Diff for /imach/src/imach.c between versions 1.256 and 1.280

version 1.256, 2017/03/27 05:50:23 version 1.280, 2018/02/21 07:58:13
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.280  2018/02/21 07:58:13  brouard
     Summary: 0.99r15
   
     New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
   
     Revision 1.279  2017/07/20 13:35:01  brouard
     Summary: temporary working
   
     Revision 1.278  2017/07/19 14:09:02  brouard
     Summary: Bug for mobil_average=0 and prevforecast fixed(?)
   
     Revision 1.277  2017/07/17 08:53:49  brouard
     Summary: BOM files can be read now
   
     Revision 1.276  2017/06/30 15:48:31  brouard
     Summary: Graphs improvements
   
     Revision 1.275  2017/06/30 13:39:33  brouard
     Summary: Saito's color
   
     Revision 1.274  2017/06/29 09:47:08  brouard
     Summary: Version 0.99r14
   
     Revision 1.273  2017/06/27 11:06:02  brouard
     Summary: More documentation on projections
   
     Revision 1.272  2017/06/27 10:22:40  brouard
     Summary: Color of backprojection changed from 6 to 5(yellow)
   
     Revision 1.271  2017/06/27 10:17:50  brouard
     Summary: Some bug with rint
   
     Revision 1.270  2017/05/24 05:45:29  brouard
     *** empty log message ***
   
     Revision 1.269  2017/05/23 08:39:25  brouard
     Summary: Code into subroutine, cleanings
   
     Revision 1.268  2017/05/18 20:09:32  brouard
     Summary: backprojection and confidence intervals of backprevalence
   
     Revision 1.267  2017/05/13 10:25:05  brouard
     Summary: temporary save for backprojection
   
     Revision 1.266  2017/05/13 07:26:12  brouard
     Summary: Version 0.99r13 (improvements and bugs fixed)
   
     Revision 1.265  2017/04/26 16:22:11  brouard
     Summary: imach 0.99r13 Some bugs fixed
   
     Revision 1.264  2017/04/26 06:01:29  brouard
     Summary: Labels in graphs
   
     Revision 1.263  2017/04/24 15:23:15  brouard
     Summary: to save
   
     Revision 1.262  2017/04/18 16:48:12  brouard
     *** empty log message ***
   
     Revision 1.261  2017/04/05 10:14:09  brouard
     Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
   
     Revision 1.260  2017/04/04 17:46:59  brouard
     Summary: Gnuplot indexations fixed (humm)
   
     Revision 1.259  2017/04/04 13:01:16  brouard
     Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
   
     Revision 1.258  2017/04/03 10:17:47  brouard
     Summary: Version 0.99r12
   
     Some cleanings, conformed with updated documentation.
   
     Revision 1.257  2017/03/29 16:53:30  brouard
     Summary: Temp
   
   Revision 1.256  2017/03/27 05:50:23  brouard    Revision 1.256  2017/03/27 05:50:23  brouard
   Summary: Temporary    Summary: Temporary
   
Line 786  Back prevalence and projections: Line 862  Back prevalence and projections:
    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;
   
    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
      Computes the transition matrix starting at age 'age' over       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
Line 954  typedef struct { Line 1030  typedef struct {
 #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 AGESUP 150
   #define AGEINF 0
 #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */  #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
Line 1045  FILE *ficrescveij; Line 1122  FILE *ficrescveij;
 char filerescve[FILENAMELENGTH];  char filerescve[FILENAMELENGTH];
 FILE  *ficresvij;  FILE  *ficresvij;
 char fileresv[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];  char title[MAXLINE];
 char model[MAXLINE]; /**< The model line */  char model[MAXLINE]; /**< The model line */
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
Line 1144  double *agedc; Line 1220  double *agedc;
 double  **covar; /**< covar[j,i], value of jth covariate for individual i,  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                   * covar=matrix(0,NCOVMAX,1,n);                     * covar=matrix(0,NCOVMAX,1,n); 
                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
 double **coqvar; /* Fixed quantitative covariate iqv */  double **coqvar; /* Fixed quantitative covariate nqv */
 double ***cotvar; /* Time varying covariate itv */  double ***cotvar; /* Time varying covariate ntv */
 double ***cotqvar; /* Time varying quantitative covariate itqv */  double ***cotqvar; /* Time varying quantitative covariate itqv */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
Line 1174  int *TvarsQind; Line 1250  int *TvarsQind;
   
