebegin, ageend;
   
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
Line 2169  double ***hpxij(double ***po, int nhstep Line 2609  double ***hpxij(double ***po, int nhstep
       newm=savm;        newm=savm;
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
         cov[3]= agexact*agexact;                                  cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=cptcovn;k++) 
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];                                  cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */                          /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */                                  /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];                                  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */                          /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];                                  cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */                          /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
   
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                           /* right multiplication of oldm by the current matrix */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         /* if((int)age == 70){ */
         /*        printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
         /*        for(i=1; i<=nlstate+ndeath; i++) { */
         /*          printf("%d pmmij ",i); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",pmmij[i][j]); */
         /*          } */
         /*          printf(" oldm "); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",oldm[i][j]); */
         /*          } */
         /*          printf("\n"); */
         /*        } */
         /* } */
         savm=oldm;
         oldm=newm;
       }
       for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
                                   po[i][j][h]=newm[i][j];
                                   /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
       /*printf("h=%d ",h);*/
     } /* end h */
           /*     printf("\n H=%d \n",h); */
     return po;
   }
   
   /************* Higher Back Matrix Product ***************/
   /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
   double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
   {
     /* 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.
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step
        (typically every 2 years instead of every month which is too big
        for the memory).
        Model is determined by parameters x and covariates have to be
        included manually here.
   
     */
   
     int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
     double **newm;
     double agexact;
     double agebegin, ageend;
     double **oldm, **savm;
   
     oldm=oldms;savm=savms;
     /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
         newm=savm;
         /* Covariates have to be included here again */
         cov[1]=1.;
         agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
         /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
         cov[2]=agexact;
         if(nagesqr==1)
           cov[3]= agexact*agexact;
         for (k=1; k<=cptcovn;k++)
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
         for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
           /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
                           
                           
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         /* Careful transposed matrix */
         /* age is in cov[2] */
         /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
         /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
         out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                      1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         /* if((int)age == 70){ */
         /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
         /*        for(i=1; i<=nlstate+ndeath; i++) { */
         /*          printf("%d pmmij ",i); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",pmmij[i][j]); */
         /*          } */
         /*          printf(" oldm "); */
         /*          for(j=1;j<=nlstate+ndeath;j++) { */
         /*            printf("%f ",oldm[i][j]); */
         /*          } */
         /*          printf("\n"); */
         /*        } */
         /* } */
       savm=oldm;        savm=oldm;
       oldm=newm;        oldm=newm;
     }      }
Line 2199  double ***hpxij(double ***po, int nhstep Line 2743  double ***hpxij(double ***po, int nhstep
       }        }
     /*printf("h=%d ",h);*/      /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
 /*     printf("\n H=%d \n",h); */    /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
   
 #ifdef NLOPT  #ifdef NLOPT
   double  myfunc(unsigned n, const double *p1, double *grad, void *pd){    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   double fret;    double fret;
Line 2346  double func( double *x) Line 2891  double func( double *x)
 /*        else */  /*        else */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #endif */  /* #endif */
             lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
             
         } else if  (s2==-2) {          } else if  ( s2==-1 ) { /* alive */
           for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           /*survp += out[s1][j]; */            /*survp += out[s1][j]; */
           lli= log(survp);            lli= log(survp);
         }          }
           
         else if  (s2==-4) {           else if  (s2==-4) { 
           for (j=3,survp=0. ; j<=nlstate; j++)              for (j=3,survp=0. ; j<=nlstate; j++)  
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);             lli= log(survp); 
         }           } 
   
         else if  (s2==-5) {           else if  (s2==-5) { 
           for (j=1,survp=0. ; j<=2; j++)              for (j=1,survp=0. ; j<=2; j++)  
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);             lli= log(survp); 
         }           } 
           
         else{          else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
Line 2478  double func( double *x) Line 3020  double func( double *x)
         s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
         if( s2 > nlstate){           if( s2 > nlstate){ 
           lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
           } else if  ( s2==-1 ) { /* alive */
             for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += out[s1][j];
             lli= log(survp);
         }else{          }else{
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          }
Line 2540  double funcone( double *x) Line 3086  double funcone( double *x)
   int s1, s2;    int s1, s2;
   double bbh, survp;    double bbh, survp;
   double agexact;    double agexact;
     double agebegin, ageend;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 2558  double funcone( double *x) Line 3105  double funcone( double *x)
           oldm[ii][j]=(ii==j ? 1.0 : 0.0);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           savm[ii][j]=(ii==j ? 1.0 : 0.0);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }          }
       for(d=0; d<dh[mi][i]; d++){        
         agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
         ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
           /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
             and mw[mi+1][i]. dh depends on stepm.*/
         newm=savm;          newm=savm;
         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
         cov[2]=agexact;          cov[2]=agexact;
Line 2579  double funcone( double *x) Line 3131  double funcone( double *x)
               
       s1=s[mw[mi][i]][i];        s1=s[mw[mi][i]][i];
       s2=s[mw[mi+1][i]][i];        s2=s[mw[mi+1][i]][i];
         /* if(s2==-1){ */
         /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
         /*        /\* exit(1); *\/ */
         /* } */
       bbh=(double)bh[mi][i]/(double)stepm;         bbh=(double)bh[mi][i]/(double)stepm; 
       /* bias is positive if real duration        /* 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.
        */         */
       if( s2 > nlstate && (mle <5) ){  /* Jackson */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         lli=log(out[s1][s2] - savm[s1][s2]);          lli=log(out[s1][s2] - savm[s1][s2]);
       } else if  (s2==-2) {        } else if  ( s2==-1 ) { /* alive */
         for (j=1,survp=0. ; j<=nlstate; j++)           for (j=1,survp=0. ; j<=nlstate; j++) 
           survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         lli= log(survp);          lli= log(survp);
Line 2606  double funcone( double *x) Line 3162  double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        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]); */        /*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){        if(globpr){
         fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\          fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           llt +=ll[k]*gipmx/gsw;            llt +=ll[k]*gipmx/gsw;
Line 2646  void likelione(FILE *ficres,double p[], Line 3202  void likelione(FILE *ficres,double p[],
       printf("Problem with resultfile: %s\n", fileresilk);        printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     }      }
     fprintf(ficresilk, "#individual(line's_record) count age s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");      fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %weight 2wlli out sav ");      fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(k=1; k<=nlstate; k++)       for(k=1; k<=nlstate; k++) 
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
Line 2662  void likelione(FILE *ficres,double p[], Line 3218  void likelione(FILE *ficres,double p[],
     else if(mle >=1)      else if(mle >=1)
       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       
       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \  
 <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  
       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \  
 <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  
       fflush(fichtm);  
               
       for (k=1; k<= nlstate ; k++) {      for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \        fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
 <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);  <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
       }      }
       fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
   <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
   <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       fflush(fichtm);
   }    }
   return;    return;
 }  }
Line 2937  double hessij( double x[], double **hess Line 3493  double hessij( double x[], double **hess
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k, kmax=1;    int k, kmax=1;
   double v1, v2, cv12, lc1, lc2;    double v1, v2, cv12, lc1, lc2;
   
     int firstime=0;
       
   fx=func(x);    fx=func(x);
   for (k=1; k<=kmax; k=k+10) {    for (k=1; k<=kmax; k=k+10) {
Line 2958  double hessij( double x[], double **hess Line 3516  double hessij( double x[], double **hess
     k4=func(p2)-fx;      k4=func(p2)-fx;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */      res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
     if(k1*k2*k3*k4 <0.){      if(k1*k2*k3*k4 <0.){
         firstime=1;
       kmax=kmax+10;        kmax=kmax+10;
       if(kmax >=10){      }
       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);      if(kmax >=10 || firstime ==1){
       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);        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);
         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);
       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);        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);        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);
       }  
     }      }
 #ifdef DEBUGHESSIJ  #ifdef DEBUGHESSIJ
     v1=hess[thetai][thetai];      v1=hess[thetai][thetai];
Line 3118  void pstamp(FILE *fichier) Line 3677  void pstamp(FILE *fichier)
 }  }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
 {  /* Some frequencies */                                                                           int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],  \
                                                                              int firstpass,  int lastpass, int stepm, int weightopt, char model[])
   int i, m, jk, j1, bool, z1,j;   {  /* Some frequencies */
   int first;    
   double ***freq; /* Frequencies */           int i, m, jk, j1, bool, z1,j;
   double *pp, **prop;           int iind=0, iage=0;
   double pos,posprop, k2, dateintsum=0,k2cpt=0;           int mi; /* Effective wave */
   char fileresp[FILENAMELENGTH];           int first;
              double ***freq; /* Frequencies */
   pp=vector(1,nlstate);           double *pp, **prop, *posprop, *pospropt;
   prop=matrix(1,nlstate,iagemin,iagemax+3);           double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
   strcpy(fileresp,"P_");           char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
   strcat(fileresp,fileresu);           double agebegin, ageend;
   if((ficresp=fopen(fileresp,"w"))==NULL) {      
     printf("Problem with prevalence resultfile: %s\n", fileresp);           pp=vector(1,nlstate);
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);           prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
     exit(0);           posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
   }           pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);           /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
   j1=0;           strcpy(fileresp,"P_");
              strcat(fileresp,fileresu);
   j=cptcoveff;           /*strcat(fileresphtm,fileresu);*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           if((ficresp=fopen(fileresp,"w"))==NULL) {
                    printf("Problem with prevalence resultfile: %s\n", fileresp);
                    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));
                    fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
                    fflush(ficlog);
                    exit(70); 
            }
            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\
   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);
       
            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{
                    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\
   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);
   
            freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
            j1=0;
     
            j=cptcoveff;
            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 
            */
   
   first=1;           for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
                    posproptt=0.;
                    /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                            scanf("%d", i);*/
                    for (i=-5; i<=nlstate+ndeath; i++)  
                            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;
                    }
         
                    dateintsum=0;
                    k2cpt=0;
   
   /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */                   for (iind=1; iind<=imx; iind++) { /* For each individual iind */
   /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */                           bool=1;
   /*    j1++; */                           if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){                                   for (z1=1; z1<=cptcoveff; z1++) {      
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);                                           if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
         scanf("%d", i);*/                                                   /* Tests if the value of each of the covariates of i is equal to filter j1 */
       for (i=-5; i<=nlstate+ndeath; i++)                                                     bool=0;
         for (jk=-5; jk<=nlstate+ndeath; jk++)                                                     /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
           for(m=iagemin; m <= iagemax+3; m++)  
             freq[i][jk][m]=0;  
         
       for (i=1; i<=nlstate; i++)    
         for(m=iagemin; m <= iagemax+3; m++)  
           prop[i][m]=0;  
         
       dateintsum=0;  
       k2cpt=0;  
       for (i=1; i<=imx; i++) {  
         bool=1;  
         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */  
           for (z1=1; z1<=cptcoveff; z1++)         
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){  
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */  
               bool=0;  
               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",   
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                 j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/                                                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
             }                                            } 
         }                                   } /* end z1 */
                             } /* cptcovn > 0 */
         if (bool==1){  
           for(m=firstpass; m<=lastpass; m++){                           if (bool==1){
             k2=anint[m][i]+(mint[m][i]/12.);                                   /* for(m=firstpass; m<=lastpass; m++){ */
             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/                                   for(mi=1; mi<wav[iind];mi++){
               if(agev[m][i]==0) agev[m][i]=iagemax+1;                                           m=mw[mi][iind];
               if(agev[m][i]==1) agev[m][i]=iagemax+2;                                           /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];                                                          and mw[mi+1][iind]. dh depends on stepm. */
               if (m<lastpass) {                                           agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                                           ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
                 freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];                                           if(m >=firstpass && m <=lastpass){
               }                                                   k2=anint[m][iind]+(mint[m][iind]/12.);
                                                                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
               if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {                                                   if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                 dateintsum=dateintsum+k2;                                                   if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                 k2cpt++;                                                   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]); */
       } /* end i */                                                           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.));
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/                                                           freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
       pstamp(ficresp);                                                           /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
       if  (cptcovn>0) {                                                           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 */
         fprintf(ficresp, "\n#********** Variable ");                                                    }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                                           }  
         fprintf(ficresp, "**********\n#");                                           if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
         fprintf(ficlog, "\n#********** Variable ");                                                    dateintsum=dateintsum+k2;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                                                   k2cpt++;
         fprintf(ficlog, "**********\n#");                                                   /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
       }                                           }
       for(i=1; i<=nlstate;i++)                                            /*}*/
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);                                   } /* end m */
       fprintf(ficresp, "\n");                           } /* end bool */
                          } /* end iind = 1 to imx */
       for(i=iagemin; i <= iagemax+3; i++){         /* prop[s][age] is feeded for any initial and valid live state as well as
         if(i==iagemax+3){                                          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
           fprintf(ficlog,"Total");  
         }else{  
           if(first==1){                   /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             first=0;                   pstamp(ficresp);
             printf("See log file for details...\n");                   if  (cptcovn>0) {
           }                           fprintf(ficresp, "\n#********** Variable "); 
           fprintf(ficlog,"Age %d", i);                           fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
         }                           fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
         for(jk=1; jk <=nlstate ; jk++){                           for (z1=1; z1<=cptcoveff; z1++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                                   fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             pp[jk] += freq[jk][m][i];                                    fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         }                                   fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         for(jk=1; jk <=nlstate ; jk++){                           }
           for(m=-1, pos=0; m <=0 ; m++)                           fprintf(ficresp, "**********\n#");
             pos += freq[jk][m][i];                           fprintf(ficresphtm, "**********</h3>\n");
           if(pp[jk]>=1.e-10){                           fprintf(ficresphtmfr, "**********</h3>\n");
             if(first==1){                           fprintf(ficlog, "\n#********** Variable "); 
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }                           fprintf(ficlog, "**********\n");
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                   }
           }else{                   fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
             if(first==1)                   for(i=1; i<=nlstate;i++) {
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                           fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
           }                   }
         }                   fprintf(ficresp, "\n");
                    fprintf(ficresphtm, "\n");
         for(jk=1; jk <=nlstate ; jk++){        
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)                   /* Header of frequency table by age */
             pp[jk] += freq[jk][m][i];                   fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
         }                          fprintf(ficresphtmfr,"<th>Age</th> ");
         for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){                   for(jk=-1; jk <=nlstate+ndeath; jk++){
           pos += pp[jk];                           for(m=-1; m <=nlstate+ndeath; m++){
           posprop += prop[jk][i];                                   if(jk!=0 && m!=0)
         }                                           fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
         for(jk=1; jk <=nlstate ; jk++){                           }
           if(pos>=1.e-5){                   }
             if(first==1)                   fprintf(ficresphtmfr, "\n");
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                   /* For each age */
           }else{                   for(iage=iagemin; iage <= iagemax+3; iage++){
             if(first==1)                           fprintf(ficresphtm,"<tr>");
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                           if(iage==iagemax+1){
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                                   fprintf(ficlog,"1");
           }                                   fprintf(ficresphtmfr,"<tr><th>0</th> ");
           if( i <= iagemax){                           }else if(iage==iagemax+2){
             if(pos>=1.e-5){                                   fprintf(ficlog,"0");
               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);                                   fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
               /*probs[i][jk][j1]= pp[jk]/pos;*/                           }else if(iage==iagemax+3){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/                                   fprintf(ficlog,"Total");
             }                                   fprintf(ficresphtmfr,"<tr><th>Total</th> ");
             else                           }else{
               fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);                                   if(first==1){
           }                                           first=0;
         }                                           printf("See log file for details...\n");
                                            }
         for(jk=-1; jk <=nlstate+ndeath; jk++)                                   fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
           for(m=-1; m <=nlstate+ndeath; m++)                                   fprintf(ficlog,"Age %d", iage);
             if(freq[jk][m][i] !=0 ) {                           }
             if(first==1)                           for(jk=1; jk <=nlstate ; jk++){
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                                   for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);                                           pp[jk] += freq[jk][m][iage]; 
             }                           }
         if(i <= iagemax)                           for(jk=1; jk <=nlstate ; jk++){
           fprintf(ficresp,"\n");                                   for(m=-1, pos=0; m <=0 ; m++)
         if(first==1)                                           pos += freq[jk][m][iage];
           printf("Others in log...\n");                                   if(pp[jk]>=1.e-10){
         fprintf(ficlog,"\n");                                           if(first==1){
       }                                                   printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       /*}*/                                           }
   }                                           fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   dateintmean=dateintsum/k2cpt;                                    }else{
                                             if(first==1)
   fclose(ficresp);                                                   printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);                                           fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   free_vector(pp,1,nlstate);                                   }
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);                           }
   /* End of Freq */  
 }                           for(jk=1; jk <=nlstate ; jk++){ 
                                    /* posprop[jk]=0; */
                                    for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
                                            pp[jk] += freq[jk][m][iage];
                            }      /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
   
