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version 1.217, 2015/12/23 17:18:31 version 1.218, 2016/02/12 11:29:23
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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    Revision 1.217  2015/12/23 17:18:31  brouard
   Summary: Experimental backcast    Summary: Experimental backcast
   
Line 651 Line 654
   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 789  typedef struct { Line 809  typedef struct {
 #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-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 821  int cptcovage=0; /**< Number of covariat Line 843  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 843  double jmean=1; /* Mean space between 2 Line 866  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, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
 FILE *ficlog, *ficrespow;  FILE *ficlog, *ficrespow;
Line 950  int *ncodemaxwundef;  /* ncodemax[j]= Nu Line 975  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; /* New global variable */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   
Line 2033  void powell(double p[], double **xi, int Line 2059  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= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
   /* Wx is row vector: population in state 1, population in state 2, population dead */    /* Wx is row vector: population in state 1, population in state 2, population dead */
Line 2056  double **prevalim(double **prlim, int nl Line 2082  double **prevalim(double **prlim, int nl
   int i, ii,j,k;    int i, ii,j,k;
   double *min, *max, *meandiff, 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=200. ; /* 100 Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
Line 2065  double **prevalim(double **prlim, int nl Line 2091  double **prevalim(double **prlim, int nl
   max=vector(1,nlstate);    max=vector(1,nlstate);
   meandiff=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 2083  double **prevalim(double **prlim, int nl Line 2110  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 2098  double **prevalim(double **prlim, int nl Line 2126  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;
Line 2147  Earliest age to start was %d-%d=%d, ncvl Line 2176  Earliest age to start was %d-%d=%d, ncvl
   
  /**** Back Prevalence limit (stable or period prevalence)  ****************/   /**** Back Prevalence limit (stable or period prevalence)  ****************/
   
 double **bprevalim(double **bprlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)   /* 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 by left multiplying the unit    /* 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 */       matrix by transitions matrix until convergence is reached with precision ftolpl */
   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */    /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */
   /* Wx is row vector: population in state 1, population in state 2, population dead */    /* Wx is row vector: population in state 1, population in state 2, population dead */
Line 2174  double **bprevalim(double **bprlim, int Line 2205  double **bprevalim(double **bprlim, int
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
   double **newm;    double **newm;
     double         **dnewm, **doldm, **dsavm;  /* for use */
     double         **oldm, **savm;  /* for use */
   
   double agefin, delaymax=200. ; /* 100 Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
       
Line 2181  double **bprevalim(double **bprlim, int Line 2215  double **bprevalim(double **bprlim, int
   max=vector(1,nlstate);    max=vector(1,nlstate);
   meandiff=vector(1,nlstate);    meandiff=vector(1,nlstate);
   
   for (ii=1;ii<=nlstate+ndeath;ii++)          dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
     for (j=1;j<=nlstate+ndeath;j++){          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);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
       
Line 2190  double **bprevalim(double **bprlim, int Line 2228  double **bprevalim(double **bprlim, int
       
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* 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 */    /* 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){    /* 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++;      ncvloop++;
     newm=savm;      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 */      /* Covariates have to be included here again */
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
Line 2214  double **bprevalim(double **bprlim, int Line 2254  double **bprevalim(double **bprlim, int
     /*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 *\/ */
     out=matprod2(newm, oldm ,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate)); /* 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;      savm=oldm;
     oldm=newm;      oldm=newm;
   
     for(j=1; j<=nlstate; j++){      for(j=1; j<=nlstate; j++){
       max[j]=0.;        max[j]=0.;
       min[j]=1.;        min[j]=1.;
     }      }
       /* sumnew=0; */  
       /* for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; */  
     for(j=1; j<=nlstate; j++){       for(j=1; j<=nlstate; j++){ 
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         /* bprlim[i][j]= newm[i][j]/(1-sumnew); */                                  /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
         bprlim[i][j]= newm[i][j];                                  bprlim[i][j]= newm[i][j];
         max[i]=FMAX(max[i],bprlim[i][j]);                                  max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
         min[i]=FMIN(min[i],bprlim[i][j]);                                  min[i]=FMIN(min[i],bprlim[i][j]);
       }        }
     }      }
                   
     maxmax=0.;      maxmax=0.;
     for(i=1; i<=nlstate; i++){      for(i=1; i<=nlstate; i++){
       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
Line 2241  double **bprevalim(double **bprlim, int Line 2284  double **bprevalim(double **bprlim, int
       /* 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); */        /* 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 */      } /* j loop */
     *ncvyear= -( (int)age- (int)agefin);      *ncvyear= -( (int)age- (int)agefin);
     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */      /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);        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(min,1,nlstate);
Line 2282  double **pmij(double **ps, double *cov, Line 2325  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) */                          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */                          /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }                  }
       for(j=i+1; j<=nlstate+ndeath;j++){                  for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){                          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/                                  /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];                                  lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */                                  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         }                          }
         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */                          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }                  }
     }          }
         
     for(i=1; i<= nlstate; i++){          for(i=1; i<= nlstate; i++){
       s1=0;                  s1=0;
       for(j=1; j<i; j++){                  for(j=1; j<i; j++){
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */                          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */                          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }                  }
       for(j=i+1; j<=nlstate+ndeath; j++){                  for(j=i+1; j<=nlstate+ndeath; j++){
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */                          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */                          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }                  }
       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */                  /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       ps[i][i]=1./(s1+1.);                  ps[i][i]=1./(s1+1.);
       /* Computing other pijs */                  /* Computing other pijs */
       for(j=1; j<i; j++)                  for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];                          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)                  for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];                          ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */                  /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */          } /* end i */
         