 #define MAXRESULTLINES 10  #define MAXRESULTLINES 10
 int nresult=0;  int nresult=0;
   int parameterline=0; /* # of the parameter (type) line */
 int TKresult[MAXRESULTLINES];  int TKresult[MAXRESULTLINES];
 int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */  int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
 int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */  int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
Line 2447  void powell(double p[], double **xi, int Line 2524  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, int nres)    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
   {    {
     /* Computes the prevalence limit in each live state at age x and for covariate combination ij       /**< Computes the prevalence limit in each live state at age x and for covariate combination ij 
        (and selected quantitative values in nres)       *   (and selected quantitative values in nres)
        by left multiplying the unit       *  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
   /* or prevalence in state 1, prevalence in state 2, 0 */       * or prevalence in state 1, prevalence in state 2, 0
   /* newm is the matrix after multiplications, its rows are identical at a factor */       * newm is the matrix after multiplications, its rows are identical at a factor.
   /* Initial matrix pimij */       * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
        * Output is prlim.
        * Initial matrix pimij 
        */
   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
   /*  0,                   0                  , 1} */    /*  0,                   0                  , 1} */
Line 2591  Earliest age to start was %d-%d=%d, ncvl Line 2671  Earliest age to start was %d-%d=%d, ncvl
  /* 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 **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, int nres)    double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
 {  {
   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit    /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
      matrix by transitions matrix until convergence is reached with precision ftolpl */       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 2627  Earliest age to start was %d-%d=%d, ncvl Line 2707  Earliest age to start was %d-%d=%d, ncvl
   max=vector(1,nlstate);    max=vector(1,nlstate);
   meandiff=vector(1,nlstate);    meandiff=vector(1,nlstate);
   
         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;    dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
         oldm=oldms; savm=savms;    oldm=oldms; savm=savms;
     
         /* Starting with matrix unity */    /* Starting with matrix unity */
         for (ii=1;ii<=nlstate+ndeath;ii++)    for (ii=1;ii<=nlstate+ndeath;ii++)
                 for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
       
Line 2652  Earliest age to start was %d-%d=%d, ncvl Line 2732  Earliest age to start was %d-%d=%d, ncvl
     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       /* printf("bprevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */        /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
     }      }
     /* for (k=1; k<=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])]; *\/ */
Line 2706  Earliest age to start was %d-%d=%d, ncvl Line 2786  Earliest age to start was %d-%d=%d, ncvl
     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, 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, 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 */      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
       /* if((int)age == 86 || (int)age == 87){ */
       /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
       /*   for(i=1; i<=nlstate+ndeath; i++) { */
       /*  printf("%d newm= ",i); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",newm[i][j]); */
       /*  } */
       /*  printf("oldm * "); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",oldm[i][j]); */
       /*  } */
       /*  printf(" bmmij "); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",pmmij[i][j]); */
       /*  } */
       /*  printf("\n"); */
       /*   } */
       /* } */
     savm=oldm;      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.;
Line 2726  Earliest age to start was %d-%d=%d, ncvl Line 2825  Earliest age to start was %d-%d=%d, ncvl
       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
       maxmax=FMAX(maxmax,meandiff[i]);        maxmax=FMAX(maxmax,meandiff[i]);
       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */        /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
     } /* j loop */      } /* i loop */
     *ncvyear= -( (int)age- (int)agefin);      *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 2758  Oldest age to start was %d-%d=%d, ncvloo Line 2857  Oldest age to start was %d-%d=%d, ncvloo
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   /* According to parameters values stored in x and the covariate's values stored in cov,    /* According to parameters values stored in x and the covariate's values stored in cov,
      computes the probability to be observed in state j being in state i by appying the       computes the probability to be observed in state j (after stepm years) being in state i by appying the
      model to the ncovmodel covariates (including constant and age).       model to the ncovmodel covariates (including constant and age).
      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
      and, according on how parameters are entered, the position of the coefficient xij(nc) of the       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
Line 2767  double **pmij(double **ps, double *cov, Line 2866  double **pmij(double **ps, double *cov,
      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
      Outputs ps[i][j] the probability to be observed in j being in j according to       Outputs ps[i][j] or probability to be observed in j being in i according to
      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
        Sum on j ps[i][j] should equal to 1.
   */    */
   double s1, lnpijopii;    double s1, lnpijopii;
   /*double t34;*/    /*double t34;*/
Line 2832  double **pmij(double **ps, double *cov, Line 2932  double **pmij(double **ps, double *cov,
   /*    /*
     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; /* Pointer is unchanged since its call */
 }  }
   