                            for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
                                    pos += pp[jk]; /* pos is the total number of transitions until this age */
                                    posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
                                                                                                                                                                            from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                                    pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
                                                                                                                                                                            from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
                            }
                            for(jk=1; jk <=nlstate ; jk++){
                                    if(pos>=1.e-5){
                                            if(first==1)
                                                    printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                                            fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                                    }else{
                                            if(first==1)
                                                    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                                            fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                                    }
                                    if( iage <= iagemax){
                                            if(pos>=1.e-5){
                                                    fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                                                    fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                                                    /*probs[iage][jk][j1]= pp[jk]/pos;*/
                                                    /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
                                            }
                                            else{
                                                    fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
                                                    fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
                                            }
                                    }
                                    pospropt[jk] +=posprop[jk];
                            } /* end loop jk */
                            /* pospropt=0.; */
                            for(jk=-1; jk <=nlstate+ndeath; jk++){
                                    for(m=-1; m <=nlstate+ndeath; m++){
                                            if(freq[jk][m][iage] !=0 ) { /* minimizing output */
                                                    if(first==1){
                                                            printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
                                                    }
                                                    fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
                                            }
                                            if(jk!=0 && m!=0)
                                                    fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
                                    }
                            } /* end loop jk */
                            posproptt=0.; 
                            for(jk=1; jk <=nlstate; jk++){
                                    posproptt += pospropt[jk];
                            }
                            fprintf(ficresphtmfr,"</tr>\n ");
                            if(iage <= iagemax){
                                    fprintf(ficresp,"\n");
                                    fprintf(ficresphtm,"</tr>\n");
                            }
                            if(first==1)
                                    printf("Others in log...\n");
                            fprintf(ficlog,"\n");
                    } /* end loop age iage */
                    fprintf(ficresphtm,"<tr><th>Tot</th>");
                    for(jk=1; jk <=nlstate ; jk++){
                            if(posproptt < 1.e-5){
                                    fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);  
                            }else{
                                    fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);   
                            }
                    }
                    fprintf(ficresphtm,"</tr>\n");
                    fprintf(ficresphtm,"</table>\n");
                    fprintf(ficresphtmfr,"</table>\n");
                    if(posproptt < 1.e-5){
                            fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
                            fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
                            fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
                            invalidvarcomb[j1]=1;
                    }else{
                            fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
                            invalidvarcomb[j1]=0;
                    }
                    fprintf(ficresphtmfr,"</table>\n");
            } /* end selected combination of covariate j1 */
            dateintmean=dateintsum/k2cpt; 
                    
            fclose(ficresp);
            fclose(ficresphtm);
            fclose(ficresphtmfr);
            free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
            free_vector(pospropt,1,nlstate);
            free_vector(posprop,1,nlstate);
            free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
            free_vector(pp,1,nlstate);
            /* End of Freq */
    }
   
 /************ Prevalence ********************/  /************ 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;
      int mi; /* Effective wave */
   double **prop;     int iage;
   double posprop;      double agebegin, ageend;
   double  y2; /* in fractional years */  
   int iagemin, iagemax;     double **prop;
   int first; /** to stop verbosity which is redirected to log file */     double posprop; 
      double  y2; /* in fractional years */
   iagemin= (int) agemin;     int iagemin, iagemax;
   iagemax= (int) agemax;     int first; /** to stop verbosity which is redirected to log file */
   /*pp=vector(1,nlstate);*/  
   prop=matrix(1,nlstate,iagemin,iagemax+3);      iagemin= (int) agemin;
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/     iagemax= (int) agemax;
   j1=0;     /*pp=vector(1,nlstate);*/
        prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   /*j=cptcoveff;*/     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}     j1=0;
       
   first=1;     /*j=cptcoveff;*/
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     /*for(i1=1; i1<=ncodemax[k1];i1++){    
       j1++;*/     first=1;
            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(m=iagemin; m <= iagemax+3; m++)         for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
           prop[i][m]=0.0;           prop[i][iage]=0.0;
            
       for (i=1; i<=imx; i++) { /* Each individual */       for (i=1; i<=imx; i++) { /* Each individual */
         bool=1;         bool=1;
         if  (cptcovn>0) {         if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           for (z1=1; z1<=cptcoveff; z1++)            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*/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
               bool=0;               bool=0;
         }          } 
         if (bool==1) {          if (bool==1) { /* For this combination of covariates values, this individual fits */
           for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/           /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */           for(mi=1; mi<wav[i];mi++){
             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */             m=mw[mi][i];
               if(agev[m][i]==0) agev[m][i]=iagemax+1;             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
               if(agev[m][i]==1) agev[m][i]=iagemax+2;             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
               if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);              if(m >=firstpass && m <=lastpass){
               if (s[m][i]>0 && s[m][i]<=nlstate) {                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                 /*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 ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 prop[s[m][i]][(int)agev[m][i]] += weight[i];                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 prop[s[m][i]][iagemax+3] += weight[i];                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
               }                  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); 
           } /* end selection of waves */                   exit(1);
         }                 }
       }                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for(i=iagemin; i <= iagemax+3; i++){                     /*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]]);*/
         for(jk=1,posprop=0; jk <=nlstate ; jk++) {                    prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
           posprop += prop[jk][i];                    prop[s[m][i]][iagemax+3] += weight[i]; 
         }                  } /* end valid statuses */ 
                        } /* end selection of dates */
         for(jk=1; jk <=nlstate ; jk++){                  } /* end selection of waves */
           if( i <=  iagemax){            } /* end effective waves */
             if(posprop>=1.e-5){          } /* end bool */
               probs[i][jk][j1]= prop[jk][i]/posprop;       }
             } else{       for(i=iagemin; i <= iagemax+3; i++){  
               if(first==1){         for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                 first=0;           posprop += prop[jk][i]; 
                 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]);         } 
               }        
             }         for(jk=1; jk <=nlstate ; jk++){      
           }            if( i <=  iagemax){ 
         }/* end jk */              if(posprop>=1.e-5){ 
       }/* end i */                probs[i][jk][j1]= prop[jk][i]/posprop;
     /*} *//* end i1 */             } else{
   } /* end j1 */               if(first==1){
                    first=0;
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/                 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]);
   /*free_vector(pp,1,nlstate);*/               }
   free_matrix(prop,1,nlstate, iagemin,iagemax+3);             }
 }  /* End of prevalence */           } 
          }/* end jk */ 
        }/* end i */ 
        /*} *//* end i1 */
      } /* end j1 */
     
      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
    }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
Line 3391  void  concatwav(int wav[], int **dh, int Line 4104  void  concatwav(int wav[], int **dh, int
   int i, mi, m;    int i, mi, m;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      double sum=0., jmean=0.;*/       double sum=0., jmean=0.;*/
   int first;    int first, firstwo, firsthree, firstfour;
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
     firstwo=0;
     firsthree=0;
     firstfour=0;
   jmin=100000;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;      mi=0;
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){      while(s[m][i] <= nlstate){  /* a live state */
       if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)        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;
       if(m >=lastpass)        }
         if(m >=lastpass){
           if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
             if(firsthree == 0){
               printf("Information! Unknown health 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.\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;
             }
             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.\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;
           }
           if(s[m][i]==-2){ /* Vital status is really unknown */
             nbwarn++;
             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);
               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.\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);
             }
             break;
           }
         break;          break;
         }
       else        else
         m++;          m++;
     }/* end while */      }/* end while */
     if (s[m][i] > nlstate){      
       /* After last pass */
       if (s[m][i] > nlstate){  /* In a death state */
       mi++;     /* Death is another wave */        mi++;     /* Death is another wave */
       /* if(mi==0)  never been interviewed correctly before death */        /* 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;        mw[mi][i]=m;
       }else if ((int) andc[i] != 9999) { /* Status is either death or 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; */
         nberr++;
         if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
           if(firstwo==0){
             printf("Error! Death for individual %ld line=%d  occurred %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;
           }
           fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %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 */
           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 );
             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 );
         }
     }      }
   
     wav[i]=mi;      wav[i]=mi;
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
Line 3428  void  concatwav(int wav[], int **dh, int Line 4183  void  concatwav(int wav[], int **dh, int
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
     /* wav and mw are no more changed */
   
     
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
Line 3520  void  concatwav(int wav[], int **dh, int Line 4277  void  concatwav(int wav[], int **dh, int
  }   }
   
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)   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 2 (V2)     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
    * nbcode[Tvar[j]][1]=      * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][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;
Line 3535  void tricode(int *Tvar, int **nbcode, in Line 4292  void tricode(int *Tvar, int **nbcode, in
   int modmincovj=0; /* Modality min of covariates j */    int modmincovj=0; /* Modality min of covariates j */
   
   
   cptcoveff=0;     /* cptcoveff=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 */
   
Line 3543  void tricode(int *Tvar, int **nbcode, in Line 4301  void tricode(int *Tvar, int **nbcode, in
   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
     for (k=-1; k < maxncov; k++) Ndum[k]=0;      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       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*/                                                                                                                                   modality of this covariate Vj*/ 
       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i        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 product of Vn*Vm, still boolean *:
                                     * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables                                                                                                                                                  * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                     * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */                                                                                                                                                  * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       /* Finds for covariate j, n=Tvar[j] of Vn . ij is the        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                       modality of the nth covariate of individual i. */                                        modality of the nth covariate of individual i. */
       if (ij > modmaxcovj)        if (ij > modmaxcovj)
         modmaxcovj=ij;           modmaxcovj=ij; 
       else if (ij < modmincovj)         else if (ij < modmincovj) 
         modmincovj=ij;                                   modmincovj=ij; 
       if ((ij < -1) && (ij > NCOVMAX)){        if ((ij < -1) && (ij > NCOVMAX)){
         printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );                                  printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
         exit(1);                                  exit(1);
       }else        }else
       Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
Line 3574  void tricode(int *Tvar, int **nbcode, in Line 4332  void tricode(int *Tvar, int **nbcode, in
       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */        if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
         if( k != -1){                                  if( k != -1){
           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th                                          ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
                              covariate for which somebody answered excluding                                                                                                                    covariate for which somebody answered excluding 
                              undefined. Usually 2: 0 and 1. */                                                                                                                   undefined. Usually 2: 0 and 1. */
         }                                  }
         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th                                  ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
                              covariate for which somebody answered including                                                                                                                                   covariate for which somebody answered including 
                              undefined. Usually 3: -1, 0 and 1. */                                                                                                                                  undefined. Usually 3: -1, 0 and 1. */
       }        }
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */                                   historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     } /* Ndum[-1] number of undefined modalities */      } /* Ndum[-1] number of undefined modalities */
                   
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.       /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
        If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;         If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
Line 3603  void tricode(int *Tvar, int **nbcode, in Line 4361  void tricode(int *Tvar, int **nbcode, in
     ij=0; /* ij is similar to i but can jump over null modalities */      ij=0; /* ij is similar to i but can jump over null modalities */
     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
         if (Ndum[i] == 0) { /* If nobody responded to this modality k */          if (Ndum[i] == 0) { /* If nobody responded to this modality k */
           break;                                  break;
         }                          }
         ij++;          ij++;
         nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/          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.*/
         cptcode = ij; /* New max modality for covar j */          cptcode = ij; /* New max modality for covar j */
Line 3625  void tricode(int *Tvar, int **nbcode, in Line 4383  void tricode(int *Tvar, int **nbcode, in
     /*   }  /\* end of loop on modality k *\/ */      /*   }  /\* end of loop on modality k *\/ */
   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       
  for (k=-1; k< maxncov; k++) Ndum[k]=0;           for (k=-1; k< maxncov; k++) Ndum[k]=0; 
       
   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */     for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/                   /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
    ij=Tvar[i]; /* Tvar might be -1 if status was unknown */                   ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
    Ndum[ij]++; /* Might be supersed V1 + V1*age */                  Ndum[ij]++; /* Might be supersed V1 + V1*age */
  }           } 
           
  ij=0;          ij=0;
  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */          for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/                  /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){                  if((Ndum[i]!=0) && (i<=ncovcol)){
      ij++;                          ij++;
      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/                          /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
      Tvaraff[ij]=i; /*For printing (unclear) */                          Tvaraff[ij]=i; /*For printing (unclear) */
    }else{                  }else{
        /* Tvaraff[ij]=0; */                          /* Tvaraff[ij]=0; */
    }                  }
  }          }
  /* ij--; */          /* ij--; */
  cptcoveff=ij; /*Number of total covariates*/          /* cptcoveff=ij; /\*Number of total covariates*\/ */
           *cptcov=ij; /*Number of total covariates*/
           
 }  }
   
   
Line 3764  void cvevsij(double ***eij, double x[], Line 4523  void cvevsij(double ***eij, double x[],
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
    to initial status i, ei. .       to initial status i, ei. .
   */    */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
Line 3858  void cvevsij(double ***eij, double x[], Line 4617  void cvevsij(double ***eij, double x[],
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
                   
     /* If stepm=6 months */      /* If stepm=6 months */
     /* Computed by stepm unit matrices, product of hstepma matrices, stored      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                   
     /* Computing  Variances of health expectancies */      /* Computing  Variances of health expectancies */
     /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        decrease memory allocation */         decrease memory allocation */
Line 3875  void cvevsij(double ***eij, double x[], Line 4634  void cvevsij(double ***eij, double x[],
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                             
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
           for(h=0; h<=nhstepm-1; h++){            for(h=0; h<=nhstepm-1; h++){
Line 3884  void cvevsij(double ***eij, double x[], Line 4643  void cvevsij(double ***eij, double x[],
           }            }
         }          }
       }        }
                                
       for(ij=1; ij<= nlstate*nlstate; ij++)        for(ij=1; ij<= nlstate*nlstate; ij++)
         for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
           gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
Line 3897  void cvevsij(double ***eij, double x[], Line 4656  void cvevsij(double ***eij, double x[],
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
           
                   
      for(ij=1;ij<=nlstate*nlstate;ij++)      for(ij=1;ij<=nlstate*nlstate;ij++)
       for(ji=1;ji<=nlstate*nlstate;ji++)        for(ji=1;ji<=nlstate*nlstate;ji++)
         varhe[ij][ji][(int)age] =0.;          varhe[ij][ji][(int)age] =0.;
                   
      printf("%d|",(int)age);fflush(stdout);      printf("%d|",(int)age);fflush(stdout);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      for(h=0;h<=nhstepm-1;h++){      for(h=0;h<=nhstepm-1;h++){
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
Line 3913  void cvevsij(double ***eij, double x[], Line 4672  void cvevsij(double ***eij, double x[],
             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
                   