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){                  for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;                          ps[ii][jj]=0;
         ps[ii][ii]=1;                          ps[ii][ii]=1;
       }                  }
     }          }
         
         
     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */          /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */          /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */          /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     /*   } */          /*   } */
     /*   printf("\n "); */          /*   printf("\n "); */
     /* } */          /* } */
     /* printf("\n ");printf("%lf ",cov[2]);*/          /* printf("\n ");printf("%lf ",cov[2]);*/
     /*          /*
       for(i=1; i<= npar; i++) printf("%f ",x[i]);                  for(i=1; i<= npar; i++) printf("%f ",x[i]);
       goto end;*/                  goto end;*/
     return ps;          return ps;
 }  }
   
   /*************** backward transition probabilities ***************/ 
   
    /* 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 ) */
   /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
    double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
   {
           /* Computes the backward probability at age agefin and covariate ij
            * and returns in **ps as well as **bmij.
            */
     int i, ii, j,k;
   
           double **out, **pmij();
           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) */
           bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
           /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
           /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
           /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
           /* left Product of this matrix by diag matrix of prevalences (savm) */
           for (j=1;j<=nlstate+ndeath;j++){
                   for (ii=1;ii<=nlstate+ndeath;ii++){
                           dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
                   }
           } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
           ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
           /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
           /* end bmij */
           return ps; 
   }
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
 double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  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,    /* According to parameters values stored in x and the covariate's values stored in cov,
      computes the probability to be observed in state j being in state i by appying the       computes the probability to be observed in state j being in state i by appying the
Line 2364  double **bmij(double **ps, double *cov, Line 2468  double **bmij(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) */                          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */                          /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }                  }
       for(j=i+1; j<=nlstate+ndeath;j++){                  for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){                          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/                                  /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];                                  lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */                                  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         }                          }
         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */                          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }                  }
     }          }
               
     for(i=1; i<= nlstate; i++){          for(i=1; i<= nlstate; i++){
       s1=0;                  s1=0;
       for(j=1; j<i; j++){                  for(j=1; j<i; j++){
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */                          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */                          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }                  }
       for(j=i+1; j<=nlstate+ndeath; j++){                  for(j=i+1; j<=nlstate+ndeath; j++){
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */                          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */                          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }                  }
       /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */                  /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       ps[i][i]=1./(s1+1.);                  ps[i][i]=1./(s1+1.);
       /* Computing other pijs */                  /* Computing other pijs */
       for(j=1; j<i; j++)                  for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];                          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)                  for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];                          ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */                  /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */          } /* end i */
               
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){                  for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;                          ps[ii][jj]=0;
         ps[ii][ii]=1;                          ps[ii][ii]=1;
       }                  }
     }          }
     /* Added for backcast */          /* Added for backcast */ /* Transposed matrix too */
     for(jj=1; jj<= nlstate; jj++){          for(jj=1; jj<= nlstate+ndeath; jj++){
       s1=0.;                  s1=0.;
       for(ii=1; ii<= nlstate; ii++){                  for(ii=1; ii<= nlstate+ndeath; ii++){
         s1+=ps[ii][jj];                          s1+=ps[ii][jj];
       }                  }
       for(ii=1; ii<= nlstate; ii++){                  for(ii=1; ii<= nlstate; ii++){
         ps[ii][jj]=ps[ii][jj]/s1;                          ps[ii][jj]=ps[ii][jj]/s1;
       }                  }
     }          }
                /* Transposition */
     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */          for(jj=1; jj<= nlstate+ndeath; jj++){
     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */                  for(ii=jj; ii<= nlstate+ndeath; ii++){
     /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */                          s1=ps[ii][jj];
     /*   } */                          ps[ii][jj]=ps[jj][ii];
     /*   printf("\n "); */                          ps[jj][ii]=s1;
     /* } */                  }
     /* printf("\n ");printf("%lf ",cov[2]);*/          }
     /*          /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       for(i=1; i<= npar; i++) printf("%f ",x[i]);          /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       goto end;*/          /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     return ps;          /*   } */
           /*   printf("\n "); */
           /* } */
           /* printf("\n ");printf("%lf ",cov[2]);*/
           /*
                   for(i=1; i<= npar; i++) printf("%f ",x[i]);
                   goto end;*/
           return ps;
 }  }
   
   
Line 2459  double **matprod2(double **out, double * Line 2570  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 2492  double ***hpxij(double ***po, int nhstep Line 2603  double ***hpxij(double ***po, int nhstep
       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;        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){ */        /* if((int)age == 70){ */
Line 2528  double ***hpxij(double ***po, int nhstep Line 2640  double ***hpxij(double ***po, int nhstep
     }      }
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
         po[i][j][h]=newm[i][j];                                  po[i][j][h]=newm[i][j];
         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/                                  /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
     /*printf("h=%d ",h);*/      /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
 /*     printf("\n H=%d \n",h); */          /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
 /************* Higher Back Matrix Product ***************/  /************* 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, int nlstate, int stepm, double **oldm, double **savm, 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     /* Computes the transition matrix starting at age 'age' 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.
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        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        (typically every 2 years instead of every month which is too big
      for the memory).       for the memory).
      Model is determined by parameters x and covariates have to be        Model is determined by parameters x and covariates have to be
      included manually here.        included manually here.
   