 /*************** backward transition probabilities ***************/   /*************** backward transition probabilities ***************/ 
Line 2841  double **pmij(double **ps, double *cov, Line 2941  double **pmij(double **ps, double *cov,
 /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
 {  {
   /* Computes the backward probability at age agefin and covariate ij    /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
    * and returns in **ps as well as **bmij.     * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
    */     */
   int i, ii, j,k;    int i, ii, j,k;
       
   double **out, **pmij();    double **out, **pmij();
   double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
       double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */
   double **dnewm, **dsavm, **doldm;    double **dnewm, **dsavm, **doldm;
   double **bbmij;    double **bbmij;
       
Line 2858  double **pmij(double **ps, double *cov, Line 2958  double **pmij(double **ps, double *cov,
   dsavm=ddsavms;    dsavm=ddsavms;
       
   agefin=cov[2];    agefin=cov[2];
     /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
   /* bmij *//* age is cov[2], ij is included in cov, but we need for    /* bmij *//* age is cov[2], ij is included in cov, but we need for
      the observed prevalence (with this covariate ij) */       the observed prevalence (with this covariate ij) at beginning of transition */
   dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);    /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   /* We do have the matrix Px in savm  and we need pij */  
     /* P_x */
     pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
     /* outputs pmmij which is a stochastic matrix in row */
   
     /* Diag(w_x) */
     /* Problem with prevacurrent which can be zero */
     sumnew=0.;
     /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
     for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
       /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]);  */
       sumnew+=prevacurrent[(int)agefin][ii][ij];
     }
     if(sumnew >0.01){  /* At least some value in the prevalence */
       for (ii=1;ii<=nlstate+ndeath;ii++){
         for (j=1;j<=nlstate+ndeath;j++)
           doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
       }
     }else{
       for (ii=1;ii<=nlstate+ndeath;ii++){
         for (j=1;j<=nlstate+ndeath;j++)
         doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
       }
       /* if(sumnew <0.9){ */
       /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
       /* } */
     }
     k3=0.0;  /* We put the last diagonal to 0 */
     for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
         doldm[ii][ii]= k3;
     }
     /* End doldm, At the end doldm is diag[(w_i)] */
     
     /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
     bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
   
     /* Diag(Sum_i w^i_x p^ij_x */
     /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
   for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
     sumnew=0.; /* w1 p11 + w2 p21 only on live states */      sumnew=0.;
     for (ii=1;ii<=nlstate;ii++){      for (ii=1;ii<=nlstate;ii++){
       sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];        /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
         sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */      } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
     for (ii=1;ii<=nlstate+ndeath;ii++){      for (ii=1;ii<=nlstate+ndeath;ii++){
       if(sumnew >= 1.e-10){  
         /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */          /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */          /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */          /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
         /* }else */          /* }else */
         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);        dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
       }else{  
         ;  
         /* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */  
       }  
     } /*End ii */      } /*End ii */
   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */    } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */  
   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */    ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */    /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */  
   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */  
   /* left Product of this matrix by diag matrix of prevalences (savm) */  
   for (j=1;j<=nlstate+ndeath;j++){  
     for (ii=1;ii<=nlstate+ndeath;ii++){  
       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);  
     }  
   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */  
   ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */  
   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */  
   /* end bmij */    /* end bmij */
   return ps;     return ps; /*pointer is unchanged */
 }  }
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
Line 3108  double ***hpxij(double ***po, int nhstep Line 3232  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, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
 double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
 {  {
   /* Computes the transition matrix starting at age 'age' over    /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
      'nhstepm*hstepm*stepm' months (i.e. until       '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 3129  double ***hbxij(double ***po, int nhstep Line 3253  double ***hbxij(double ***po, int nhstep
      (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. Then we use a call to bmij(x and cov)
        The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
   */    */
   