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                                                     
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                                           
         }          }
                   
     fprintf(ficresstdeij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     for(i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++){
       eip=0.;        eip=0.;
Line 3938  void cvevsij(double ***eij, double x[], Line 4697  void cvevsij(double ***eij, double x[],
       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
     fprintf(ficresstdeij,"\n");      fprintf(ficresstdeij,"\n");
                   
     fprintf(ficrescveij,"%3.0f",age );      fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
Line 3951  void cvevsij(double ***eij, double x[], Line 4710  void cvevsij(double ***eij, double x[],
           }            }
       }        }
     fprintf(ficrescveij,"\n");      fprintf(ficrescveij,"\n");
                      
   }    }
   free_matrix(gm,0,nhstepm,1,nlstate*nlstate);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   free_matrix(gp,0,nhstepm,1,nlstate*nlstate);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
Line 3961  void cvevsij(double ***eij, double x[], Line 4720  void cvevsij(double ***eij, double x[],
   free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("\n");    printf("\n");
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
           
   free_vector(xm,1,npar);    free_vector(xm,1,npar);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(dnewm,1,nlstate*nlstate,1,npar);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 }  }
   
 /************ 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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])  
 {  
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   /* double **newm;*/  
   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/  
     
   int movingaverage();  
   double **dnewm,**doldm;  
   double **dnewmp,**doldmp;  
   int i, j, nhstepm, hstepm, h, nstepm ;  
   int k;  
   double *xp;  
   double **gp, **gm;  /* for var eij */  
   double ***gradg, ***trgradg; /*for var eij */  
   double **gradgp, **trgradgp; /* for var p point j */  
   double *gpp, *gmp; /* for var p point j */  
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */  
   double ***p3mat;  
   double age,agelim, hf;  
   double ***mobaverage;  
   int theta;  
   char digit[4];  
   char digitp[25];  
   
   char fileresprobmorprev[FILENAMELENGTH];  
   
   if(popbased==1){  
     if(mobilav!=0)  
       strcpy(digitp,"-POPULBASED-MOBILAV_");  
     else strcpy(digitp,"-POPULBASED-NOMOBIL_");  
   }  
   else   
     strcpy(digitp,"-STABLBASED_");  
   
   if (mobilav!=0) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){  
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
       printf(" Error in movingaverage mobilav=%d\n",mobilav);  
     }  
   }  
   
   strcpy(fileresprobmorprev,"PRMORPREV-");   
   sprintf(digit,"%-d",ij);  
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/  
   strcat(fileresprobmorprev,digit); /* Tvar to be done */  
   strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */  
   strcat(fileresprobmorprev,fileresu);  
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobmorprev);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);  
   }  
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);  
    
   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,"# Age cov=%-d",ij);  
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){  
     fprintf(ficresprobmorprev," p.%-d SE",j);  
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);  
   }    
   fprintf(ficresprobmorprev,"\n");  
   fprintf(ficgp,"\n# Routine varevsij");  
   fprintf(ficgp,"\nunset title \n");  
 /* fprintf(fichtm, "#Local time at start: %s", strstart);*/  
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");  
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);  
 /*   } */  
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   pstamp(ficresvij);  
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");  
   if(popbased==1)  
     fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);  
   else  
     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");  
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);  
   fprintf(ficresvij,"\n");  
   
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);  
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);  
   
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);  
   gpp=vector(nlstate+1,nlstate+ndeath);  
   gmp=vector(nlstate+1,nlstate+ndeath);  
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
     
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  
   else  hstepm=estepm;     
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.   
      nhstepm is the number of hstepm from age to agelim   
      nstepm is the number of stepm from age to agelin.   
      Look at function hpijx to understand why (it is linked to memory size questions) */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed every two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same   
      results. So we changed our mind and took the option of the best precision.  
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */   
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  
   
   
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);  
   
       if (popbased==1) {  
         if(mobilav ==0){  
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][ij];  
         }else{ /* mobilav */   
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=mobaverage[(int)age][i][ij];  
         }  
       }  
     
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  
       }  
       /* This for computing probability of death (h=1 means  
          computed over hstepm matrices product = hstepm*stepm months)   
          as a weighted average of prlim.  
       */  
       for(j=nlstate+1;j<=nlstate+ndeath;j++){  
         for(i=1,gpp[j]=0.; i<= nlstate; i++)  
           gpp[j] += prlim[i][i]*p3mat[i][j][1];  
       }      
       /* end probability of death */  
   
       for(i=1; i<=npar; i++) /* Computes gradient x - delta */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);  
     
       if (popbased==1) {  /************ Variance ******************/
         if(mobilav ==0){   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[])
           for(i=1; i<=nlstate;i++)   {
             prlim[i][i]=probs[(int)age][i][ij];     /* Variance of health expectancies */
         }else{ /* mobilav */      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           for(i=1; i<=nlstate;i++)     /* double **newm;*/
             prlim[i][i]=mobaverage[(int)age][i][ij];     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
         }    
       }     /* int movingaverage(); */
      double **dnewm,**doldm;
       for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */     double **dnewmp,**doldmp;
         for(h=0; h<=nhstepm; h++){     int i, j, nhstepm, hstepm, h, nstepm ;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)     int k;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];     double *xp;
         }     double **gp, **gm;  /* for var eij */
       }     double ***gradg, ***trgradg; /*for var eij */
       /* This for computing probability of death (h=1 means     double **gradgp, **trgradgp; /* for var p point j */
          computed over hstepm matrices product = hstepm*stepm months)      double *gpp, *gmp; /* for var p point j */
          as a weighted average of prlim.     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       */     double ***p3mat;
       for(j=nlstate+1;j<=nlstate+ndeath;j++){     double age,agelim, hf;
         for(i=1,gmp[j]=0.; i<= nlstate; i++)     /* double ***mobaverage; */
          gmp[j] += prlim[i][i]*p3mat[i][j][1];     int theta;
       }         char digit[4];
       /* end probability of death */     char digitp[25];
   
       for(j=1; j<= nlstate; j++) /* vareij */     char fileresprobmorprev[FILENAMELENGTH];
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];     if(popbased==1){
         }       if(mobilav!=0)
          strcpy(digitp,"-POPULBASED-MOBILAV_");
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */       else strcpy(digitp,"-POPULBASED-NOMOBIL_");
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];     }
       }     else 
        strcpy(digitp,"-STABLBASED_");
     } /* End theta */  
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */  
   
     for(h=0; h<=nhstepm; h++) /* veij */  
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  
   
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */  
       for(theta=1; theta <=npar; theta++)  
         trgradgp[j][theta]=gradgp[theta][j];  
     
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;  
   
     for(h=0;h<=nhstepm;h++){     /* if (mobilav!=0) { */
       for(k=0;k<=nhstepm;k++){     /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);     /*   if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);     /*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
         for(i=1;i<=nlstate;i++)     /*     printf(" Error in movingaverage mobilav=%d\n",mobilav); */
           for(j=1;j<=nlstate;j++)     /*   } */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;     /* } */
       }  
     }     strcpy(fileresprobmorprev,"PRMORPREV-"); 
      sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(fileresprobmorprev,fileresu);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      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,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
      fprintf(ficresprobmorprev,"\n");
     
      fprintf(ficgp,"\n# Routine varevsij");
      fprintf(ficgp,"\nunset title \n");
      /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      /*   } */
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      pstamp(ficresvij);
      fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
        fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
      else
        fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
      fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
      fprintf(ficresvij,"\n");
   
      xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       
     /* pptj */     if(estepm < stepm){
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       printf ("Problem %d lower than %d\n",estepm, stepm);
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);     }
     for(j=nlstate+1;j<=nlstate+ndeath;j++)     else  hstepm=estepm;   
       for(i=nlstate+1;i<=nlstate+ndeath;i++)     /* For example we decided to compute the life expectancy with the smallest unit */
         varppt[j][i]=doldmp[j][i];     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     /* end ppptj */        nhstepm is the number of hstepm from age to agelim 
     /*  x centered again */        nstepm is the number of stepm from age to agelim. 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);          Look at function hpijx to understand why because of memory size limitations, 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);        we decided (b) to get a life expectancy respecting the most precise curvature of the
          survival function given by stepm (the optimization length). Unfortunately it
     if (popbased==1) {        means that if the survival funtion is printed every two years of age and if
       if(mobilav ==0){        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(i=1; i<=nlstate;i++)        results. So we changed our mind and took the option of the best precision.
           prlim[i][i]=probs[(int)age][i][ij];     */
       }else{ /* mobilav */      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for(i=1; i<=nlstate;i++)     agelim = AGESUP;
           prlim[i][i]=mobaverage[(int)age][i][ij];     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       }       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* This for computing probability of death (h=1 means       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        computed over hstepm (estepm) matrices product = hstepm*stepm months)        gp=matrix(0,nhstepm,1,nlstate);
        as a weighted average of prlim.       gm=matrix(0,nhstepm,1,nlstate);
                   
                   
        for(theta=1; theta <=npar; theta++){
          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);
                           
          if (popbased==1) {
            if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
                           
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* 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++)
                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
          }
          /* Next for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
          /* end probability of death */
                           
          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);
                           
          if (popbased==1) {
            if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
            }
          }
                           
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                           
          for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
            for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
          }
          /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
          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];
          }    
          /* end probability of death */
                           
          for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
                           
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
                           
        } /* End theta */
                   
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                   
        for(h=0; h<=nhstepm; h++) /* veij */
          for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
                   
        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
                   
                   
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        for(i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
                   
        for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
            for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
        }
                   
        /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
        /* end ppptj */
        /*  x centered again */
                   
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
                   
        if (popbased==1) {
          if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
            for(i=1; i<=nlstate;i++)
              prlim[i][i]=mobaverage[(int)age][i][ij];
          }
        }
                   
        /* This for computing probability of death (h=1 means
           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);  
        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]; 
        }    
        /* end probability of death */
                   
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
        } 
        fprintf(ficresprobmorprev,"\n");
                   
        fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          }
        fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
      free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
      fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
      /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
      /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
     */      */
     for(j=nlstate+1;j<=nlstate+ndeath;j++){     /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
       for(i=1,gmp[j]=0.;i<= nlstate; i++)      fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
         gmp[j] += prlim[i][i]*p3mat[i][j][1];   
     }      
     /* end probability of death */  
   
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);  
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));  
       for(i=1; i<=nlstate;i++){  
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);  
       }  
     }   
     fprintf(ficresprobmorprev,"\n");  
   
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  
       }  
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  
   free_vector(gpp,nlstate+1,nlstate+ndeath);  
   free_vector(gmp,nlstate+1,nlstate+ndeath);  
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);  
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
   /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */  
   fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");  
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */  
   fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");  
   fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);  
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */  
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));  
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));  
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);  
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);  
 */  
 /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */  
   fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);  
   
   free_vector(xp,1,npar);     free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);     free_matrix(doldm,1,nlstate,1,nlstate);
   free_matrix(dnewm,1,nlstate,1,npar);     free_matrix(dnewm,1,nlstate,1,npar);
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   fclose(ficresprobmorprev);     fclose(ficresprobmorprev);
   fflush(ficgp);     fflush(ficgp);
   fflush(fichtm);      fflush(fichtm); 
 }  /* end varevsij */   }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ 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 *ncvyear, 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[])
 {  {
   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
Line 4290  void cvevsij(double ***eij, double x[], Line 5053  void cvevsij(double ***eij, double x[],
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
     double **mgm, **mgp;
   double age,agelim;    double age,agelim;
   int theta;    int theta;
       
Line 4312  void cvevsij(double ***eij, double x[], Line 5076  void cvevsij(double ***eij, double x[],
     if (stepm >= YEARM) hstepm=1;      if (stepm >= YEARM) hstepm=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     gradg=matrix(1,npar,1,nlstate);      gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
     gp=vector(1,nlstate);      gp=vector(1,nlstate);
     gm=vector(1,nlstate);      gm=vector(1,nlstate);
   
Line 4319  void cvevsij(double ***eij, double x[], Line 5085  void cvevsij(double ***eij, double x[],
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
               mgp[theta][i] = prlim[i][i];
         }
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);        if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
       for(i=1;i<=nlstate;i++)          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         else
           prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
         for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
           mgm[theta][i] = prlim[i][i];
         }
       for(i=1;i<=nlstate;i++)        for(i=1;i<=nlstate;i++)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
     } /* End theta */      } /* End theta */
   
     trgradg =matrix(1,nlstate,1,npar);      trgradg =matrix(1,nlstate,1,npar);
Line 4338  void cvevsij(double ***eij, double x[], Line 5113  void cvevsij(double ***eij, double x[],
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       for(theta=1; theta <=npar; theta++)        for(theta=1; theta <=npar; theta++)
         trgradg[j][theta]=gradg[theta][j];          trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] =0.;        varpl[i][(int)age] =0.;
     if((int)age==67 ||(int)age== 66 ){      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     }else{      }else{
Line 4357  void cvevsij(double ***eij, double x[], Line 5150  void cvevsij(double ***eij, double x[],
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
     free_vector(gp,1,nlstate);      free_vector(gp,1,nlstate);
     free_vector(gm,1,nlstate);      free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
     free_matrix(gradg,1,npar,1,nlstate);      free_matrix(gradg,1,npar,1,nlstate);
     free_matrix(trgradg,1,nlstate,1,npar);      free_matrix(trgradg,1,nlstate,1,npar);
   } /* End age */    } /* End age */
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(doldm,1,nlstate,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_matrix(dnewm,1,nlstate,1,nlstate);
   
 }  
   
 /************ Variance of one-step probabilities  ******************/  
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  
 {  
   int i, j=0,  k1, l1, tj;  
   int k2, l2, j1,  z1;  
   int k=0, l;  
   int first=1, first1, first2;  
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;  
   double **dnewm,**doldm;  
   double *xp;  
   double *gp, *gm;  
   double **gradg, **trgradg;  
   double **mu;  
   double age, cov[NCOVMAX+1];  
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  
   int theta;  
   char fileresprob[FILENAMELENGTH];  
   char fileresprobcov[FILENAMELENGTH];  
   char fileresprobcor[FILENAMELENGTH];  
   double ***varpij;  
   
   strcpy(fileresprob,"PROB_");   
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  
   }  
   strcpy(fileresprobcov,"PROBCOV_");   
   strcat(fileresprobcov,fileresu);  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcov);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);  
   }  
   strcpy(fileresprobcor,"PROBCOR_");   
   strcat(fileresprobcor,fileresu);  
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcor);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);  
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  
   pstamp(ficresprob);  
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");  
   fprintf(ficresprob,"# Age");  
   pstamp(ficresprobcov);  
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");  
   fprintf(ficresprobcov,"# Age");  
   pstamp(ficresprobcor);  
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  
   fprintf(ficresprobcor,"# Age");  
   
   
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }    
  /* fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");  
   fprintf(ficresprobcor,"\n");  
  */  
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  
   first=1;  
   fprintf(ficgp,"\n# Routine varprob");  
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");  
   fprintf(fichtm,"\n");  
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);  
   fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);  
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \  
 and drawn. It helps understanding how is the covariance between two incidences.\  
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");  
   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \  
 It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \  
 would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \  
 standard deviations wide on each axis. <br>\  
  Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\  
  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\  
 To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");  
   
   cov[1]=1;  
   /* tj=cptcoveff; */  
   tj = (int) pow(2,cptcoveff);  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}  
   j1=0;  
   for(j1=1; j1<=tj;j1++){  
     /*for(i1=1; i1<=ncodemax[t];i1++){ */  
     /*j1++;*/  
       if  (cptcovn>0) {  
         fprintf(ficresprob, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
         fprintf(ficresprob, "**********\n#\n");  
         fprintf(ficresprobcov, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
         fprintf(ficresprobcov, "**********\n#\n");  
           
         fprintf(ficgp, "\n#********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
         fprintf(ficgp, "**********\n#\n");  
           
           
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");  
           
         fprintf(ficresprobcor, "\n#********** Variable ");      
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
         fprintf(ficresprobcor, "**********\n#");      
       }  
         