      */       */
   
Line 2558  double ***hbxij(double ***po, int nhstep Line 2670  double ***hbxij(double ***po, int nhstep
   double **newm;    double **newm;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
           double **oldm, **savm;
   
           oldm=oldms;savm=savms;
   /* 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++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
Line 2575  double ***hbxij(double ***po, int nhstep Line 2689  double ***hbxij(double ***po, int nhstep
       /* 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;        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]);*/
       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,         /* Careful transposed matrix */
                   oldm);                          /* 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){ */        /* if((int)age == 70){ */
       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */        /*        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++) { */        /*        for(i=1; i<=nlstate+ndeath; i++) { */
Line 2611  double ***hbxij(double ***po, int nhstep Line 2729  double ***hbxij(double ***po, int nhstep
     }      }
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
         po[i][j][h]=newm[i][j];                                  po[i][j][h]=newm[i][j];
         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/                                  /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
     /*printf("h=%d ",h);*/      /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
 /*     printf("\n H=%d \n",h); */          /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
Line 3393  double hessij( double x[], double **hess Line 3511  double hessij( double x[], double **hess
       kmax=kmax+10;        kmax=kmax+10;
     }      }
     if(kmax >=10 || firstime ==1){      if(kmax >=10 || firstime ==1){
       printf("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; 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);
     }      }
Line 3565  void  freqsummary(char fileres[], int ia Line 3683  void  freqsummary(char fileres[], int ia
   double agebegin, ageend;    double agebegin, ageend;
           
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin,iagemax+3);    prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
     /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
   strcpy(fileresp,"P_");    strcpy(fileresp,"P_");
   strcat(fileresp,fileresu);    strcat(fileresp,fileresu);
   /*strcat(fileresphtm,fileresu);*/    /*strcat(fileresphtm,fileresu);*/
Line 3605  Title=%s <br>Datafile=%s Firstpass=%d La Line 3724  Title=%s <br>Datafile=%s Firstpass=%d La
   }    }
   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
   
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
   j1=0;    j1=0;
       
   j=cptcoveff;    j=cptcoveff;
Line 3814  Title=%s <br>Datafile=%s Firstpass=%d La Line 3933  Title=%s <br>Datafile=%s Firstpass=%d La
   fclose(ficresp);    fclose(ficresp);
   fclose(ficresphtm);    fclose(ficresphtm);
   fclose(ficresphtmfr);    fclose(ficresphtmfr);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin, iagemax+3);    free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
   /* End of Freq */    /* End of Freq */
 }  }
   
Line 3842  void prevalence(double ***probs, double Line 3961  void prevalence(double ***probs, double
   iagemin= (int) agemin;    iagemin= (int) agemin;
   iagemax= (int) agemax;    iagemax= (int) agemax;
   /*pp=vector(1,nlstate);*/    /*pp=vector(1,nlstate);*/
   prop=matrix(1,nlstate,iagemin,iagemax+3);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;    j1=0;
       
Line 3852  void prevalence(double ***probs, double Line 3971  void prevalence(double ***probs, double
   first=1;    first=1;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
     for (i=1; i<=nlstate; i++)        for (i=1; i<=nlstate; i++)  
       for(iage=iagemin; iage <= iagemax+3; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
         prop[i][iage]=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) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */        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++) 
           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(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*\/ */
         for(mi=1; mi<wav[i];mi++){                                  for(mi=1; mi<wav[i];mi++){
           m=mw[mi][i];                                          m=mw[mi][i];
           agebegin=agev[m][i]; /* Age at beginning of wave before transition*/                                          agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
           /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */                                          /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
           if(m >=firstpass && m <=lastpass){                                          if(m >=firstpass && m <=lastpass){
             y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */                                                  y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */                                                  if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               if(agev[m][i]==0) agev[m][i]=iagemax+1;                                                          if(agev[m][i]==0) agev[m][i]=iagemax+1;
               if(agev[m][i]==1) agev[m][i]=iagemax+2;                                                          if(agev[m][i]==1) agev[m][i]=iagemax+2;
               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((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
               if (s[m][i]>0 && s[m][i]<=nlstate) {                                                                   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); 
                 /*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]]);*/                                                                  exit(1);
                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */                                                          }
                 prop[s[m][i]][iagemax+3] += weight[i];                                                           if (s[m][i]>0 && s[m][i]<=nlstate) { 
               } /* end valid statuses */                                                                   /*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]]);*/
             } /* end selection of dates */                                                                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
           } /* end selection of waves */                                                                  prop[s[m][i]][iagemax+3] += weight[i]; 
         } /* end effective waves */                                                          } /* end valid statuses */ 
                                                   } /* end selection of dates */
                                           } /* end selection of waves */
                                   } /* end effective waves */
       } /* end bool */        } /* end bool */
     }      }
     for(i=iagemin; i <= iagemax+3; i++){        for(i=iagemin; i <= iagemax+3; i++){  
       for(jk=1,posprop=0; jk <=nlstate ; jk++) {         for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         posprop += prop[jk][i];                                   posprop += prop[jk][i]; 
       }         } 
               