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1], **bmij();
   double **newm;    double **newm, ***newmm;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
   double **oldm, **savm;    double **oldm, **savm;
   
   oldm=oldms;savm=savms;    newmm=po; /* To be saved */
     oldm=oldms;savm=savms; /* Global pointers */
   /* Hstepm could be zero and should return the unit matrix */    /* 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 3153  double ***hbxij(double ***po, int nhstep Line 3278  double ***hbxij(double ***po, int nhstep
       newm=savm;        newm=savm;
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */        agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */        /* 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 */          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];        }
       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
           cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
           /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
         }
         for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
           if(Dummy[Tvar[Tage[k]]]){
             cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           } else{
             cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
           }
           /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
         }
         for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */        }                 
                           
                           
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("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]);*/
   
       /* Careful transposed matrix */        /* Careful transposed matrix */
       /* age is in cov[2] */        /* age is in cov[2], prevacurrent at beginning of transition. */
       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
       /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
Line 3198  double ***hbxij(double ***po, int nhstep Line 3334  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 %.1f ",h, agexact); */
   } /* end h */    } /* end h */
   /*     printf("\n H=%d \n",h); */    /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
   return po;    return po;
 }  }
   
Line 3657  double funcone( double *x) Line 3794  double funcone( double *x)
       s1=s[mw[mi][i]][i];        s1=s[mw[mi][i]][i];
       s2=s[mw[mi+1][i]][i];        s2=s[mw[mi+1][i]][i];
       /* if(s2==-1){ */        /* if(s2==-1){ */
       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */        /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
       /*        /\* exit(1); *\/ */        /*        /\* exit(1); *\/ */
       /* } */        /* } */
       bbh=(double)bh[mi][i]/(double)stepm;         bbh=(double)bh[mi][i]/(double)stepm; 
Line 3690  double funcone( double *x) Line 3827  double funcone( double *x)
         fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\          fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           llt +=ll[k]*gipmx/gsw;            llt +=ll[k]*gipmx/gsw;
           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
Line 3743  void likelione(FILE *ficres,double p[], Line 3880  void likelione(FILE *ficres,double p[],
     else if(mle >=1)      else if(mle >=1)
       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model); 
               
     for (k=1; k<= nlstate ; k++) {      for (k=1; k<= nlstate ; k++) {
       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \        fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
Line 4210  void pstamp(FILE *fichier) Line 4347  void pstamp(FILE *fichier)
   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
 int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {  
   
   /* y=a+bx regression */  
   double   sumx = 0.0;                        /* sum of x                      */  
   double   sumx2 = 0.0;                       /* sum of x**2                   */  
   double   sumxy = 0.0;                       /* sum of x * y                  */  
   double   sumy = 0.0;                        /* sum of y                      */  
   double   sumy2 = 0.0;                       /* sum of y**2                   */  
   double   sume2; /* sum of square or residuals */  
   double yhat;  
     
   double denom=0;  
   int i;  
   int ne=*no;  
     
   for ( i=ifi, ne=0;i<=ila;i++) {  
     if(!isfinite(x[i]) || !isfinite(y[i])){  
       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */  
       continue;  
     }  
     ne=ne+1;  
     sumx  += x[i];         
     sumx2 += x[i]*x[i];    
     sumxy += x[i] * y[i];  
     sumy  += y[i];        
     sumy2 += y[i]*y[i];   
     denom = (ne * sumx2 - sumx*sumx);  
     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */  
   }   
     
   denom = (ne * sumx2 - sumx*sumx);  
   if (denom == 0) {  
     // vertical, slope m is infinity  
     *b = INFINITY;  
     *a = 0;  
     if (r) *r = 0;  
     return 1;  
   }  
     
   *b = (ne * sumxy  -  sumx * sumy) / denom;  
   *a = (sumy * sumx2  -  sumx * sumxy) / denom;  
   if (r!=NULL) {  
     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */  
       sqrt((sumx2 - sumx*sumx/ne) *  
            (sumy2 - sumy*sumy/ne));  
   }  
   *no=ne;  
   for ( i=ifi, ne=0;i<=ila;i++) {  
     if(!isfinite(x[i]) || !isfinite(y[i])){  
       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */  
       continue;  
     }  
     ne=ne+1;  
     yhat = y[i] - *a -*b* x[i];  
     sume2  += yhat * yhat ;         
       
     denom = (ne * sumx2 - sumx*sumx);  
     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */  
   }   
   *sb = sqrt(sume2/(ne-2)/(sumx2 - sumx * sumx /ne));  
   *sa= *sb * sqrt(sumx2/ne);  
     
   return 0;   
 }  
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \  void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
Line 4281  void  freqsummary(char fileres[], double Line 4355  void  freqsummary(char fileres[], double
                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies as well as proposing some starting values */  {  /* Some frequencies as well as proposing some starting values */
       