       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));  
       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
       gp=vector(1,(nlstate)*(nlstate+ndeath));  
       gm=vector(1,(nlstate)*(nlstate+ndeath));  
       for (age=bage; age<=fage; age ++){   
         cov[2]=age;  
         if(nagesqr==1)  
           cov[3]= age*age;  
         for (k=1; k<=cptcovn;k++) {  
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];  
           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4  
                                                          * 1  1 1 1 1  
                                                          * 2  2 1 1 1  
                                                          * 3  1 2 1 1  
                                                          */  
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/  
         }  
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
         for (k=1; k<=cptcovprod;k++)  
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];  
           
       
         for(theta=1; theta <=npar; theta++){  
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);  
             
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
             
           k=0;  
           for(i=1; i<= (nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;  
               gp[k]=pmmij[i][j];  
             }  
           }  
             
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);  
       
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
           k=0;  
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;  
               gm[k]=pmmij[i][j];  
             }  
           }  
        
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)   
             gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];    
         }  
   
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];  
           
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);   
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
   
         pmij(pmmij,cov,ncovmodel,x,nlstate);  }
           
         k=0;  
         for(i=1; i<=(nlstate); i++){  
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;  
             mu[k][(int) age]=pmmij[i][j];  
           }  
         }  
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  
             varpij[i][j][(int)age] = doldm[i][j];  
   
         /*printf("\n%d ",(int)age);  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
           }*/  
   
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);  
         fprintf(ficresprobcor,"\n%d ",(int)age);  
   
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)  
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  
         }  
         i=0;  
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){   
             i++;  
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);  
             for (j=1; j<=i;j++){  
               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */  
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);  
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  
             }  
           }  
         }/* end of loop for state */  
       } /* end of loop for age */  
       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  
       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
         
       /* Confidence intervalle of pij  */  
       /*  
         fprintf(ficgp,"\nunset parametric;unset label");  
         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");  
         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);  
         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);  
         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);  
         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);  
       */  
   
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/  /************ Variance of one-step probabilities  ******************/
       first1=1;first2=2;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
       for (k2=1; k2<=(nlstate);k2++){   {
         for (l2=1; l2<=(nlstate+ndeath);l2++){      int i, j=0,  k1, l1, tj;
           if(l2==k2) continue;     int k2, l2, j1,  z1;
           j=(k2-1)*(nlstate+ndeath)+l2;     int k=0, l;
           for (k1=1; k1<=(nlstate);k1++){     int first=1, first1, first2;
             for (l1=1; l1<=(nlstate+ndeath);l1++){      double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
               if(l1==k1) continue;     double **dnewm,**doldm;
               i=(k1-1)*(nlstate+ndeath)+l1;     double *xp;
               if(i<=j) continue;     double *gp, *gm;
               for (age=bage; age<=fage; age ++){      double **gradg, **trgradg;
                 if ((int)age %5==0){     double **mu;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;     double age, cov[NCOVMAX+1];
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;     int theta;
                   mu1=mu[i][(int) age]/stepm*YEARM ;     char fileresprob[FILENAMELENGTH];
                   mu2=mu[j][(int) age]/stepm*YEARM;     char fileresprobcov[FILENAMELENGTH];
                   c12=cv12/sqrt(v1*v2);     char fileresprobcor[FILENAMELENGTH];
                   /* Computing eigen value of matrix of covariance */     double ***varpij;
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;  
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;     strcpy(fileresprob,"PROB_"); 
                   if ((lc2 <0) || (lc1 <0) ){     strcat(fileresprob,fileres);
                     if(first2==1){     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
                       first1=0;       printf("Problem with resultfile: %s\n", fileresprob);
                     printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
                     }     }
                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);     strcpy(fileresprobcov,"PROBCOV_"); 
                     /* lc1=fabs(lc1); */ /* If we want to have them positive */     strcat(fileresprobcov,fileresu);
                     /* lc2=fabs(lc2); */     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
                   }       printf("Problem with resultfile: %s\n", fileresprobcov);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
      strcpy(fileresprobcor,"PROBCOR_"); 
      strcat(fileresprobcor,fileresu);
      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      pstamp(ficresprob);
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
      pstamp(ficresprobcov);
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
      pstamp(ficresprobcor);
      fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      fprintf(ficresprobcor,"# Age");
   
   
      for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
      /* fprintf(ficresprob,"\n");
         fprintf(ficresprobcov,"\n");
         fprintf(ficresprobcor,"\n");
      */
      xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
      fprintf(ficgp,"\n# Routine varprob");
      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
   
      fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
      fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
                   /* Eigen vectors */     cov[1]=1;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));     /* tj=cptcoveff; */
                   /*v21=sqrt(1.-v11*v11); *//* error */     tj = (int) pow(2,cptcoveff);
                   v21=(lc1-v1)/cv12*v11;     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
                   v12=-v21;     j1=0;
                   v22=v11;     for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates */
                   tnalp=v21/v11;       if  (cptcovn>0) {
                   if(first1==1){         fprintf(ficresprob, "\n#********** Variable "); 
                     first1=0;         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);         fprintf(ficresprob, "**********\n#\n");
                   }         fprintf(ficresprobcov, "\n#********** Variable "); 
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                   /*printf(fignu*/         fprintf(ficresprobcov, "**********\n#\n");
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */                          
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */         fprintf(ficgp, "\n#********** Variable "); 
                   if(first==1){         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                     first=0;         fprintf(ficgp, "**********\n#\n");
                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");                          
                     fprintf(ficgp,"\nset parametric;unset label");                          
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                     fprintf(ficgp,"\nset ter svg size 640, 480");         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\                          
          fprintf(ficresprobcor, "\n#********** Variable ");    
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
          fprintf(ficresprobcor, "**********\n#");    
          if(invalidvarcomb[j1]){
            fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
            fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
            continue;
          }
        }
        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        gp=vector(1,(nlstate)*(nlstate+ndeath));
        gm=vector(1,(nlstate)*(nlstate+ndeath));
        for (age=bage; age<=fage; age ++){ 
          cov[2]=age;
          if(nagesqr==1)
            cov[3]= age*age;
          for (k=1; k<=cptcovn;k++) {
            cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
            /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                                       * 1  1 1 1 1
                                                                       * 2  2 1 1 1
                                                                       * 3  1 2 1 1
                                                                       */
            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
          }
          /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
          for (k=1; k<=cptcovprod;k++)
            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                           
                           
          for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++)
              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                                   
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                   
            k=0;
            for(i=1; i<= (nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
                gp[k]=pmmij[i][j];
              }
            }
                                   
            for(i=1; i<=npar; i++)
              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                                   
            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            k=0;
            for(i=1; i<=(nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
                gm[k]=pmmij[i][j];
              }
            }
                                   
            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
          }
   
          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            for(theta=1; theta <=npar; theta++)
              trgradg[j][theta]=gradg[theta][j];
                           
          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                           
          pmij(pmmij,cov,ncovmodel,x,nlstate);
                           
          k=0;
          for(i=1; i<=(nlstate); i++){
            for(j=1; j<=(nlstate+ndeath);j++){
              k=k+1;
              mu[k][(int) age]=pmmij[i][j];
            }
          }
          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
              varpij[i][j][(int)age] = doldm[i][j];
                           
          /*printf("\n%d ",(int)age);
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
            }*/
                           
          fprintf(ficresprob,"\n%d ",(int)age);
          fprintf(ficresprobcov,"\n%d ",(int)age);
          fprintf(ficresprobcor,"\n%d ",(int)age);
                           
          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
          }
          i=0;
          for (k=1; k<=(nlstate);k++){
            for (l=1; l<=(nlstate+ndeath);l++){ 
              i++;
              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
              for (j=1; j<=i;j++){
                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
              }
            }
          }/* end of loop for state */
        } /* end of loop for age */
        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       
        /* Confidence intervalle of pij  */
        /*
          fprintf(ficgp,"\nunset parametric;unset label");
          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
        */
                   
        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
        first1=1;first2=2;
        for (k2=1; k2<=(nlstate);k2++){
          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
            if(l2==k2) continue;
            j=(k2-1)*(nlstate+ndeath)+l2;
            for (k1=1; k1<=(nlstate);k1++){
              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                if(l1==k1) continue;
                i=(k1-1)*(nlstate+ndeath)+l1;
                if(i<=j) continue;
                for (age=bage; age<=fage; age ++){ 
                  if ((int)age %5==0){
                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                    mu1=mu[i][(int) age]/stepm*YEARM ;
                    mu2=mu[j][(int) age]/stepm*YEARM;
                    c12=cv12/sqrt(v1*v2);
                    /* Computing eigen value of matrix of covariance */
                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                    if ((lc2 <0) || (lc1 <0) ){
                      if(first2==1){
                        first1=0;
                        printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                      }
                      fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                      /* lc1=fabs(lc1); */ /* If we want to have them positive */
                      /* lc2=fabs(lc2); */
                    }
                                                                   
                    /* Eigen vectors */
                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                    /*v21=sqrt(1.-v11*v11); *//* error */
                    v21=(lc1-v1)/cv12*v11;
                    v12=-v21;
                    v22=v11;
                    tnalp=v21/v11;
                    if(first1==1){
                      first1=0;
                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                    }
                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                    /*printf(fignu*/
                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                    if(first==1){
                      first=0;
                      fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                      fprintf(ficgp,"\nset parametric;unset label");
                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                      fprintf(ficgp,"\nset ter svg size 640, 480");
                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
 %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   }else{                   }else{
                     first=0;                     first=0;
                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   }/* if first */                   }/* if first */
                 } /* age mod 5 */                 } /* age mod 5 */
               } /* end loop age */               } /* end loop age */
               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
               first=1;               first=1;
             } /*l12 */             } /*l12 */
           } /* k12 */           } /* k12 */
         } /*l1 */         } /*l1 */
       }/* k1 */       }/* k1 */
       /* } */ /* loop covariates */     }  /* loop on combination of covariates j1 */
   }     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);     free_vector(xp,1,npar);
   free_vector(xp,1,npar);     fclose(ficresprob);
   fclose(ficresprob);     fclose(ficresprobcov);
   fclose(ficresprobcov);     fclose(ficresprobcor);
   fclose(ficresprobcor);     fflush(ficgp);
   fflush(ficgp);     fflush(fichtmcov);
   fflush(fichtmcov);   }
 }  
   
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int estepm ,\                    int popforecast, int prevfcast, int backcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                   double jprev2, double mprev2,double anprev2){                    double jprev2, double mprev2,double anprev2, double dateprev2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     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 \     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
 </ul>");  </ul>");
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\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,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
      fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
      fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));             stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
    - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
      fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n",     <a href=\"%s\">%s</a> <br>\n",
            estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));             estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
    fprintf(fichtm,"\     if(prevfcast==1){
  - Population projections by age and states: \       fprintf(fichtm,"\
    - Prevalence projections by age and states:                            \
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
      }
   
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");     m=pow(2,cptcoveff);
      if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  m=pow(2,cptcoveff);     jj1=0;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     for(k1=1; k1<=m;k1++){
   
  jj1=0;       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
  for(k1=1; k1<=m;k1++){  
    /* for(i1=1; i1<=ncodemax[k1];i1++){ */  
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
Line 4748  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 5556  fprintf(fichtm," \n<ul><li><b>Graphs</b>
          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);           printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
        }         }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
            printf("\nCombination (%d) ignored because no cases \n",k1); 
            continue;
          }
      }       }
      /* aij, bij */       /* aij, bij */
      fprintf(fichtm,"<br>- Logit model, 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.svg\">%s_%d-1.svg</a><br> \
 <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);  <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>\n- Pij 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.svg\">%s_%d-2.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.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       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,\   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 hPij \   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: hPij/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.svg\">%s_%d-3.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.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
      /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
Line 4768  divided by h: hPij/h : <a href=\"%s_%d-3 Line 5581  divided by h: hPij/h : <a href=\"%s_%d-3
      }       }
      /* State specific survival functions (period) */       /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\         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.\   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.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);
      }       }
      /* Period (stable) prevalence in each health state */       /* Period (stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       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.svg\">%s_%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.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
      }       }
        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> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
          }
        }
        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> \
   <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);
          }
        }
            
      for(cpt=1; cpt<=nlstate;cpt++) {       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.svg\">%s_%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.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
      }       }
    /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
   
  fprintf(fichtm,"\     fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
Line 4797  variances but at the covariance matrix. Line 5625  variances but at the covariance matrix.
 covariance matrix of the one-step probabilities. \  covariance matrix of the one-step probabilities. \
 See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);  See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",     fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));             subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));             subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));             subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
          estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
          estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 4830  See page 'Matrix of variance-covariance Line 5658  See page 'Matrix of variance-covariance
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
  fflush(fichtm);     fflush(fichtm);
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
  m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
    /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++) 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
          if(invalidvarcomb[k1]){
            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
            continue;
          }
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \         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 <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%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.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       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) \  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\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg<br>\   observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%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.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
    /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
  fflush(fichtm);     fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){   void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    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,ij=0,l=0;
     int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
           int ioffset; /* variable offset for columns */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 4891  void printinggnuplot(char fileresu[], ch Line 5728  void printinggnuplot(char fileresu[], ch
 /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */  /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */      /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));      fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));      fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));      fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));      fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
     for (i=1; i<= nlstate ; i ++) {      for (i=1; i<= nlstate ; i ++) {
       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);        fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));        fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
       fprintf(ficgp,"  u  2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);        fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
       for (j=2; j<= nlstate+ndeath ; j ++) {        for (j=2; j<= nlstate+ndeath ; j ++) {
         fprintf(ficgp,",\\\n \"\" u  2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);                                  fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
       }        }
       fprintf(ficgp,";\nset out; unset ylabel;\n");         fprintf(ficgp,";\nset out; unset ylabel;\n"); 
     }      }
Line 4912  void printinggnuplot(char fileresu[], ch Line 5749  void printinggnuplot(char fileresu[], ch
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
  /* 1eme*/   /* 1eme*/
   fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
   for (cpt=1; cpt<= nlstate ; cpt ++) {      for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
     for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
      fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
      fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
      fprintf(ficgp,"set xlabel \"Age\" \n\                                  lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
 set ylabel \"Probability\" \n\                                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
 set ter svg size 640, 480\n\                                  /* 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 is the value of the covariate lv, 0 or 1 */
                           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
                                   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,"V_"),cpt,k1);
                           fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
                           fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n   \
   set ter svg size 640, 480\n     \
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
                           
      for (i=1; i<= nlstate ; i ++) {                          for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");                                  if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else        fprintf(ficgp," %%*lf (%%*lf)");                                  else        fprintf(ficgp," %%*lf (%%*lf)");
      }                          }
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);                          fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {                          for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");                                  if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," %%*lf (%%*lf)");                                  else fprintf(ficgp," %%*lf (%%*lf)");
      }                           } 
      fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);                           fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {                          for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");                                  if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," %%*lf (%%*lf)");                                  else fprintf(ficgp," %%*lf (%%*lf)");
      }                            }  
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));                          fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
      fprintf(ficgp,"\nset out \n");                          if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
                                   /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
                                   fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
                                   kl=0;
                                   for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                                           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                           vlv= nbcode[Tvaraff[k]][lv];
                                           kl++;
                                           /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                                           /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                                           /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                                           /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                                           if(k==cptcoveff){
                                                           fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                                                                                           6+(cpt-1),  cpt );
                                           }else{
                                                   fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                                                   kl++;
                                           }
                                   } /* end covariate */
                           }
                           fprintf(ficgp,"\nset out \n");
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
   /*2 eme*/    /*2 eme*/
   fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");  
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     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*/        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       if(vpopbased==0)        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);                                  lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
       else                                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
         fprintf(ficgp,"\nreplot ");                                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
       for (i=1; i<= nlstate+1 ; i ++) {                                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         k=2*i;                                  vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);                                  fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         for (j=1; j<= nlstate+1 ; j ++) {        }
           if (j==i) fprintf(ficgp," %%lf (%%lf)");        fprintf(ficgp,"\n#\n");
           else fprintf(ficgp," %%*lf (%%*lf)");                          if(invalidvarcomb[k1]){
         }                                                     fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);                                                  continue;
         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 ++) {                          fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
           if (j==i) fprintf(ficgp," %%lf (%%lf)");                          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           else fprintf(ficgp," %%*lf (%%*lf)");                                  if(vpopbased==0)
         }                                             fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
         fprintf(ficgp,"\" t\"\" w l lt 0,");                                  else
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);                                          fprintf(ficgp,"\nreplot ");
         for (j=1; j<= nlstate+1 ; j ++) {                                  for (i=1; i<= nlstate+1 ; i ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");                                          k=2*i;
           else fprintf(ficgp," %%*lf (%%*lf)");                                          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
         }                                             for (j=1; j<= nlstate+1 ; j ++) {
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");                                                  if (j==i) fprintf(ficgp," %%lf (%%lf)");
         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");                                                  else fprintf(ficgp," %%*lf (%%*lf)");
       } /* state */                                          }   
     } /* vpopbased */                                          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */                                          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 */    } /* k1 */
           