       for(jk=1; jk <=nlstate ; jk++){               for(jk=1; jk <=nlstate ; jk++){       
         if( i <=  iagemax){                                   if( i <=  iagemax){ 
           if(posprop>=1.e-5){                                           if(posprop>=1.e-5){ 
             probs[i][jk][j1]= prop[jk][i]/posprop;                                                  probs[i][jk][j1]= prop[jk][i]/posprop;
           } else{                                          } else{
             if(first==1){                                                  if(first==1){
               first=0;                                                          first=0;
               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]);                                                          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]);
             }                                                  }
           }                                          }
         }                                   } 
       }/* end jk */         }/* end jk */ 
     }/* end i */       }/* end i */ 
     /*} *//* end i1 */      /*} *//* end i1 */
Line 3907  void prevalence(double ***probs, double Line 4029  void prevalence(double ***probs, double
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/    /*free_vector(pp,1,nlstate);*/
   free_matrix(prop,1,nlstate, iagemin,iagemax+3);    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
 }  /* End of prevalence */  }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
Line 3924  void  concatwav(int wav[], int **dh, int Line 4046  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, firstwo, firsthree;    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;    firstwo=0;
   firsthree=0;    firsthree=0;
     firstfour=0;
   jmin=100000;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
Line 3944  void  concatwav(int wav[], int **dh, int Line 4067  void  concatwav(int wav[], int **dh, int
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
           if(firsthree == 0){            if(firsthree == 0){
             printf("Information! Unknown 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);              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);
             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.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);  
             firsthree=1;              firsthree=1;
           }else{  
             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.\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);  
           }            }
             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;            mw[++mi][i]=m;
         }          }
         if(s[m][i]==-2){ /* Vital status is really unknown */          if(s[m][i]==-2){ /* Vital status is really unknown */
Line 3977  void  concatwav(int wav[], int **dh, int Line 4098  void  concatwav(int wav[], int **dh, int
       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */        /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
       /* mw[mi][i]=m; */        /* mw[mi][i]=m; */
       nberr++;        nberr++;
       if(firstwo==0){        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         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 );          if(firstwo==0){
         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.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            printf("Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
         firstwo=1;            firstwo=1;
       }else if(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.\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 );          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;
Line 4429  void cvevsij(double ***eij, double x[], Line 4557  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 */
     for(theta=1; theta <=npar; theta++){      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){         for(i=1; i<=npar; i++){ 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                                  xp[i] = x[i] + (i==theta ?delti[theta]:0);
         xm[i] = x[i] - (i==theta ?delti[theta]:0);                                  xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       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++){
             gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;                                                  gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
             gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;                                                  gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           }                                          }
         }                                  }
       }        }
                                
       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];
         }                                  }
     }/* End theta */      }/* End theta */
           
           
     for(h=0; h<=nhstepm-1; h++)      for(h=0; h<=nhstepm-1; h++)
       for(j=1; j<=nlstate*nlstate;j++)        for(j=1; j<=nlstate*nlstate;j++)
         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]);
         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] += 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.;
       vip=0.;        vip=0.;
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
         eip += eij[i][j][(int)age];                                  eip += eij[i][j][(int)age];
         for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */                                  for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
           vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];                                          vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
         fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );                                  fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       }        }
       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++){
         cptj= (j-1)*nlstate+i;                                  cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)                                  for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){                                          for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;                                                  cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)                                                  if(cptj2 <= cptj)
               fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);                                                          fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           }                                          }
       }        }
     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 4532  void cvevsij(double ***eij, double x[], Line 4660  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 ******************/  /************ Variance ******************/
  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
 {   {
   /* Variance of health expectancies */     /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /* double **newm;*/     /* double **newm;*/
   /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
       
   int movingaverage();     /* int movingaverage(); */
   double **dnewm,**doldm;     double **dnewm,**doldm;
   double **dnewmp,**doldmp;     double **dnewmp,**doldmp;
   int i, j, nhstepm, hstepm, h, nstepm ;     int i, j, nhstepm, hstepm, h, nstepm ;
   int k;     int k;
   double *xp;     double *xp;
   double **gp, **gm;  /* for var eij */     double **gp, **gm;  /* for var eij */
   double ***gradg, ***trgradg; /*for var eij */     double ***gradg, ***trgradg; /*for var eij */
   double **gradgp, **trgradgp; /* for var p point j */     double **gradgp, **trgradgp; /* for var p point j */
   double *gpp, *gmp; /* for var p point j */     double *gpp, *gmp; /* for var p point j */
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   double ***p3mat;     double ***p3mat;
   double age,agelim, hf;     double age,agelim, hf;
   double ***mobaverage;     /* double ***mobaverage; */
   int theta;     int theta;
   char digit[4];     char digit[4];
   char digitp[25];     char digitp[25];
   
   char fileresprobmorprev[FILENAMELENGTH];     char fileresprobmorprev[FILENAMELENGTH];
   
   if(popbased==1){     if(popbased==1){
     if(mobilav!=0)       if(mobilav!=0)
       strcpy(digitp,"-POPULBASED-MOBILAV_");         strcpy(digitp,"-POPULBASED-MOBILAV_");
     else strcpy(digitp,"-POPULBASED-NOMOBIL_");       else strcpy(digitp,"-POPULBASED-NOMOBIL_");
   }     }
   else      else 
     strcpy(digitp,"-STABLBASED_");       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 agelim.   
      Look at function hpijx to understand why because of memory size limitations,   
      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);  
       }  
   