   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0;    int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
   int iind=0, iage=0;    int iind=0, iage=0;
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */    double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
   int no;    int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
   double *meanq;    double *meanq;
   double **meanqt;    double **meanqt;
   double *pp, **prop, *posprop, *pospropt;    double *pp, **prop, *posprop, *pospropt;
Line 4360  Title=%s <br>Datafile=%s Firstpass=%d La Line 4434  Title=%s <br>Datafile=%s Firstpass=%d La
   k2cpt=0;    k2cpt=0;
   
   if(cptcoveff == 0 )    if(cptcoveff == 0 )
     nl=1;  /* Constant model only */      nl=1;  /* Constant and age model only */
   else    else
     nl=2;      nl=2;
   
     /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
     /* Loop on nj=1 or 2 if dummy covariates j!=0
      *   Loop on j1(1 to 2**cptcoveff) covariate combination
      *     freq[s1][s2][iage] =0.
      *     Loop on iind
      *       ++freq[s1][s2][iage] weighted
      *     end iind
      *     if covariate and j!0
      *       headers Variable on one line
      *     endif cov j!=0
      *     header of frequency table by age
      *     Loop on age
      *       pp[s1]+=freq[s1][s2][iage] weighted
      *       pos+=freq[s1][s2][iage] weighted
      *       Loop on s1 initial state
      *         fprintf(ficresp
      *       end s1
      *     end age
      *     if j!=0 computes starting values
      *     end compute starting values
      *   end j1
      * end nl 
      */
   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */    for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
     if(nj==1)      if(nj==1)
       j=0;  /* First pass for the constant */        j=0;  /* First pass for the constant */
     else      else{
       j=cptcoveff; /* Other passes for the covariate values */        j=cptcoveff; /* Other passes for the covariate values */
       }
     first=1;      first=1;
     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */      for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
       posproptt=0.;        posproptt=0.;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
       for (i=-5; i<=nlstate+ndeath; i++)          for (i=-5; i<=nlstate+ndeath; i++)  
         for (jk=-5; jk<=nlstate+ndeath; jk++)            for (s2=-5; s2<=nlstate+ndeath; s2++)  
           for(m=iagemin; m <= iagemax+3; m++)            for(m=iagemin; m <= iagemax+3; m++)
             freq[i][jk][m]=0;              freq[i][s2][m]=0;
               
       for (i=1; i<=nlstate; i++)  {        for (i=1; i<=nlstate; i++)  {
         for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
Line 4394  Title=%s <br>Datafile=%s Firstpass=%d La Line 4493  Title=%s <br>Datafile=%s Firstpass=%d La
       /* dateintsum=0; */        /* dateintsum=0; */
       /* k2cpt=0; */        /* k2cpt=0; */
               
       /* For that combination of covariate j1, we count and print the frequencies in one pass */        /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
       for (iind=1; iind<=imx; iind++) { /* For each individual iind */        for (iind=1; iind<=imx; iind++) { /* For each individual iind */
         bool=1;          bool=1;
         if(j !=0){          if(j !=0){
Line 4410  Title=%s <br>Datafile=%s Firstpass=%d La Line 4509  Title=%s <br>Datafile=%s Firstpass=%d La
                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                 /* }else  */                  /* }else  */
                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */                  if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
                   /* Tests if this individual iind responded to combination j1 (V4=1 V3=0) */                    /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */                    bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
                   /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",                     /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                      bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                       bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
Line 4421  Title=%s <br>Datafile=%s Firstpass=%d La Line 4520  Title=%s <br>Datafile=%s Firstpass=%d La
             } /* cptcovn > 0 */              } /* cptcovn > 0 */
           } /* end any */            } /* end any */
         }/* end j==0 */          }/* end j==0 */
         if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */          if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
           /* for(m=firstpass; m<=lastpass; m++){ */            /* for(m=firstpass; m<=lastpass; m++){ */
           for(mi=1; mi<wav[iind];mi++){ /* For that wave */            for(mi=1; mi<wav[iind];mi++){ /* For that wave */
             m=mw[mi][iind];              m=mw[mi][iind];
Line 4483  Title=%s <br>Datafile=%s Firstpass=%d La Line 4582  Title=%s <br>Datafile=%s Firstpass=%d La
               