           
   /*3eme*/    /*3eme*/
     
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
   
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                   lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                   /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                   /* 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;
                           }
                           
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        k=2+(nlstate+1)*(cpt-1);
       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
       fprintf(ficgp,"set ter svg size 640, 480\n\        fprintf(ficgp,"set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),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);
     }      }
   }    }
       
           /* 4eme */
   /* Survival functions (period) from state i in state j by initial state i */    /* 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 multivariate if any */
   
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;        fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, 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);
         }
         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.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
 set ter svg size 640, 480\n\  set ter svg size 640, 480\n                                                                                                                                                                                     \
 unset log y\n\  unset log y\n                                                                                                                                                                                                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3;
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
         if(i==1)                                  if(i==1){
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));                                          fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else                                  }else{
           fprintf(ficgp,", '' ");                                          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);                                  l=(nlstate+ndeath)*(i-1)+1;
         for (j=2; j<= nlstate+ndeath ; j ++)                                  fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           fprintf(ficgp,"+$%d",k+l+j-1);                                  for (j=2; j<= nlstate+ndeath ; j ++)
         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);                                          fprintf(ficgp,"+$%d",k+l+j-1);
                                   fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
           
   /* 5eme */
   /* Survival functions (period) from state i in state j by final state j */    /* Survival functions (period) from state i in state j by final state j */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */    for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
       k=3;  
       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);        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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
 set ter svg size 640, 480\n\  set ter svg size 640, 480\n                                                                                                                                                                                     \
 unset log y\n\  unset log y\n                                                                                                                                                                                                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3;
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
         if(j==1)                                  if(j==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));                                          fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else                                  else
           fprintf(ficgp,", '' ");                                          fprintf(ficgp,", '' ");
         l=(nlstate+ndeath)*(cpt-1) +j;                                  l=(nlstate+ndeath)*(cpt-1) +j;
         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);                                  fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
         /* for (i=2; i<= nlstate+ndeath ; i ++) */                                  /* for (i=2; i<= nlstate+ndeath ; i ++) */
         /*   fprintf(ficgp,"+$%d",k+l+i-1); */                                  /*   fprintf(ficgp,"+$%d",k+l+i-1); */
         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);                                  fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,", '' ");        fprintf(ficgp,", '' ");
       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);        fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */        for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
         l=(nlstate+ndeath)*(cpt-1) +j;                                  l=(nlstate+ndeath)*(cpt-1) +j;
         if(j < nlstate)                                  if(j < nlstate)
           fprintf(ficgp,"$%d +",k+l);                                          fprintf(ficgp,"$%d +",k+l);
         else                                  else
           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);                                          fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
       }        }
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
           
   /* 6eme */
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */    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 */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       k=3;  
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' 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 */
                                   /* 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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n\  set ter svg size 640, 480\n\
 unset log y\n\  unset log y\n\
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
         if(i==1)                                  if(i==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));                                          fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else                                  else
           fprintf(ficgp,", '' ");                                          fprintf(ficgp,", '' ");
         l=(nlstate+ndeath)*(i-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);                                  fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
         for (j=2; j<= nlstate ; j ++)                                  for (j=2; j<= nlstate ; j ++)
           fprintf(ficgp,"+$%d",k+l+j-1);                                          fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);                                  fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
   
   /* proba elementaires */  
   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");  /* 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 (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                   fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
                                   for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                           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,"PB_"),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,"PIJB_"));
                                           else
                                                   fprintf(ficgp,", '' ");
                                           /* l=(nlstate+ndeath)*(i-1)+1; */
                                           l=(nlstate+ndeath)*(cpt-1)+1;
                                           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
                                           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
                                           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
                                           /* 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);
                                   } /* nlstate */
                                   fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* End if backcast */
     
           /* 8eme */
     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 (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                   fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
                                   for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
                                           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                           vlv= nbcode[Tvaraff[k]][lv];
                                           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                   }
                                   fprintf(ficgp,"\n#\n");
                                   if(invalidvarcomb[k1]){
                                                                   fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                                   continue;
                                   }
                                   
                                   fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
                                   fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
                                   fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\n     \
   unset log y\n   \
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
                                   for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                                           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
                                           if(i==1){
                                                   fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
                                           }else{
                                                   fprintf(ficgp,",\\\n '' ");
                                           }
                                           if(cptcoveff ==0){ /* No covariate */
                                                   ioffset=2; /* Age is in 2 */
                                                   /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                   /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                   /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                   /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                   fprintf(ficgp," u %d:(", ioffset); 
                                                   if(i==nlstate+1)
                                                           fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",                    \
                                                                                           ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                   else
                                                           fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",                    \
                                                                                           ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                           }else{ /* more than 2 covariates */
                                                   if(cptcoveff ==1){
                                                           ioffset=4; /* Age is in 4 */
                                                   }else{
                                                           ioffset=6; /* Age is in 6 */
                                                   /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                   /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                                                   }   
                                                   fprintf(ficgp," u %d:(",ioffset); 
                                                   kl=0;
                                                   strcpy(gplotcondition,"(");
                                                   for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                                                           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                                                           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                                           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                                           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                                           vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                                                           kl++;
                                                           sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                                                           kl++;
                                                           if(k <cptcoveff && cptcoveff>1)
                                                                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
                                                   }
                                                   strcpy(gplotcondition+strlen(gplotcondition),")");
                                                   /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                                                   /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                                                   /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                                                   /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                                                   if(i==nlstate+1){
                                                           fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
                                                                                           ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                   }else{
                                                                   fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                                                                                                   ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                                   }
                                           } /* end if covariate */
                                   } /* nlstate */
                                   fprintf(ficgp,"\nset out\n");
                           } /* end cpt state*/
                   } /* end covariate */
           } /* End if prevfcast */
           
           
           /* proba elementaires */
           fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
     fprintf(ficgp,"# initial state %d\n",i);      fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
Line 5174  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6272  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                else                 else
                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                   fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
              }               }
              if(ng != 1){             }else{
                fprintf(ficgp,")/(1");               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++){                for(k1=1; k1 <=nlstate; k1++){ 
                  if(nagesqr==0)                 if(nagesqr==0)
                    fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  else /* nagesqr =1 */                 else /* nagesqr =1 */
                    fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);                   fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
                                   
                  ij=1;                 ij=1;
                  for(j=3; j <=ncovmodel-nagesqr; j++){                 for(j=3; j <=ncovmodel-nagesqr; j++){
                    if(ij <=cptcovage) { /* Bug valgrind */                   if(ij <=cptcovage) { /* Bug valgrind */
                      if((j-2)==Tage[ij]) { /* Bug valgrind */                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                        fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                       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])]); */                       /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                        ij++;                       ij++;
                      }  
                    }                     }
                    else  
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);  
                  }                   }
                  fprintf(ficgp,")");                   else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
                if(ng ==2)  
                  fprintf(ficgp," t \"p%d%d\" ", k2,k);  
                else /* ng= 3 */  
                  fprintf(ficgp," t \"i%d%d\" ", k2,k);  
              }else{ /* end ng <> 1 */  
                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);  
              }               }
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");               fprintf(ficgp,")");
              i=i+ncovmodel;               if(ng ==2)
                  fprintf(ficgp," t \"p%d%d\" ", k2,k);
                else /* ng= 3 */
                  fprintf(ficgp," t \"i%d%d\" ", k2,k);
              }else{ /* end ng <> 1 */
                if( k !=k2) /* logit p11 is hard to draw */
                  fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
            }             }
              if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
                fprintf(ficgp,",");
              if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
                fprintf(ficgp,",");
              i=i+ncovmodel;
          } /* end k */           } /* end k */
        } /* end k2 */         } /* end k2 */
        fprintf(ficgp,"\n set out\n");         fprintf(ficgp,"\n set out\n");
Line 5219  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6326  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   
   
 /*************** Moving average **************/  /*************** Moving average **************/
 int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){  /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
    int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
   int i, cpt, cptcod;     
   int modcovmax =1;     int i, cpt, cptcod;
   int mobilavrange, mob;     int modcovmax =1;
   double age;     int mobilavrange, mob;
      int iage=0;
   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose   
                            a covariate has 2 modalities */     double sum=0.;
   if (cptcovn<1) modcovmax=1; /* At least 1 pass */     double age;
      double *sumnewp, *sumnewm;
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){     double *agemingood, *agemaxgood; /* Currently identical for all covariates */
     if(mobilav==1) mobilavrange=5; /* default */    
     else mobilavrange=mobilav;    
     for (age=bage; age<=fage; age++)     /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
       for (i=1; i<=nlstate;i++)     /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
         for (cptcod=1;cptcod<=modcovmax;cptcod++)  
           mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];     sumnewp = vector(1,ncovcombmax);
     /* We keep the original values on the extreme ages bage, fage and for      sumnewm = vector(1,ncovcombmax);
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2     agemingood = vector(1,ncovcombmax);  
        we use a 5 terms etc. until the borders are no more concerned.      agemaxgood = vector(1,ncovcombmax);
     */   
     for (mob=3;mob <=mobilavrange;mob=mob+2){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){       sumnewm[cptcod]=0.;
         for (i=1; i<=nlstate;i++){       sumnewp[cptcod]=0.;
           for (cptcod=1;cptcod<=modcovmax;cptcod++){       agemingood[cptcod]=0;
             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];       agemaxgood[cptcod]=0;
               for (cpt=1;cpt<=(mob-1)/2;cpt++){     }
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];    
               }     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
             mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;       if(mobilav==1) mobilavrange=5; /* default */
           }       else mobilavrange=mobilav;
         }       for (age=bage; age<=fage; age++)
       }/* end age */         for (i=1; i<=nlstate;i++)
     }/* end mob */           for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
   }else return -1;             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   return 0;       /* We keep the original values on the extreme ages bage, fage and for 
 }/* End movingaverage */          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
        */ 
        for (mob=3;mob <=mobilavrange;mob=mob+2){
          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
            for (i=1; i<=nlstate;i++){
              for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                }
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
              }
            }
          }/* end age */
        }/* end mob */
      }else
        return -1;
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
        /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
        if(invalidvarcomb[cptcod]){
          printf("\nCombination (%d) ignored because no cases \n",cptcod); 
          continue;
        }
   
        agemingood[cptcod]=fage-(mob-1)/2;
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemingood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        /* From youngest, finding the oldest wrong */
        agemaxgood[cptcod]=bage+(mob-1)/2;
        for (age=bage+(mob-1)/2; age<=fage; age++){
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
            agemaxgood[cptcod]=age;
          }else{ /* bad */
            for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            } /* i */
          } /* end bad */
        }/* age */
        sum=0.;
        for (i=1; i<=nlstate;i++){
          sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
        }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
          /* for (i=1; i<=nlstate;i++){ */
          /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* } /\* i *\/ */
        } /* end bad */
                   
        for (age=bage; age<=fage; age++){
          printf("%d %d ", cptcod, (int)age);
          sumnewp[cptcod]=0.;
          sumnewm[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewp[cptcod]+=probs[(int)age][i][cptcod];
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
          }
          /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
        }
        /* printf("\n"); */
        /* } */
        /* brutal averaging */
        for (i=1; i<=nlstate;i++){
          for (age=1; age<=bage; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }        
          for (age=fage; age<=AGESUP; age++){
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
            /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
          }
        } /* end i status */
        for (i=nlstate+1; i<=nlstate+ndeath;i++){
          for (age=1; age<=AGESUP; age++){
            /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
            mobaverage[(int)age][i][cptcod]=0.;
          }
        }
      }/* end cptcod */
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      free_vector(agemaxgood,1, ncovcombmax);
      free_vector(agemingood,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
    
   
 /************** Forecasting ******************/  /************** 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){
Line 5272  void prevforecast(char fileres[], double Line 6492  void prevforecast(char fileres[], double
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    /* double ***mobaverage; */
   char fileresf[FILENAMELENGTH];    char fileresf[FILENAMELENGTH];
   
   agelim=AGESUP;    agelim=AGESUP;
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
     /*          firstpass, lastpass,  stepm,  weightopt, model); */
     
   strcpy(fileresf,"F_");     strcpy(fileresf,"F_"); 
   strcat(fileresf,fileresu);    strcat(fileresf,fileresu);
Line 5284  void prevforecast(char fileres[], double Line 6509  void prevforecast(char fileres[], double
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   }    }
   printf("Computing forecasting: result on file '%s' \n", fileresf);    printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   if (mobilav!=0) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){  
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
       printf(" Error in movingaverage mobilav=%d\n",mobilav);  
     }  
   }  
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
Line 5326  void prevforecast(char fileres[], double Line 6544  void prevforecast(char fileres[], double
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#******");        fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                  fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficresf,"******\n");        fprintf(ficresf," yearproj age");
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");  
       for(j=1; j<=nlstate+ndeath;j++){         for(j=1; j<=nlstate+ndeath;j++){ 
         for(i=1; i<=nlstate;i++)                                                for(i=1; i<=nlstate;i++)              
           fprintf(ficresf," p%d%d",i,j);            fprintf(ficresf," p%d%d",i,j);
         fprintf(ficresf," p.%d",j);                                  fprintf(ficresf," wp.%d",j);
       }        }
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
         fprintf(ficresf,"\n");                                  fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);                                     fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
                                   for (agec=fage; agec>=(ageminpar-1); agec--){ 
         for (agec=fage; agec>=(ageminpar-1); agec--){                                           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm=(int) rint((agelim-agec)*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,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);                                            
                                                   for (h=0; h<=nhstepm; h++){
           for (h=0; h<=nhstepm; h++){                                                  if (h*hstepm/YEARM*stepm ==yearp) {
             if (h*hstepm/YEARM*stepm ==yearp) {  
               fprintf(ficresf,"\n");                fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++)                 for(j=1;j<=cptcoveff;j++) 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);                                                          fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             }                                                   } 
             for(j=1; j<=nlstate+ndeath;j++) {                                                  for(j=1; j<=nlstate+ndeath;j++) {
               ppij=0.;                                                          ppij=0.;
               for(i=1; i<=nlstate;i++) {                                                          for(i=1; i<=nlstate;i++) {
                 if (mobilav==1)                                                                   if (mobilav==1) 
                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];                                                                          ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                 else {                                                                  else {
                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];                                                                          ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                 }                                                                  }
                 if (h*hstepm/YEARM*stepm== yearp) {                                                                  if (h*hstepm/YEARM*stepm== yearp) {
                   fprintf(ficresf," %.3f", p3mat[i][j][h]);                                                                          fprintf(ficresf," %.3f", p3mat[i][j][h]);
                 }                                                                  }
               } /* end i */                                                          } /* end i */
               if (h*hstepm/YEARM*stepm==yearp) {                                                          if (h*hstepm/YEARM*stepm==yearp) {
                 fprintf(ficresf," %.3f", ppij);                                                                  fprintf(ficresf," %.3f", ppij);
               }                                                          }
             }/* end j */                                                  }/* end j */
           } /* end h */                                          } /* end h */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */                                  } /* end agec */
       } /* end yearp */        } /* end yearp */
     } /* end cptcod */      } /* end cptcod */
   } /* end  cptcov */    } /* end  cptcov */
                  