       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++){     /* 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. 
         Look at function hpijx to understand why because of memory size limitations, 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,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);
     */      */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);       /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
     for(j=nlstate+1;j<=nlstate+ndeath;j++){     fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
       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);  
 */  
 /*   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 *ncvyearp, int ij, char strstart[])   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[])
Line 5480  See page 'Matrix of variance-covariance Line 5608  See page 'Matrix of variance-covariance
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      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 */
Line 5497  true period expectancies (those weighted Line 5625  true period expectancies (those weighted
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
     void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, 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];
   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;
Line 5581  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 5709  plot [%.f:%.f] \"%s\" every :::%d::%d u
        if (i==cpt) fprintf(ficgp," %%lf (%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," %%*lf (%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
                    if(backcast==1){
                            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,"\nset out \n");       fprintf(ficgp,"\nset out \n");
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
Line 5782  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 5913  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
     if(backcast == 1){
     /* CV back preval stable (period) for each covariate */      /* CV back preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (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 */
       fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         vlv= nbcode[Tvaraff[lv]][lv];            vlv= nbcode[Tvaraff[lv]][lv];
         fprintf(ficgp," V%d=%d ",k,vlv);            fprintf(ficgp," V%d=%d ",k,vlv);
       }          }
       fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
           
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);          fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),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 */          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,"PIJB_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
         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); /* a vérifier */            l=(nlstate+ndeath)*(cpt-1)+1;
         for (j=2; j<= nlstate ; j ++)            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
           fprintf(ficgp,"+$%d",k+l+j-1);            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);            fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
       } /* nlstate */            /* for (j=2; j<= nlstate ; j ++) */
       fprintf(ficgp,"\nset out\n");            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
     } /* end cpt state*/             /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
   } /* end covariate */              fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
           } /* nlstate */
           fprintf(ficgp,"\nset out\n");
         } /* end cpt state*/ 
       } /* end covariate */  
     } /* End if backcast */
     
   if(prevfcast==1){    if(prevfcast==1){
   /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to stable (period) for each covariate */
       
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (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 */
         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
Line 6039  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6175  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 i, cpt, cptcod;
   int modcovmax =1;    int modcovmax =1;
   int mobilavrange, mob;    int mobilavrange, mob;
   double age;    double age;
     int iage=0;
     double *sumnewp, *sumnewm;
     double *agemingood, *agemaxgood; /* Currently identical for all covariates */
     
     sumnewp = vector(1,modcovmax);
     sumnewm = vector(1,modcovmax);
     agemingood = vector(1,modcovmax);     
     agemaxgood = vector(1,modcovmax);
     
     
   modcovmax=2*cptcoveff;/* Max number of modalities. We suppose     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                            a covariate has 2 modalities */                             a covariate has 2 modalities, should be equal to ncovcombmax  */
   if (cptcovn<1) modcovmax=1; /* At least 1 pass */    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     if(mobilav==1) mobilavrange=5; /* default */      if(mobilav==1) mobilavrange=5; /* default */
     else mobilavrange=mobilav;      else mobilavrange=mobilav;
Line 6066  int movingaverage(double ***probs, doubl Line 6212  int movingaverage(double ***probs, doubl
         for (i=1; i<=nlstate;i++){          for (i=1; i<=nlstate;i++){
           for (cptcod=1;cptcod<=modcovmax;cptcod++){            for (cptcod=1;cptcod<=modcovmax;cptcod++){
             mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
               for (cpt=1;cpt<=(mob-1)/2;cpt++){              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] +=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;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
           }            }
         }          }
       }/* end age */        }/* end age */
     }/* end mob */      }/* end mob */
   }else return -1;    }else
       return -1;
     for (cptcod=1;cptcod<=modcovmax;cptcod++){
       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
       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 */
       /* 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 */
       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, modcovmax);
     free_vector(sumnewp,1, modcovmax);
     free_vector(agemaxgood,1, modcovmax);
     free_vector(agemingood,1, modcovmax);
   return 0;    return 0;
 }/* End movingaverage */  }/* 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 6092  void prevforecast(char fileres[], double Line 6304  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;
Line 6102  void prevforecast(char fileres[], double Line 6314  void prevforecast(char fileres[], double
   */    */
   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */    /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
   /*          firstpass, lastpass,  stepm,  weightopt, model); */    /*          firstpass, lastpass,  stepm,  weightopt, model); */
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);  
     
   strcpy(fileresf,"F_");     strcpy(fileresf,"F_"); 
   strcat(fileresf,fileresu);    strcat(fileresf,fileresu);
Line 6115  void prevforecast(char fileres[], double Line 6326  void prevforecast(char fileres[], double
   