               
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       pstamp(ficresp);        if(cptcoveff==0 && nj==1) /* no covariate and first pass */
           pstamp(ficresp);
       if  (cptcoveff>0 && j!=0){        if  (cptcoveff>0 && j!=0){
           pstamp(ficresp);
         printf( "\n#********** Variable ");           printf( "\n#********** Variable "); 
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
Line 4512  Title=%s <br>Datafile=%s Firstpass=%d La Line 4613  Title=%s <br>Datafile=%s Firstpass=%d La
         fprintf(ficlog, "**********\n");          fprintf(ficlog, "**********\n");
       }        }
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
         if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
           fprintf(ficresp, " Age");
         if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       for(i=1; i<=nlstate;i++) {        for(i=1; i<=nlstate;i++) {
         fprintf(ficresp, " Age Prev(%d)  N(%d)  N  ",i,i);          if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       }        }
       fprintf(ficresp, "\n");        if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");        fprintf(ficresphtm, "\n");
               
       /* Header of frequency table by age */        /* Header of frequency table by age */
       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
       fprintf(ficresphtmfr,"<th>Age</th> ");        fprintf(ficresphtmfr,"<th>Age</th> ");
       for(jk=-1; jk <=nlstate+ndeath; jk++){        for(s2=-1; s2 <=nlstate+ndeath; s2++){
         for(m=-1; m <=nlstate+ndeath; m++){          for(m=-1; m <=nlstate+ndeath; m++){
           if(jk!=0 && m!=0)            if(s2!=0 && m!=0)
             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);              fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
         }          }
       }        }
       fprintf(ficresphtmfr, "\n");        fprintf(ficresphtmfr, "\n");
Line 4550  Title=%s <br>Datafile=%s Firstpass=%d La Line 4654  Title=%s <br>Datafile=%s Firstpass=%d La
           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);            fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
           fprintf(ficlog,"Age %d", iage);            fprintf(ficlog,"Age %d", iage);
         }          }
         for(jk=1; jk <=nlstate ; jk++){          for(s1=1; s1 <=nlstate ; s1++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
             pp[jk] += freq[jk][m][iage];               pp[s1] += freq[s1][m][iage]; 
         }          }
         for(jk=1; jk <=nlstate ; jk++){          for(s1=1; s1 <=nlstate ; s1++){
           for(m=-1, pos=0; m <=0 ; m++)            for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][iage];              pos += freq[s1][m][iage];
           if(pp[jk]>=1.e-10){            if(pp[s1]>=1.e-10){
             if(first==1){              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
             }              }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
           }else{            }else{
             if(first==1)              if(first==1)
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
           }            }
         }          }
               
         for(jk=1; jk <=nlstate ; jk++){           for(s1=1; s1 <=nlstate ; s1++){ 
           /* posprop[jk]=0; */            /* posprop[s1]=0; */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */            for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
             pp[jk] += freq[jk][m][iage];              pp[s1] += freq[s1][m][iage];
         }       /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */          }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
               
         for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){          for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
           pos += pp[jk]; /* pos is the total number of transitions until this age */            pos += pp[s1]; /* pos is the total number of transitions until this age */
           posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state            posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
                                             from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */                                              from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state            pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
                                           from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */                                            from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           }
           