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   
   fclose(ficresf);    fclose(ficresf);
     printf("End of Computing forecasting \n");
     fprintf(ficlog,"End of Computing forecasting\n");
   
 }  }
   
   /* /\************** Back Forecasting ******************\/ */
   /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
   /*   /\* back1, year, month, day of starting backection  */
   /*      agemin, agemax range of age */
   /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
   /*      anback2 year of en of backection (same day and month as back1). */
   /*   *\/ */
   /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
   /*   double agec; /\* generic age *\/ */
   /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
   /*   double *popeffectif,*popcount; */
   /*   double ***p3mat; */
   /*   /\* double ***mobaverage; *\/ */
   /*   char fileresfb[FILENAMELENGTH]; */
           
   /*   agelim=AGESUP; */
   /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
   /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
   /*      We still use firstpass and lastpass as another selection. */
   /*   *\/ */
   /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
   /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
   /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
           
   /*   strcpy(fileresfb,"FB_");  */
   /*   strcat(fileresfb,fileresu); */
   /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
   /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
   /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
   /*   } */
   /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
   /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
           
   /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
           
   /*   /\* if (mobilav!=0) { *\/ */
   /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
   /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
   /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
   /*   /\*   } *\/ */
   /*   /\* } *\/ */
           
   /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
   /*   if (stepm<=12) stepsize=1; */
   /*   if(estepm < stepm){ */
   /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
   /*   } */
   /*   else  hstepm=estepm;    */
           
   /*   hstepm=hstepm/stepm;  */
   /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
   /*                                fractional in yp1 *\/ */
   /*   anprojmean=yp; */
   /*   yp2=modf((yp1*12),&yp); */
   /*   mprojmean=yp; */
   /*   yp1=modf((yp2*30.5),&yp); */
   /*   jprojmean=yp; */
   /*   if(jprojmean==0) jprojmean=1; */
   /*   if(mprojmean==0) jprojmean=1; */
           
   /*   i1=cptcoveff; */
   /*   if (cptcovn < 1){i1=1;} */
     
   /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
     
   /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
           
   /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
   /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
   /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
   /*       k=k+1; */
   /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
   /*       for(j=1;j<=cptcoveff;j++) { */
   /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*       } */
   /*       fprintf(ficresfb," yearbproj age"); */
   /*       for(j=1; j<=nlstate+ndeath;j++){  */
   /*                              for(i=1; i<=nlstate;i++)               */
   /*           fprintf(ficresfb," p%d%d",i,j); */
   /*                              fprintf(ficresfb," p.%d",j); */
   /*       } */
   /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
   /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
   /*                              fprintf(ficresfb,"\n"); */
   /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
   /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
   /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
   /*                                      nhstepm = nhstepm/hstepm;  */
   /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*                                      oldm=oldms;savm=savms; */
   /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
   /*                                      for (h=0; h<=nhstepm; h++){ */
   /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
   /*               fprintf(ficresfb,"\n"); */
   /*               for(j=1;j<=cptcoveff;j++)  */
   /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
   /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
   /*                                              }  */
   /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
   /*                                                      ppij=0.; */
   /*                                                      for(i=1; i<=nlstate;i++) { */
   /*                                                              if (mobilav==1)  */
   /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
   /*                                                              else { */
   /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
   /*                                                              } */
   /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */
   /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
   /*                                                              } */
   /*                                                      } /\* end i *\/ */
   /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */
   /*                                                              fprintf(ficresfb," %.3f", ppij); */
   /*                                                      } */
   /*                                              }/\* end j *\/ */
   /*                                      } /\* end h *\/ */
   /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
   /*                              } /\* end agec *\/ */
   /*       } /\* end yearp *\/ */
   /*     } /\* end cptcod *\/ */
   /*   } /\* end  cptcov *\/ */
           
   /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
           
   /*   fclose(ficresfb); */
   /*   printf("End of Computing Back forecasting \n"); */
   /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */
           
   /* } */
   
 /************** Forecasting *****not tested NB*************/  /************** 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 dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
       
Line 5391  void populforecast(char fileres[], doubl Line 6738  void populforecast(char fileres[], doubl
   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);
Line 5413  void populforecast(char fileres[], doubl Line 6760  void populforecast(char fileres[], doubl
   
   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;
Line 5428  void populforecast(char fileres[], doubl Line 6775  void populforecast(char fileres[], doubl
       
   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);
Line 5440  void populforecast(char fileres[], doubl Line 6787  void populforecast(char fileres[], doubl
           
     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++) {
Line 5460  void populforecast(char fileres[], doubl Line 6807  void populforecast(char fileres[], doubl
       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);
Line 5483  void populforecast(char fileres[], doubl Line 6830  void populforecast(char fileres[], doubl
               }                }
               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)) for(j=1; j<=nlstate;j++)               if (h==(int)(calagedatem+12*cpt))
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                for(j=1; j<=nlstate;j++) 
                   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--){ 
Line 5528  void populforecast(char fileres[], doubl Line 6876  void populforecast(char fileres[], doubl
           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);
Line 5542  void populforecast(char fileres[], doubl Line 6890  void populforecast(char fileres[], doubl
   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)  int fileappend(FILE *fichier, char *optionfich)
 {  {
   if((fichier=fopen(optionfich,"a"))==NULL) {    if((fichier=fopen(optionfich,"a"))==NULL) {
Line 5683  double gompertz(double x[]) Line 7031  double gompertz(double x[])
   double A,B,L=0.0,sump=0.,num=0.;    double A,B,L=0.0,sump=0.,num=0.;
   int i,n=0; /* n is the size of the sample */    int i,n=0; /* n is the size of the sample */
   
   for (i=0;i<=imx-1 ; i++) {    for (i=1;i<=imx ; i++) {
     sump=sump+weight[i];      sump=sump+weight[i];
     /*    sump=sump+1;*/      /*    sump=sump+1;*/
     num=num+1;      num=num+1;
Line 5817  int readdata(char datafile[], int firsto Line 7165  int readdata(char datafile[], int firsto
   
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
   }    }
   
   i=1;    i=1;
Line 6195  int decodemodel ( char model[], int last Line 7543  int decodemodel ( char model[], int last
 int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 {  {
   int i, m;    int i, m;
     int firstone=0;
     
   for (i=1; i<=imx; i++) {    for (i=1; i<=imx; i++) {
     for(m=2; (m<= maxwav); m++) {      for(m=2; (m<= maxwav); m++) {
       if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){        if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
         anint[m][i]=9999;          anint[m][i]=9999;
         s[m][i]=-1;          if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
             s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
         *nberr = *nberr + 1;          *nberr = *nberr + 1;
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);          if(firstone == 0){
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);            firstone=1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
           }
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
Line 6220  int calandcheckages(int imx, int maxwav, Line 7573  int calandcheckages(int imx, int maxwav,
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
     for(m=firstpass; (m<= lastpass); m++){      for(m=firstpass; (m<= lastpass); m++){
       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){        if(s[m][i] >0  || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
         if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
           if(agedc[i]>0){            if(agedc[i]>0){
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999){              if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
               agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
             }else {              }else {
               if ((int)andc[i]!=9999){                if ((int)andc[i]!=9999){
                 nbwarn++;                  nbwarn++;
Line 6235  int calandcheckages(int imx, int maxwav, Line 7588  int calandcheckages(int imx, int maxwav,
               }                }
             }              }
           } /* agedc > 0 */            } /* agedc > 0 */
         }          } /* end if */
         else if(s[m][i] !=9){ /* Standard case, age in fractional          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                  years but with the precision of a month */                                   years but with the precision of a month */
           agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
Line 6251  int calandcheckages(int imx, int maxwav, Line 7604  int calandcheckages(int imx, int maxwav,
           }            }
           /*agev[m][i]=anint[m][i]-annais[i];*/            /*agev[m][i]=anint[m][i]-annais[i];*/
           /*     agev[m][i] = age[i]+2*m;*/            /*     agev[m][i] = age[i]+2*m;*/
         }          } /* en if 9*/
         else { /* =9 */          else { /* =9 */
             /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
           agev[m][i]=1;            agev[m][i]=1;
           s[m][i]=-1;            s[m][i]=-1;
         }          }
       }        }
       else /*= 0 Unknown */        else if(s[m][i]==0) /*= 0 Unknown */
         agev[m][i]=1;          agev[m][i]=1;
     }        else{
               printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); 
           agev[m][i]=0;
         }
       } /* End for lastpass */
   }    }
       
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){      for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {        if (s[m][i] > (nlstate+ndeath)) {
Line 6485  void syscompilerinfo(int logged) Line 7844  void syscompilerinfo(int logged)
 #endif  #endif
         
   
  }  }
   
  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   int i, j, k, i1 ;    int i, j, k, i1 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
   double tot;    double tot;
   
   strcpy(filerespl,"PL_");    strcpy(filerespl,"PL_");
   strcat(filerespl,fileresu);    strcat(filerespl,fileresu);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      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;      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     }
     printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing 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 ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
     agebase=ageminpar;
     agelim=agemaxpar;
   
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
   
     for(k=1; k<=i1;k++){
     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       /* k=k+1; */
       /* to clean */
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
       fprintf(ficrespl,"#******");
       printf("#******");
       fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff;j++) {
         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(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);
         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 */
     return 0;
   }
   
   int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
           /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
           
           /* Computes the back prevalence limit  for any combination      of covariate values 
      * at any age between ageminpar and agemaxpar
            */
     int i, j, k, i1 ;
     /* double ftolpl = 1.e-10; */
     double age, agebase, agelim;
     double tot;
     /* double ***mobaverage; */
     /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
   
     strcpy(fileresplb,"PLB_");
     strcat(fileresplb,fileresu);
     if((ficresplb=fopen(fileresplb,"w"))==NULL) {
       printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
       fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
   }    }
   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
   pstamp(ficrespl);    pstamp(ficresplb);
   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficrespl,"#Age ");    fprintf(ficresplb,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
   fprintf(ficrespl,"\n");    fprintf(ficresplb,"\n");
       
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */    
     /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
     agebase=ageminpar;    
     agelim=agemaxpar;    agebase=ageminpar;
     agelim=agemaxpar;
     i1=pow(2,cptcoveff);    
     if (cptcovn < 1){i1=1;}    
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){          for(k=1; k<=i1;k++){ 
     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */      /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;      /* k=k+1; */
         /* to clean */      /* to clean */
         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));      //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
         fprintf(ficrespl,"#******");      fprintf(ficresplb,"#******");
         printf("#******");      printf("#******");
         fprintf(ficlog,"#******");      fprintf(ficlog,"#******");
         for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }      }
         fprintf(ficrespl,"******\n");      fprintf(ficresplb,"******\n");
         printf("******\n");      printf("******\n");
         fprintf(ficlog,"******\n");      fprintf(ficlog,"******\n");
                   if(invalidvarcomb[k]){
         fprintf(ficrespl,"#Age ");                                                  printf("\nCombination (%d) ignored because no cases \n",k); 
         for(j=1;j<=cptcoveff;j++) {                                                  fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                                  fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
         }                                                  continue;
         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);                  }
         fprintf(ficrespl,"Total Years_to_converge\n");      
               fprintf(ficresplb,"#Age ");
         for (age=agebase; age<=agelim; age++){      for(j=1;j<=cptcoveff;j++) {
         /* for (age=agebase; age<=agebase; age++){ */        fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);      }
           fprintf(ficrespl,"%.0f ",age );      for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
           for(j=1;j<=cptcoveff;j++)      fprintf(ficresplb,"Total Years_to_converge\n");
             fprintf(ficrespl,"%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 +=  prlim[i][i];        /* for (age=agebase; age<=agebase; age++){ */
             fprintf(ficrespl," %.5f", prlim[i][i]);        if(mobilavproj > 0){
           }          /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
           fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);          /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
         } /* Age */                                  bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
         /* 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);
         return 0;                                  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(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 */
     } /* cptcov */
     
     /* hBijx(p, bage, fage); */
     /* fclose(ficrespijb); */
     
     return 0;
 }  }
    
 int hPijx(double *p, int bage, int fage){  int hPijx(double *p, int bage, int fage){
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
   
Line 6585  int hPijx(double *p, int bage, int fage) Line 8054  int hPijx(double *p, int bage, int fage)
     agelim=AGESUP;      agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */      hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                   
     /* hstepm=1;   aff par mois*/      /* hstepm=1;   aff par mois*/
     pstamp(ficrespij);      pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,cptcoveff);      i1= pow(2,cptcoveff);
    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*   k=k+1;  */                  /*      k=k+1;  */
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
Line 6626  int hPijx(double *p, int bage, int fage) Line 8095  int hPijx(double *p, int bage, int fage)
       }        }
       /*}*/        /*}*/
     }      }
         return 0;      return 0;
 }  }
    
    int hBijx(double *p, int bage, int fage, double ***prevacurrent){
       /*------------- h Bij x at various ages ------------*/
   
     int stepsize;
     /* int agelim; */
           int ageminl;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
           
     double agedeb;
     double ***p3mat;
           
     strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
     if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
       printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
       fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
     }
     printf("Computing pij back: result on file '%s' \n", filerespijb);
     fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
     
     /* agelim=AGESUP; */
     ageminl=30;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
     
     /* hstepm=1;   aff par mois*/
     pstamp(ficrespijb);
     fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
     i1= pow(2,cptcoveff);
     /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
     /*    k=k+1;  */
     for (k=1; k <= (int) pow(2,cptcoveff); k++){
       fprintf(ficrespijb,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;
       }
       
       /* 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) */
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
         
         /*          nhstepm=nhstepm*YEARM; aff par mois*/
         
         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,prevacurrent,nlstate,stepm, k);
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");
         for (h=0; h<=nhstepm; h++){
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           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");
       }
       /*}*/
     }
     return 0;
    } /*  hBijx */
   
   
 /***********************************************/  /***********************************************/
Line 6645  int main(int argc, char *argv[]) Line 8195  int main(int argc, char *argv[])
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;    int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   int ncvyearnp=0;    int ncvyear=0; /* Number of years needed for the period prevalence to converge */
   int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */  
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
   int num_filled;    int num_filled;
Line 6661  int main(int argc, char *argv[]) Line 8210  int main(int argc, char *argv[])
   double agedeb=0.;    double agedeb=0.;
   
   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;    double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
     double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
   
   double fret;    double fret;
   double dum=0.; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    /* double ***mobaverage; */
   
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
Line 6681  int main(int argc, char *argv[]) Line 8231  int main(int argc, char *argv[])
   
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int backcast=0;
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm=0, nhstepm=0;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
Line 6691  int main(int argc, char *argv[]) Line 8242  int main(int argc, char *argv[])
   double bage=0, fage=110., age, agelim=0., agebase=0.;    double bage=0, fage=110., age, agelim=0., agebase=0.;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
     double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
   double  *p;    double  *p;
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
Line 6702  int main(int argc, char *argv[]) Line 8254  int main(int argc, char *argv[])
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
   