   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 6202  void prevforecast(char fileres[], double Line 6406  void prevforecast(char fileres[], double
     } /* 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");    printf("End of Computing forecasting \n");
   fprintf(ficlog,"End of Computing forecasting\n");    fprintf(ficlog,"End of Computing forecasting\n");
   
 }  }
   
 /************** Back Forecasting ******************/  /* /\************** Back Forecasting ******************\/ */
 void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){  /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
   /* back1, year, month, day of starting backection   /*   /\* back1, year, month, day of starting backection  */
      agemin, agemax range of age  /*      agemin, agemax range of age */
      dateprev1 dateprev2 range of dates during which prevalence is computed  /*      dateprev1 dateprev2 range of dates during which prevalence is computed */
      anback2 year of en of backection (same day and month as back1).  /*      anback2 year of en of backection (same day and month as back1). */
   */  /*   *\/ */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;  /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
   double agec; /* generic age */  /*   double agec; /\* generic age *\/ */
   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 fileresfb[FILENAMELENGTH];  /*   char fileresfb[FILENAMELENGTH]; */
           
   agelim=AGESUP;  /*   agelim=AGESUP; */
   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people  /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
      in each health status at the date of interview (if between dateprev1 and dateprev2).  /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */
      We still use firstpass and lastpass as another selection.  /*      We still use firstpass and lastpass as another selection. */
   */  /*   *\/ */
   /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */  /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
   /*          firstpass, lastpass,  stepm,  weightopt, model); */  /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);  /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
            
   strcpy(fileresfb,"FB_");   /*   strcpy(fileresfb,"FB_");  */
   strcat(fileresfb,fileresu);  /*   strcat(fileresfb,fileresu); */
   if((ficresfb=fopen(fileresfb,"w"))==NULL) {  /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
     printf("Problem with back forecast resultfile: %s\n", fileresfb);  /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */
     fprintf(ficlog,"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);  /*   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);  /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
           
   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; */
   if(estepm < stepm){  /*   if(estepm < stepm){ */
     printf ("Problem %d lower than %d\n",estepm, stepm);  /*     printf ("Problem %d lower than %d\n",estepm, stepm); */
   }  /*   } */
   else  hstepm=estepm;     /*   else  hstepm=estepm;    */
           
   hstepm=hstepm/stepm;   /*   hstepm=hstepm/stepm;  */
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and  /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */
                                fractional in yp1 */  /*                                fractional in yp1 *\/ */
   anprojmean=yp;  /*   anprojmean=yp; */
   yp2=modf((yp1*12),&yp);  /*   yp2=modf((yp1*12),&yp); */
   mprojmean=yp;  /*   mprojmean=yp; */
   yp1=modf((yp2*30.5),&yp);  /*   yp1=modf((yp2*30.5),&yp); */
   jprojmean=yp;  /*   jprojmean=yp; */
   if(jprojmean==0) jprojmean=1;  /*   if(jprojmean==0) jprojmean=1; */
   if(mprojmean==0) jprojmean=1;  /*   if(mprojmean==0) jprojmean=1; */
           
   i1=cptcoveff;  /*   i1=cptcoveff; */
   if (cptcovn < 1){i1=1;}  /*   if (cptcovn < 1){i1=1;} */
       
   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);   /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */
       
   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");  /*   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,nlstate,stepm,oldm,savm, k);    
                   
           for (h=0; h<=nhstepm; h++){  /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */
             if (h*hstepm/YEARM*stepm ==yearp) {  /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
               fprintf(ficresfb,"\n");  /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
               for(j=1;j<=cptcoveff;j++)   /*       k=k+1; */
                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
               fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm);  /*       for(j=1;j<=cptcoveff;j++) { */
             }   /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
             for(j=1; j<=nlstate+ndeath;j++) {  /*       } */
               ppij=0.;  /*       fprintf(ficresfb," yearbproj age"); */
               for(i=1; i<=nlstate;i++) {  /*       for(j=1; j<=nlstate+ndeath;j++){  */
                 if (mobilav==1)   /*                              for(i=1; i<=nlstate;i++)               */
                   ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];  /*           fprintf(ficresfb," p%d%d",i,j); */
                 else {  /*                              fprintf(ficresfb," p.%d",j); */
                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];  /*       } */
                 }  /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */
                 if (h*hstepm/YEARM*stepm== yearp) {  /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */
                   fprintf(ficresfb," %.3f", p3mat[i][j][h]);  /*                              fprintf(ficresfb,"\n"); */
                 }  /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */
               } /* end i */  /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */
               if (h*hstepm/YEARM*stepm==yearp) {  /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */
                 fprintf(ficresfb," %.3f", ppij);  /*                                      nhstepm = nhstepm/hstepm;  */
               }  /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
             }/* end j */  /*                                      oldm=oldms;savm=savms; */
           } /* end h */  /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*                                      for (h=0; h<=nhstepm; h++){ */
         } /* end agec */  /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */
       } /* end yearp */  /*               fprintf(ficresfb,"\n"); */
     } /* end cptcod */  /*               for(j=1;j<=cptcoveff;j++)  */
   } /* end  cptcov */  /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
          /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*                                              }  */
   /*                                              for(j=1; j<=nlstate+ndeath;j++) { */
   fclose(ficresfb);  /*                                                      ppij=0.; */
   printf("End of Computing Back forecasting \n");  /*                                                      for(i=1; i<=nlstate;i++) { */
   fprintf(ficlog,"End of Computing Back forecasting\n");  /*                                                              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 6349  void populforecast(char fileres[], doubl Line 6550  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 6371  void populforecast(char fileres[], doubl Line 6572  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 6386  void populforecast(char fileres[], doubl Line 6587  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 6398  void populforecast(char fileres[], doubl Line 6599  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 6418  void populforecast(char fileres[], doubl Line 6619  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 6441  void populforecast(char fileres[], doubl Line 6642  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 6486  void populforecast(char fileres[], doubl Line 6688  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 6500  void populforecast(char fileres[], doubl Line 6702  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 6775  int readdata(char datafile[], int firsto Line 6977  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 7153  int decodemodel ( char model[], int last Line 7355  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)){
Line 7163  int calandcheckages(int imx, int maxwav, Line 7366  int calandcheckages(int imx, int maxwav,
       }        }
       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 7524  void syscompilerinfo(int logged) Line 7730  void syscompilerinfo(int logged)
         return 0;          return 0;
 }  }
   