           /* Writing ficresp */
           if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
             }
           }else if( nj==2){
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
               for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }
         }          }
         for(jk=1; jk <=nlstate ; jk++){          for(s1=1; s1 <=nlstate ; s1++){
           if(pos>=1.e-5){            if(pos>=1.e-5){
             if(first==1)              if(first==1)
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
           }else{            }else{
             if(first==1)              if(first==1)
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
           }            }
           if( iage <= iagemax){            if( iage <= iagemax){
             if(pos>=1.e-5){              if(pos>=1.e-5){
               fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);                if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
               /*probs[iage][jk][j1]= pp[jk]/pos;*/                }else if( nj==2){
               /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
             }                }
             else{                fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
               fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);                /*probs[iage][s1][j1]= pp[s1]/pos;*/
               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);                /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
               } else{
                 if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
             }              }
           }            }
           pospropt[jk] +=posprop[jk];            pospropt[s1] +=posprop[s1];
         } /* end loop jk */          } /* end loop s1 */
         /* pospropt=0.; */          /* pospropt=0.; */
         for(jk=-1; jk <=nlstate+ndeath; jk++){          for(s1=-1; s1 <=nlstate+ndeath; s1++){
           for(m=-1; m <=nlstate+ndeath; m++){            for(m=-1; m <=nlstate+ndeath; m++){
             if(freq[jk][m][iage] !=0 ) { /* minimizing output */              if(freq[s1][m][iage] !=0 ) { /* minimizing output */
               if(first==1){                if(first==1){
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);                  printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
               }                }
               /* printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); */                /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);                fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
             }              }
             if(jk!=0 && m!=0)              if(s1!=0 && m!=0)
               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);                fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
           }            }
         } /* end loop jk */          } /* end loop s1 */
         posproptt=0.;           posproptt=0.; 
         for(jk=1; jk <=nlstate; jk++){          for(s1=1; s1 <=nlstate; s1++){
           posproptt += pospropt[jk];            posproptt += pospropt[s1];
         }          }
         fprintf(ficresphtmfr,"</tr>\n ");          fprintf(ficresphtmfr,"</tr>\n ");
         if(iage <= iagemax){          fprintf(ficresphtm,"</tr>\n");
           fprintf(ficresp,"\n");          if((cptcoveff==0 && nj==1)|| nj==2 ) {
           fprintf(ficresphtm,"</tr>\n");            if(iage <= iagemax)
               fprintf(ficresp,"\n");
         }          }
         if(first==1)          if(first==1)
           printf("Others in log...\n");            printf("Others in log...\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
       } /* end loop age iage */        } /* end loop age iage */
         