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
   int *dcwave;    int *dcwave;
Line 6906  int main(int argc, char *argv[]) Line 8460  int main(int argc, char *argv[])
   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \    if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){                          &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
     if (num_filled != 8) {      if (num_filled != 8) {
       printf("Not 8\n");        printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         printf("but line=%s\n",line);
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);      printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
   }    }
   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
   ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
   /* Third parameter line */    /* Third parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
Line 7005  int main(int argc, char *argv[]) Line 8560  int main(int argc, char *argv[])
     fclose (ficlog);      fclose (ficlog);
     goto end;      goto end;
     exit(0);      exit(0);
   }    }  else if(mle==-5) { /* Main Wizard */
   else if(mle==-3) { /* Main Wizard */  
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
     hess=matrix(1,npar,1,npar);      hess=matrix(1,npar,1,npar);
   }    }  else{ /* Begin of mle != -1 or -5 */
   else{  
     /* Read guessed parameters */      /* Read guessed parameters */
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
Line 7029  int main(int argc, char *argv[]) Line 8582  int main(int argc, char *argv[])
           
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       j=0;                          j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){        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 \  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);  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);      fflush(ficlog);
Line 7080  run imach with mle=-1 to get a correct t Line 8633  run imach with mle=-1 to get a correct t
   
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        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);      fflush(ficlog);
                   
     /* Reads covariance matrix */      /* Reads covariance matrix */
     delti=delti3[1][1];      delti=delti3[1][1];
                   
                   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */      /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
                     
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
Line 7119  run imach with mle=-1 to get a correct t Line 8672  run imach with mle=-1 to get a correct t
       fputs(line,ficlog);        fputs(line,ficlog);
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
                     
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
     hess=matrix(1,npar,1,npar);      hess=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=1; j <=npar; j++) matcov[i][j]=0.;        for(j=1; j <=npar; j++) matcov[i][j]=0.;
                         
     /* Scans npar lines */      /* Scans npar lines */
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);        count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
       if(count != 3){        if(count != 3){
         printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\                                  printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
         fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\                                  fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
         exit(1);                                  exit(1);
       }else        }else{
       if(mle==1)                                  if(mle==1)
         printf("%1d%1d%1d",i1,j1,jk);                                          printf("%1d%1d%1d",i1,j1,jk);
                           }
       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);        fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);        fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
       for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);                                  fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){                                  if(mle==1){
           printf(" %.5le",matcov[i][j]);                                          printf(" %.5le",matcov[i][j]);
         }                                  }
         fprintf(ficlog," %.5le",matcov[i][j]);                                  fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);                                  fprintf(ficparo," %.5le",matcov[i][j]);
       }        }
       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");
     }      }
     /* End of read covariance matrix npar lines */      /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)        for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];                                  matcov[i][j]=matcov[j][i];
           
     if(mle==1)      if(mle==1)
       printf("\n");        printf("\n");
Line 7178  Please run with mle=-1 to get a correct Line 8732  Please run with mle=-1 to get a correct
     }      }
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
     
   /*  Main data    /*  Main data
    */     */
   n= lastobs;    n= lastobs;
Line 7187  Please run with mle=-1 to get a correct Line 8741  Please run with mle=-1 to get a correct
   annais=vector(1,n);    annais=vector(1,n);
   moisdc=vector(1,n);    moisdc=vector(1,n);
   andc=vector(1,n);    andc=vector(1,n);
     weight=vector(1,n);
   agedc=vector(1,n);    agedc=vector(1,n);
   cod=ivector(1,n);    cod=ivector(1,n);
   weight=vector(1,n);    for(i=1;i<=n;i++){
   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                  num[i]=0;
                   moisnais[i]=0;
                   annais[i]=0;
                   moisdc[i]=0;
                   andc[i]=0;
                   agedc[i]=0;
                   cod[i]=0;
                   weight[i]=1.0; /* Equal weights, 1 by default */
           }
   mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,1,n);
   anint=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 */     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
Line 7260  Please run with mle=-1 to get a correct Line 8823  Please run with mle=-1 to get a correct
   free_vector(annais,1,n);    free_vector(annais,1,n);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/       free_matrix(anint,1,maxwav,1,n);*/
   free_vector(moisdc,1,n);    /* free_vector(moisdc,1,n); */
   free_vector(andc,1,n);    /* free_vector(andc,1,n); */
   /* */    /* */
       
   wav=ivector(1,imx);    wav=ivector(1,imx);
   dh=imatrix(1,lastpass-firstpass+1,1,imx);    /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
   bh=imatrix(1,lastpass-firstpass+1,1,imx);    /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
   mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
     dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
     bh=imatrix(1,lastpass-firstpass+2,1,imx);
     mw=imatrix(1,lastpass-firstpass+2,1,imx);
         
   /* Concatenates waves */    /* Concatenates waves */
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
        mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi 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.
     */
   
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   /* */    /* */
     
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;    ncodemax[1]=1;
   Ndum =ivector(-1,NCOVMAX);      Ndum =ivector(-1,NCOVMAX);  
   if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */          cptcoveff=0;
     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
   /* Nbcode gives the value of the lth modality of jth covariate, in      tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
           }
           
           ncovcombmax=pow(2,cptcoveff);
           invalidvarcomb=ivector(1, ncovcombmax); 
           for(i=1;i<ncovcombmax;i++)
                   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).*/       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /* 1 to ncodemax[j] is the maximum value of this jth covariate */    /* 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) */    /*  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));*/    /*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).*/    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;    /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j, 
      * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded 
      * (currently 0 or 1) in the data.
      * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of 
      * corresponding modality (h,j).
      */
   
     h=0;
   /*if (cptcovn > 0) */    /*if (cptcovn > 0) */
         
    
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1            /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
            * For k=4 covariates, h goes from 1 to 2**k             * For k=4 covariates, h goes from 1 to m=2**k
            * codtabm(h,k)=  1 & (h-1) >> (k-1) ;             * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
              * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
            *     h\k   1     2     3     4             *     h\k   1     2     3     4
            *______________________________               *______________________________  
            *     1 i=1 1 i=1 1 i=1 1 i=1 1             *     1 i=1 1 i=1 1 i=1 1 i=1 1
Line 7317  Please run with mle=-1 to get a correct Line 8904  Please run with mle=-1 to get a correct
            *    15 i=8 1     2     2     2             *    15 i=8 1     2     2     2
            *    16     2     2     2     2             *    16     2     2     2     2
            */             */
   /* /\* for(h=1; h <=100 ;h++){  *\/ */    /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
   /*   /\* printf("h=%2d ", h); *\/ */       /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
   /*    /\* for(k=1; k <=10; k++){ *\/ */       * and the value of each covariate?
   /*      /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */       * V1=1, V2=1, V3=2, V4=1 ?
   /*    /\*   codtab[h][k]=codtabm(h,k); *\/ */       * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
   /*    /\* } *\/ */       * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
   /*    /\* printf("\n"); *\/ */       * In order to get the real value in the data, we use nbcode
   /* } */       * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
   /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */       * We are keeping this crazy system in order to be able (in the future?) 
   /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */       * to have more than 2 values (0 or 1) for a covariate.
   /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */       * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
   /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */       * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
   /*      h++; */       *              bbbbbbbb
   /*      if (h>m)  */       *              76543210     
   /*        h=1; */       *   h-1        00000101 (6-1=5)
   /*      codtab[h][k]=j; */       *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
   /*      /\* codtab[12][3]=1; *\/ */       *           &
   /*      /\*codtab[h][Tvar[k]]=j;*\/ */       *     1        00000001 (1)
   /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */       *              00000000        = 1 & ((h-1) >> (k-1))
   /*    }  */       *          +1= 00000001 =1 
   /*     } */       *
   /*   } */       * h=14, k=3 => h'=h-1=13, k'=k-1=2
   /* }  */       *          h'      1101 =2^3+2^2+0x2^1+2^0
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        *    >>k'            11
      codtab[1][2]=1;codtab[2][2]=2; */       *          &   00000001
   /* for(i=1; i <=m ;i++){  */       *            = 00000001
   /*    for(k=1; k <=cptcovn; k++){ */       *      +1    = 00000010=2    =  codtabm(14,3)   
   /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */       * Reverse h=6 and m=16?
   /*    } */       * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
   /*    printf("\n"); */       * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
   /* } */       * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1 
   /*   scanf("%d",i);*/       * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
        * V3=decodtabm(14,3,2**4)=2
        *          h'=13   1101 =2^3+2^2+0x2^1+2^0
        *(h-1) >> (j-1)    0011 =13 >> 2
        *          &1 000000001
        *           = 000000001
        *         +1= 000000010 =2
        *                  2211
        *                  V1=1+1, V2=0+1, V3=1+1, V4=1+1
        *                  V3=2
                    * codtabm and decodtabm are identical
        */
   
   
  free_ivector(Ndum,-1,NCOVMAX);   free_ivector(Ndum,-1,NCOVMAX);
   
Line 7395  Title=%s <br>Datafile=%s Firstpass=%d La Line 8994  Title=%s <br>Datafile=%s Firstpass=%d La
           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   
   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015</a></font><br>  \    fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 <font size=\"2\">IMaCh-%s <br> %s</font> \  <font size=\"2\">IMaCh-%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
Line 7423  Title=%s <br>Datafile=%s Firstpass=%d La Line 9022  Title=%s <br>Datafile=%s Firstpass=%d La
 #endif  #endif
                       
       
   /* Calculates basic frequencies. Computes observed prevalence at single age    /* Calculates basic frequencies. Computes observed prevalence at single age 
                    and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,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);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 7433  Youngest age at first (selected) pass %. Line 9034  Youngest age at first (selected) pass %.
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);            imx,agemin,agemax,jmin,jmax,jmean);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
   /* For Powell, parameters are in a vector p[] starting at p[1]    /* For Powell, parameters are in a vector p[] starting at p[1]
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
Line 7447  Interval (in months) between two waves: Line 9047  Interval (in months) between two waves:
   /* For mortality only */    /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(1,NDIM,1,NDIM); 
                   for(i=1;i<=NDIM;i++)
                           for(j=1;j<=NDIM;j++)
                                   ximort[i][j]=0.;
     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
Line 7456  Interval (in months) between two waves: Line 9059  Interval (in months) between two waves:
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
       for (m=firstpass; m<=lastpass; m++)        for (m=firstpass; m<=lastpass; m++)
         if (s[m][i]>nlstate) {                                  if (s[m][i]>nlstate) {
           dcwave[i]=m;                                          dcwave[i]=m;
           /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/                                          /*      printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
           break;                                          break;
         }                                  }
     }      }
                   
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) {
       if (wav[i]>0){        if (wav[i]>0){
         ageexmed[i]=agev[mw[1][i]][i];                                  ageexmed[i]=agev[mw[1][i]][i];
         j=wav[i];                                  j=wav[i];
         agecens[i]=1.;                                   agecens[i]=1.; 
                                   
         if (ageexmed[i]> 1 && wav[i] > 0){                                  if (ageexmed[i]> 1 && wav[i] > 0){
           agecens[i]=agev[mw[j][i]][i];                                          agecens[i]=agev[mw[j][i]][i];
           cens[i]= 1;                                          cens[i]= 1;
         }else if (ageexmed[i]< 1)                                   }else if (ageexmed[i]< 1) 
           cens[i]= -1;                                          cens[i]= -1;
         if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)                                  if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
           cens[i]=0 ;                                          cens[i]=0 ;
       }        }
       else cens[i]=-1;        else cens[i]=-1;
     }      }
           
     for (i=1;i<=NDIM;i++) {      for (i=1;i<=NDIM;i++) {
       for (j=1;j<=NDIM;j++)        for (j=1;j<=NDIM;j++)
         ximort[i][j]=(i == j ? 1.0 : 0.0);                                  ximort[i][j]=(i == j ? 1.0 : 0.0);
     }      }
           
     /*p[1]=0.0268; p[NDIM]=0.083;*/      /*p[1]=0.0268; p[NDIM]=0.083;*/
Line 7595  Interval (in months) between two waves: Line 9198  Interval (in months) between two waves:
   
     for(i=1; i <=NDIM; i++)      for(i=1; i <=NDIM; i++)
       for(j=i+1;j<=NDIM;j++)        for(j=i+1;j<=NDIM;j++)
         matcov[i][j]=matcov[j][i];                                  matcov[i][j]=matcov[j][i];
           
     printf("\nCovariance matrix\n ");      printf("\nCovariance matrix\n ");
     fprintf(ficlog,"\nCovariance matrix\n ");      fprintf(ficlog,"\nCovariance matrix\n ");
     for(i=1; i <=NDIM; i++) {      for(i=1; i <=NDIM; i++) {
       for(j=1;j<=NDIM;j++){         for(j=1;j<=NDIM;j++){ 
         printf("%f ",matcov[i][j]);                                  printf("%f ",matcov[i][j]);
         fprintf(ficlog,"%f ",matcov[i][j]);                                  fprintf(ficlog,"%f ",matcov[i][j]);
       }        }
       printf("\n ");  fprintf(ficlog,"\n ");        printf("\n ");  fprintf(ficlog,"\n ");
     }      }
Line 7643  Interval (in months) between two waves: Line 9246  Interval (in months) between two waves:
           
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
                   ageminpar=50;
                   agemaxpar=100;
     if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){      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\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
Line 7650  Please run with mle=-1 to get a correct Line 9255  Please run with mle=-1 to get a correct
         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\  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);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else      }else{
                           printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
                           fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
       printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);        printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
                   }
     printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \      printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
                      stepm, weightopt,\                       stepm, weightopt,\
                      model,imx,p,matcov,agemortsup);                       model,imx,p,matcov,agemortsup);
Line 7659  Please run with mle=-1 to get a correct Line 9267  Please run with mle=-1 to get a correct
     free_vector(lsurv,1,AGESUP);      free_vector(lsurv,1,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,1,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,1,AGESUP);
 #ifdef GSL      free_matrix(ximort,1,NDIM,1,NDIM);
     free_ivector(cens,1,n);      free_ivector(cens,1,n);
     free_vector(agecens,1,n);      free_vector(agecens,1,n);
     free_ivector(dcwave,1,n);      free_ivector(dcwave,1,n);
     free_matrix(ximort,1,NDIM,1,NDIM);  #ifdef GSL
 #endif  #endif
   } /* Endof if mle==-3 mortality only */    } /* Endof if mle==-3 mortality only */
   /* Standard  */    /* Standard  */
Line 7700  Please run with mle=-1 to get a correct Line 9308  Please run with mle=-1 to get a correct
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){      for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){        for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {                                  if (k != i) {
           printf("%d%d ",i,k);                                          printf("%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);                                          fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);                                          fprintf(ficres,"%1d%1d ",i,k);
           for(j=1; j <=ncovmodel; j++){                                          for(j=1; j <=ncovmodel; j++){
             printf("%12.7f ",p[jk]);                                                  printf("%12.7f ",p[jk]);
             fprintf(ficlog,"%12.7f ",p[jk]);                                                  fprintf(ficlog,"%12.7f ",p[jk]);
             fprintf(ficres,"%12.7f ",p[jk]);                                                  fprintf(ficres,"%12.7f ",p[jk]);
             jk++;                                                   jk++; 
           }                                          }
           printf("\n");                                          printf("\n");
           fprintf(ficlog,"\n");                                          fprintf(ficlog,"\n");
           fprintf(ficres,"\n");                                          fprintf(ficres,"\n");
         }                                  }
       }        }
     }      }
     if(mle != 0){      if(mle != 0){
Line 7723  Please run with mle=-1 to get a correct Line 9331  Please run with mle=-1 to get a correct
       printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");        printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
       fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");        fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
       for(i=1,jk=1; i <=nlstate; i++){        for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){                                  for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {                                          if (k != i) {
             printf("%d%d ",i,k);                                                  printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);                                                  fprintf(ficlog,"%d%d ",i,k);
             for(j=1; j <=ncovmodel; j++){                                                  for(j=1; j <=ncovmodel; j++){
               printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));                                                          printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
               fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));                                                          fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
               jk++;                                                           jk++; 
             }                                                  }
             printf("\n");                                                  printf("\n");
             fprintf(ficlog,"\n");                                                  fprintf(ficlog,"\n");
           }                                          }
         }                                  }
       }        }
     } /* end of hesscov and Wald tests */      } /* end of hesscov and Wald tests */
                   