  int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){  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) --------------*/          /*--------------- 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 ;    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;
     /* double ***mobaverage; */
     /* double      **dnewm, **doldm, **dsavm;  /\* for use *\/ */
   
   strcpy(fileresplb,"PLB_");    strcpy(fileresplb,"PLB_");
   strcat(fileresplb,fileresu);    strcat(fileresplb,fileresu);
Line 7545  void syscompilerinfo(int logged) Line 7757  void syscompilerinfo(int logged)
   for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
   fprintf(ficresplb,"\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);
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){    if (cptcovn < 1){i1=1;}
     
     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(ficresplb,"#******");      fprintf(ficresplb,"#******");
         printf("#******");      printf("#******");
         fprintf(ficlog,"#******");      fprintf(ficlog,"#******");
         for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           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(ficresplb,"******\n");      fprintf(ficresplb,"******\n");
         printf("******\n");      printf("******\n");
         fprintf(ficlog,"******\n");      fprintf(ficlog,"******\n");
       
         fprintf(ficresplb,"#Age ");      fprintf(ficresplb,"#Age ");
         for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }      }
         for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);      for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
         fprintf(ficresplb,"Total Years_to_converge\n");      fprintf(ficresplb,"Total Years_to_converge\n");
               
         for (age=agebase; age<=agelim; age++){      
         /* for (age=agebase; age<=agebase; age++){ */      for (age=agebase; age<=agelim; age++){
           bprevalim(bprlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);        /* for (age=agebase; age<=agebase; age++){ */
           fprintf(ficresplb,"%.0f ",age );        if(mobilavproj > 0){
           for(j=1;j<=cptcoveff;j++)          /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
             fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
           tot=0.;          bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
           for(i=1; i<=nlstate;i++){        }else if (mobilavproj == 0){
             tot +=  bprlim[i][i];          printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
             fprintf(ficresplb," %.5f", bprlim[i][i]);          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);
           fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);        }else{
         } /* Age */          /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
         /* was end of cptcod */          bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
     } /* cptcov */        }
         return 0;        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 7622  int hPijx(double *p, int bage, int fage) Line 7852  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 7663  int hPijx(double *p, int bage, int fage) Line 7893  int hPijx(double *p, int bage, int fage)
       }        }
       /*}*/        /*}*/
     }      }
         return 0;      return 0;
 }  }
    
  int hBijx(double *p, int bage, int fage){   int hBijx(double *p, int bage, int fage, double ***prevacurrent){
     /*------------- h Bij x at various ages ------------*/      /*------------- h Bij x at various ages ------------*/
   
   int stepsize;    int stepsize;
   int agelim;    /* int agelim; */
           int ageminl;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k;    int h, i, i1, j, k;
           
   double agedeb;    double agedeb;
   double ***p3mat;    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;  
     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");  
         
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */  
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months */  
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           
         /*        nhstepm=nhstepm*YEARM; aff par mois*/  
                   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcpy(filerespijb,"PIJB_");  strcat(filerespijb,fileresu);
         oldm=oldms;savm=savms;    if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");      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");
       
       /* 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(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);              fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
         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");          fprintf(ficrespijb,"\n");
       }        }
       /*}*/        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespijb,"\n");
     }      }
         return 0;      /*}*/
 }    }
     return 0;
    } /*  hBijx */
   
   
 /***********************************************/  /***********************************************/
Line 7769  int main(int argc, char *argv[]) Line 8004  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 8250  This is probably because your covariance Line 8486  This is probably because your covariance
 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++){
Line 8291  Please run with mle=-1 to get a correct Line 8527  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 8615  Interval (in months) between two waves: Line 8851  Interval (in months) between two waves:
     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 8634  Interval (in months) between two waves: Line 8869  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 9143  Please run with mle=-1 to get a correct Line 9378  Please run with mle=-1 to get a correct
 This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\  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, prevfcast, 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,prevfcast,backcast, estepm, \                   model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
Line 9173  Please run with mle=-1 to get a correct Line 9408  Please run with mle=-1 to get a correct
     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
     /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/  
     /*#include "prevlim.h"*/  /* Use ficresplb, ficlog */  
     bprlim=matrix(1,nlstate,1,nlstate);  
     back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);  
     fclose(ficresplb);  
   