     /*  */      /*  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");      printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){      for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){        for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {                                  if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);                                          fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);                                          printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);                                          fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){                                          for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);                                                  printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);                                                  fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);                                                  fprintf(ficres," %.5e",delti[jk]);
             jk++;                                                  jk++;
           }                                          }
           printf("\n");                                          printf("\n");
           fprintf(ficlog,"\n");                                          fprintf(ficlog,"\n");
           fprintf(ficres,"\n");                                          fprintf(ficres,"\n");
         }                                  }
       }        }
     }      }
           
Line 7782  Please run with mle=-1 to get a correct Line 9390  Please run with mle=-1 to get a correct
     for(itimes=1;itimes<=2;itimes++){      for(itimes=1;itimes<=2;itimes++){
       jj=0;        jj=0;
       for(i=1; i <=nlstate; i++){        for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){                                  for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;                                          if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){                                          for(k=1; k<=ncovmodel;k++){
             jj++;                                                  jj++;
             ca[0]= k+'a'-1;ca[1]='\0';                                                  ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){                                                  if(itimes==1){
               if(mle>=1)                                                          if(mle>=1)
                 printf("#%1d%1d%d",i,j,k);                                                                  printf("#%1d%1d%d",i,j,k);
               fprintf(ficlog,"#%1d%1d%d",i,j,k);                                                          fprintf(ficlog,"#%1d%1d%d",i,j,k);
               fprintf(ficres,"#%1d%1d%d",i,j,k);                                                          fprintf(ficres,"#%1d%1d%d",i,j,k);
             }else{                                                  }else{
               if(mle>=1)                                                          if(mle>=1)
                 printf("%1d%1d%d",i,j,k);                                                                  printf("%1d%1d%d",i,j,k);
               fprintf(ficlog,"%1d%1d%d",i,j,k);                                                          fprintf(ficlog,"%1d%1d%d",i,j,k);
               fprintf(ficres,"%1d%1d%d",i,j,k);                                                          fprintf(ficres,"%1d%1d%d",i,j,k);
             }                                                  }
             ll=0;                                                  ll=0;
             for(li=1;li <=nlstate; li++){                                                  for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){                                                          for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;                                                                  if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){                                                                  for(lk=1;lk<=ncovmodel;lk++){
                   ll++;                                                                          ll++;
                   if(ll<=jj){                                                                          if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';                                                                                  cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){                                                                                  if(ll<jj){
                       if(itimes==1){                                                                                          if(itimes==1){
                         if(mle>=1)                                                                                                  if(mle>=1)
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);                                                                                                          printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);                                                                                                  fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);                                                                                                  fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{                                                                                          }else{
                         if(mle>=1)                                                                                                  if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]);                                                                                                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]);                                                                                                   fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]);                                                                                                   fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }                                                                                          }
                     }else{                                                                                  }else{
                       if(itimes==1){                                                                                          if(itimes==1){
                         if(mle>=1)                                                                                                  if(mle>=1)
                           printf(" Var(%s%1d%1d)",ca,i,j);                                                                                                          printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);                                                                                                  fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);                                                                                                  fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{                                                                                          }else{
                         if(mle>=1)                                                                                                  if(mle>=1)
                           printf(" %.7e",matcov[jj][ll]);                                                                                                           printf(" %.7e",matcov[jj][ll]); 
                         fprintf(ficlog," %.7e",matcov[jj][ll]);                                                                                                   fprintf(ficlog," %.7e",matcov[jj][ll]); 
                         fprintf(ficres," %.7e",matcov[jj][ll]);                                                                                                   fprintf(ficres," %.7e",matcov[jj][ll]); 
                       }                                                                                          }
                     }                                                                                  }
                   }                                                                          }
                 } /* end lk */                                                                  } /* end lk */
               } /* end lj */                                                          } /* end lj */
             } /* end li */                                                  } /* end li */
             if(mle>=1)                                                  if(mle>=1)
               printf("\n");                                                          printf("\n");
             fprintf(ficlog,"\n");                                                  fprintf(ficlog,"\n");
             fprintf(ficres,"\n");                                                  fprintf(ficres,"\n");
             numlinepar++;                                                  numlinepar++;
           } /* end k*/                                          } /* end k*/
         } /*end j */                                  } /*end j */
       } /* end i */        } /* end i */
     } /* end itimes */      } /* end itimes */
           
     fflush(ficlog);      fflush(ficlog);
     fflush(ficres);      fflush(ficres);
                       while(fgets(line, MAXLINE, ficpar)) {
     while((c=getc(ficpar))=='#' && c!= EOF){                          /* If line starts with a # it is a comment */
       ungetc(c,ficpar);                          if (line[0] == '#') {
       fgets(line, MAXLINE, ficpar);                                  numlinepar++;
       fputs(line,stdout);                                  fputs(line,stdout);
       fputs(line,ficparo);                                  fputs(line,ficparo);
     }                                  fputs(line,ficlog);
     ungetc(c,ficpar);                                  continue;
                           }else
                                   break;
                   }
                   
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /* } */
       /* ungetc(c,ficpar); */
           
     estepm=0;      estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
                           
                           if (num_filled != 6) {
                                   printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
                                   fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
                                   goto end;
                           }
                           printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
                   }
                   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
                   /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
                   
       /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
     if (estepm==0 || estepm < stepm) estepm=stepm;      if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {      if (fage <= 2) {
       bage = ageminpar;        bage = ageminpar;
Line 7865  Please run with mle=-1 to get a correct Line 9496  Please run with mle=-1 to get a correct
     }      }
           
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                   
     /* Other stuffs, more or less useful */          /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
Line 7915  Please run with mle=-1 to get a correct Line 9546  Please run with mle=-1 to get a correct
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);      fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
       fprintf(ficparo,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficlog,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       fprintf(ficres,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
           
           
      /* 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); */      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){      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\  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);  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\  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);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else      }else{
       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);        printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
           }
     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\                                                                   model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                                                                   jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
                         
    /*------------ free_vector  -------------*/                  /*------------ free_vector  -------------*/
    /*  chdir(path); */                  /*  chdir(path); */
                    
     free_ivector(wav,1,imx);      /* free_ivector(wav,1,imx); */  /* Moved after last prevalence call */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);      /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
     free_lvector(num,1,n);      free_lvector(num,1,n);
     free_vector(agedc,1,n);      free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
     fclose(ficres);      fclose(ficres);
                   
                   
     /* Other results (useful)*/      /* Other results (useful)*/
                   
                   
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, ncvyear);      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
 #ifdef FREEEXIT2  
 #include "freeexit2.h"  
 #endif  
   
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
     /*#include "hpijx.h"*/      /*#include "hpijx.h"*/
     hPijx(p, bage, fage);      hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
   
   /*-------------- Variance of one-step probabilities---*/      /* ncovcombmax=  pow(2,cptcoveff); */
       /*-------------- Variance of one-step probabilities---*/
     k=1;      k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      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,NCOVMAX, 1,NCOVMAX);      probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=1;i<=AGESUP;i++)
       for(j=1;j<=NCOVMAX;j++)        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
         for(k=1;k<=NCOVMAX;k++)                                  for(k=1;k<=ncovcombmax;k++)
           probs[i][j][k]=0.;                                          probs[i][j][k]=0.;
       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(j=1;j<=nlstate;j++)
                                           for(k=1;k<=ncovcombmax;k++)
                                                   mobaverages[i][j][k]=0.;
         mobaverage=mobaverages;
         if (mobilav!=0) {
                                   if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
                                           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                                           printf(" Error in movingaverage mobilav=%d\n",mobilav);
                                   }
         }
         /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
         /* 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){
                                           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
                                           printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
                                   }
         }
       }/* end if moving average */
                   
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){      if(prevfcast==1){
       /*    if(stepm ==1){*/        /*    if(stepm ==1){*/
       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/  
       /*      }  */  
       /*      else{ */  
       /*        erreur=108; */  
       /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */  
       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */  
       /*      } */  
     }      }
       if(backcast==1){
         ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
         ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
         ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
   
         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
   
         bprlim=matrix(1,nlstate,1,nlstate);
         back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
         fclose(ficresplb);
   
         hBijx(p, bage, fage, mobaverage);
         fclose(ficrespijb);
         free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
   
         /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
            bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
         free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
         free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       }
       
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);      free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\      free_imatrix(mw,1,lastpass-firstpass+2,1,imx);   
         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);                  
     */                  
   
     if (mobilav!=0) {  
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){  
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
         printf(" Error in movingaverage mobilav=%d\n",mobilav);  
       }  
     }  
   
   
     /*---------- Health expectancies, no variances ------------*/      /*---------- Health expectancies, no variances ------------*/
                   
     strcpy(filerese,"E_");      strcpy(filerese,"E_");
     strcat(filerese,fileresu);      strcat(filerese,fileresu);
     if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }      }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);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++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {        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)]);
         }        }
         fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\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);    
               
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        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);  
         
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     }      }
     fclose(ficreseij);      fclose(ficreseij);
       printf("done evsij\n");fflush(stdout);
       fprintf(ficlog,"done evsij\n");fflush(ficlog);
                   
     /*---------- Health expectancies and variances ------------*/      /*---------- Health expectancies and variances ------------*/
                   
                   
     strcpy(filerest,"T_");      strcpy(filerest,"T_");
     strcat(filerest,fileresu);      strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }      }
     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
                   
   
     strcpy(fileresstde,"STDE_");      strcpy(fileresstde,"STDE_");
     strcat(fileresstde,fileresu);      strcat(fileresstde,fileresu);
Line 8060  Please run with mle=-1 to get a correct Line 9727  Please run with mle=-1 to get a correct
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        printf("Problem with Health 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 Health 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 Health 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 Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"CVE_");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileresu);      strcat(filerescve,fileresu);
Line 8069  Please run with mle=-1 to get a correct Line 9736  Please run with mle=-1 to get a correct
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        printf("Problem with Covar. Health 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. Health Exp. resultfile: %s\n", filerescve); exit(0);
     }      }
     printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("    Computing Covar. of Health 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 Health Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"V_");      strcpy(fileresv,"V_");
     strcat(fileresv,fileresu);      strcat(fileresv,fileresu);
Line 8078  Please run with mle=-1 to get a correct Line 9745  Please run with mle=-1 to get a correct
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"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' \n", fileresv);      printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"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(ficrest,"******\n");        fprintf(ficrest,"******\n");
         
         fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {        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)]);
         }        }
         fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
         
         fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)         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)]);
         fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
         
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
         cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);          printf(" cvevsij %d, ",k);
         /*        fprintf(ficlog, " cvevsij %d, ",k);
          */        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
         /* goto endfree; */        printf(" end cvevsij \n ");
          fprintf(ficlog, " end cvevsij \n ");
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        
         pstamp(ficrest);        /*
          */
         /* goto endfree; */
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        
           oldm=oldms;savm=savms; /* ZZ Segmentation fault */        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           cptcod= 0; /* To be deleted */        pstamp(ficrest);
           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 */        
           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)        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==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);                                  oldm=oldms;savm=savms; /* ZZ Segmentation fault */
           else                                  cptcod= 0; /* To be deleted */
             fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");                                  printf("varevsij %d \n",vpopbased);
           fprintf(ficrest,"# Age popbased mobilav e.. (std) ");                                  fprintf(ficlog, "varevsij %d \n",vpopbased);
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                                  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 */
           fprintf(ficrest,"\n");                                  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 ");
           /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */                                  if(vpopbased==1)
           epj=vector(1,nlstate+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);
           for(age=bage; age <=fage ;age++){                                  else
             prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */                                          fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             if (vpopbased==1) {                                  fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
               if(mobilav ==0){                                  for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                 for(i=1; i<=nlstate;i++)                                  fprintf(ficrest,"\n");
                   prlim[i][i]=probs[(int)age][i][k];                                  /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
               }else{ /* mobilav */                                   epj=vector(1,nlstate+1);
                 for(i=1; i<=nlstate;i++)                                  printf("Computing age specific period (stable) prevalences in each health state \n");
                   prlim[i][i]=mobaverage[(int)age][i][k];                                  fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
               }                                  for(age=bage; age <=fage ;age++){
             }                                          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
                                                   if (vpopbased==1) {
             fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);                                                  if(mobilav ==0){
             /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */                                                          for(i=1; i<=nlstate;i++)
             /* printf(" age %4.0f ",age); */                                                                  prlim[i][i]=probs[(int)age][i][k];
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                                                  }else{ /* mobilav */ 
               for(i=1, epj[j]=0.;i <=nlstate;i++) {                                                          for(i=1; i<=nlstate;i++)
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];                                                                  prlim[i][i]=mobaverage[(int)age][i][k];
                 /*ZZZ  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];                                          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 */
             /* printf(" age %4.0f \n",age); */                                          /* printf(" age %4.0f ",age); */
                                           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, vepp=0.;i <=nlstate;i++)                                                  for(i=1, epj[j]=0.;i <=nlstate;i++) {
               for(j=1;j <=nlstate;j++)                                                          epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 vepp += vareij[i][j][(int)age];                                                          /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                                                          /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
             for(j=1;j <=nlstate;j++){                                                  }
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                                                  epj[nlstate+1] +=epj[j];
             }                                          }
             fprintf(ficrest,"\n");                                          /* printf(" age %4.0f \n",age); */
           }            
         }                                          for(i=1, vepp=0.;i <=nlstate;i++)
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                                                  for(j=1;j <=nlstate;j++)
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                                                          vepp += vareij[i][j][(int)age];
         free_vector(epj,1,nlstate+1);                                          fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                                           for(j=1;j <=nlstate;j++){
                                                   fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                                           }
                                           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);
         fprintf(ficlog,"done\n");fflush(ficlog);
         
       /*}*/        /*}*/
     }      } /* End k */
     free_vector(weight,1,n);      free_vector(weight,1,n);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,1,n);
Line 8180  Please run with mle=-1 to get a correct Line 9859  Please run with mle=-1 to get a correct
     fclose(ficrescveij);      fclose(ficrescveij);
     fclose(ficresvij);      fclose(ficresvij);
     fclose(ficrest);      fclose(ficrest);
       printf("done Health expectancies\n");fflush(stdout);
       fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
     fclose(ficpar);      fclose(ficpar);
       
     /*------- Variance of period (stable) prevalence------*/         /*------- Variance of period (stable) prevalence------*/   
Line 8190  Please run with mle=-1 to get a correct Line 9871  Please run with mle=-1 to get a correct
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);      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(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficresvpl,"\n#****** ");          fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)                           for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);                                  fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficresvpl,"******\n");                          fprintf(ficresvpl,"******\n");
               
         varpl=matrix(1,nlstate,(int) bage, (int) fage);                          varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;                          oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);                          varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       /*}*/        /*}*/
     }      }
                   
     fclose(ficresvpl);      fclose(ficresvpl);
       printf("done variance-covariance of period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
   
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0 ||mobilavproj !=0)
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
   }  /* mle==-3 arrives here for freeing */      free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
  /* endfree:*/  
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     }  /* mle==-3 arrives here for freeing */
    /* 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);
Line 8233  Please run with mle=-1 to get a correct Line 9918  Please run with mle=-1 to get a correct
     free_ivector(Tvar,1,NCOVMAX);      free_ivector(Tvar,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);      free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);      free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);      free_ivector(Tage,1,NCOVMAX);
   
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);      free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
Line 8242  Please run with mle=-1 to get a correct Line 9928  Please run with mle=-1 to get a correct
       
   
   if((nberr >0) || (nbwarn>0)){    if((nberr >0) || (nbwarn>0)){
     printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);      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\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);
   }else{    }else{
     printf("End of Imach\n");      printf("End of Imach\n");
     fprintf(ficlog,"End of Imach\n");      fprintf(ficlog,"End of Imach\n");
Removed from v.1.205  
changed lines
  Added in v.1.222

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