       
 #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);
   
     hBijx(p, bage, fage);                  ncovcombmax=  pow(2,cptcoveff);
     fclose(ficrespijb);  
   
   /*-------------- Variance of one-step probabilities---*/    /*-------------- 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;j++)
         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 ) {
                           mobaverage= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
                           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)){*/
Line 9210  Please run with mle=-1 to get a correct Line 9450  Please run with mle=-1 to get a correct
       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);
     }      }
     if(backcast==1){      if(backcast==1){
       prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);                  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) --------------*/
                           /*#include "prevlim.h"*/  /* Use ficresplb, ficlog */
                           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);
                   }
     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     /* if (mobilavproj!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   
     /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/      /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
     /*      }  */      /*      }  */
     /*      else{ */      /*      else{ */
Line 9225  Please run with mle=-1 to get a correct Line 9485  Please run with mle=-1 to get a correct
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);      /* prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
     /*  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",\      /*  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",\
         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);          ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */      */
Line 9233  Please run with mle=-1 to get a correct Line 9493  Please run with mle=-1 to get a correct
     free_imatrix(dh,1,lastpass-firstpass+2,1,imx);      free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+2,1,imx);      free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+2,1,imx);         free_imatrix(mw,1,lastpass-firstpass+2,1,imx);   
                   
                   
     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, bage, fage, mobaverage,mobilav)!=0){                  /*     if (movingaverage(probs, bage, 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); */
       }                  /*     } */
     }                  /*   } */
                   
                   
     /*---------- 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) {
Line 9256  Please run with mle=-1 to get a correct Line 9516  Please run with mle=-1 to get a correct
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);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(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);                          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;                          oldm=oldms;savm=savms;
         evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);                            evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
               
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       /*}*/        /*}*/
     }      }
     fclose(ficreseij);      fclose(ficreseij);
     printf("done evsij\n");fflush(stdout);      printf("done evsij\n");fflush(stdout);
     fprintf(ficlog,"done evsij\n");fflush(ficlog);      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) {
Line 9286  Please run with mle=-1 to get a correct Line 9546  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);      printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);      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 9321  Please run with mle=-1 to get a correct Line 9581  Please run with mle=-1 to get a correct
     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);
Line 9355  Please run with mle=-1 to get a correct Line 9615  Please run with mle=-1 to get a correct
               
               
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         oldm=oldms;savm=savms; /* ZZ Segmentation fault */                                  oldm=oldms;savm=savms; /* ZZ Segmentation fault */
         cptcod= 0; /* To be deleted */                                  cptcod= 0; /* To be deleted */
         printf("varevsij %d \n",vpopbased);                                  printf("varevsij %d \n",vpopbased);
         fprintf(ficlog, "varevsij %d \n",vpopbased);                                  fprintf(ficlog, "varevsij %d \n",vpopbased);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */                                  varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");                                  fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
         if(vpopbased==1)                                  if(vpopbased==1)
           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);                                          fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
         else                                  else
           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");                                          fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");                                  fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                                  for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");                                  fprintf(ficrest,"\n");
         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */                                  /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
         epj=vector(1,nlstate+1);                                  epj=vector(1,nlstate+1);
         printf("Computing age specific period (stable) prevalences in each health state \n");                                  printf("Computing age specific period (stable) prevalences in each health state \n");
         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");                                  fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
         for(age=bage; age <=fage ;age++){                                  for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */                                          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
           if (vpopbased==1) {                                          if (vpopbased==1) {
             if(mobilav ==0){                                                  if(mobilav ==0){
               for(i=1; i<=nlstate;i++)                                                          for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];                                                                  prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */                                                   }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)                                                          for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];                                                                  prlim[i][i]=mobaverage[(int)age][i][k];
             }                                                  }
           }                                          }
                                                     
           fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);                                          fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
           /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */                                          /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
           /* printf(" age %4.0f ",age); */                                          /* printf(" age %4.0f ",age); */
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                                          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {                                                  for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];                                                          epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                                                          /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */                                                          /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
             }                                                  }
             epj[nlstate+1] +=epj[j];                                                  epj[nlstate+1] +=epj[j];
           }                                          }
           /* printf(" age %4.0f \n",age); */                                          /* printf(" age %4.0f \n",age); */
                                                     
           for(i=1, vepp=0.;i <=nlstate;i++)                                          for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)                                                  for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];                                                          vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                                          fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){                                          for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                                                  fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }                                          }
           fprintf(ficrest,"\n");                                          fprintf(ficrest,"\n");
         }                                  }
       } /* End vpopbased */        } /* End vpopbased */
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 9446  Please run with mle=-1 to get a correct Line 9706  Please run with mle=-1 to get a correct
                       
     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);      printf("done variance-covariance of period prevalence\n");fflush(stdout);
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);      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(mobaverage,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
  /* endfree:*/   /* endfree:*/
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
Removed from v.1.217  
changed lines
  Added in v.1.218

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