       fprintf(ficresphtm,"<tr><th>Tot</th>");        fprintf(ficresphtm,"<tr><th>Tot</th>");
       for(jk=1; jk <=nlstate ; jk++){        for(s1=1; s1 <=nlstate ; s1++){
         if(posproptt < 1.e-5){          if(posproptt < 1.e-5){
           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);             fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt); 
         }else{          }else{
           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);              fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);  
         }          }
       }        }
       fprintf(ficresphtm,"</tr>\n");        fprintf(ficresphtm,"</tr>\n");
Line 4647  Title=%s <br>Datafile=%s Firstpass=%d La Line 4768  Title=%s <br>Datafile=%s Firstpass=%d La
       if(posproptt < 1.e-5){        if(posproptt < 1.e-5){
         fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);          fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);          fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
         fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);          fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
           printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
         invalidvarcomb[j1]=1;          invalidvarcomb[j1]=1;
       }else{        }else{
         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);          fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
Line 4657  Title=%s <br>Datafile=%s Firstpass=%d La Line 4779  Title=%s <br>Datafile=%s Firstpass=%d La
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       if(j!=0){        if(j!=0){
         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);          printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
         for(i=1,jk=1; i <=nlstate; i++){          for(i=1,s1=1; i <=nlstate; i++){
           for(k=1; k <=(nlstate+ndeath); k++){            for(k=1; k <=(nlstate+ndeath); k++){
             if (k != i) {              if (k != i) {
               for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */                for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
                 if(jj==1){  /* Constant case (in fact cste + age) */                  if(jj==1){  /* Constant case (in fact cste + age) */
                   if(j1==1){ /* All dummy covariates to zero */                    if(j1==1){ /* All dummy covariates to zero */
                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */                      freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */                      freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
                     printf("%d%d ",i,k);                      printf("%d%d ",i,k);
                     fprintf(ficlog,"%d%d ",i,k);                      fprintf(ficlog,"%d%d ",i,k);
                     printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));                      printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
                     fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));                      fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                     pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);                      pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                   }                    }
                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */                  }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
                   for(iage=iagemin; iage <= iagemax+3; iage++){                    for(iage=iagemin; iage <= iagemax+3; iage++){
                     x[iage]= (double)iage;                      x[iage]= (double)iage;
                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);                      y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
                     /* printf("i=%d, k=%d, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */                      /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
                   }                    }
                     /* Some are not finite, but linreg will ignore these ages */
                     no=0;
                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */                    linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
                   pstart[jk]=b;                    pstart[s1]=b;
                   pstart[jk-1]=a;                    pstart[s1-1]=a;
                 }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */                   }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ 
                   printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);                    printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                   printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);                    printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                   pstart[jk]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));                    pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
                   printf("%d%d ",i,k);                    printf("%d%d ",i,k);
                   fprintf(ficlog,"%d%d ",i,k);                    fprintf(ficlog,"%d%d ",i,k);
                   printf("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));                    printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
                 }else{ /* Other cases, like quantitative fixed or varying covariates */                  }else{ /* Other cases, like quantitative fixed or varying covariates */
                   ;                    ;
                 }                  }
                 /* printf("%12.7f )", param[i][jj][k]); */                  /* printf("%12.7f )", param[i][jj][k]); */
                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */                  /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                 jk++;                   s1++; 
               } /* end jj */                } /* end jj */
             } /* end k!= i */              } /* end k!= i */
           } /* end k */            } /* end k */
         } /* end i, jk */          } /* end i, s1 */
       } /* end j !=0 */        } /* end j !=0 */
     } /* end selected combination of covariate j1 */      } /* end selected combination of covariate j1 */
     if(j==0){ /* We can estimate starting values from the occurences in each case */      if(j==0){ /* We can estimate starting values from the occurences in each case */
       printf("#Freqsummary: Starting values for the constants:\n");        printf("#Freqsummary: Starting values for the constants:\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       for(i=1,jk=1; i <=nlstate; i++){        for(i=1,s1=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){          for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {            if (k != i) {
             printf("%d%d ",i,k);              printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);              fprintf(ficlog,"%d%d ",i,k);
             for(jj=1; jj <=ncovmodel; jj++){              for(jj=1; jj <=ncovmodel; jj++){
               pstart[jk]=p[jk]; /* Setting pstart to p values by default */                pstart[s1]=p[s1]; /* Setting pstart to p values by default */
               if(jj==1){ /* Age has to be done */                if(jj==1){ /* Age has to be done */
                 pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);                  pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                 printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));                  printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                 fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));                  fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
               }                }
               /* printf("%12.7f )", param[i][jj][k]); */                /* printf("%12.7f )", param[i][jj][k]); */
               /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */                /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
               jk++;                 s1++; 
             }              }
             printf("\n");              printf("\n");
             fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
Line 4725  Title=%s <br>Datafile=%s Firstpass=%d La Line 4849  Title=%s <br>Datafile=%s Firstpass=%d La
       }        }
       printf("#Freqsummary\n");        printf("#Freqsummary\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       for(jk=-1; jk <=nlstate+ndeath; jk++){        for(s1=-1; s1 <=nlstate+ndeath; s1++){
         for(m=-1; m <=nlstate+ndeath; m++){          for(s2=-1; s2 <=nlstate+ndeath; s2++){
           /* param[i]|j][k]= freq[jk][m][iagemax+3] */            /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
           printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);            printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
           fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);            fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
           /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */            /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
           /*   printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */            /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
           /*   fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */            /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
           /* } */            /* } */
         }          }
       } /* end loop jk */        } /* end loop s1 */
               
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
Line 4780  Title=%s <br>Datafile=%s Firstpass=%d La Line 4904  Title=%s <br>Datafile=%s Firstpass=%d La
   /* End of freqsummary */    /* End of freqsummary */
 }  }
   
   /* Simple linear regression */
   int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
   
     /* y=a+bx regression */
     double   sumx = 0.0;                        /* sum of x                      */
     double   sumx2 = 0.0;                       /* sum of x**2                   */
     double   sumxy = 0.0;                       /* sum of x * y                  */
     double   sumy = 0.0;                        /* sum of y                      */
     double   sumy2 = 0.0;                       /* sum of y**2                   */
     double   sume2 = 0.0;                       /* sum of square or residuals */
     double yhat;
     
     double denom=0;
     int i;
     int ne=*no;
     
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       sumx  += x[i];       
       sumx2 += x[i]*x[i];  
       sumxy += x[i] * y[i];
       sumy  += y[i];      
       sumy2 += y[i]*y[i]; 
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     
     denom = (ne * sumx2 - sumx*sumx);
     if (denom == 0) {
       // vertical, slope m is infinity
       *b = INFINITY;
       *a = 0;
       if (r) *r = 0;
       return 1;
     }
     
     *b = (ne * sumxy  -  sumx * sumy) / denom;
     *a = (sumy * sumx2  -  sumx * sumxy) / denom;
     if (r!=NULL) {
       *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
         sqrt((sumx2 - sumx*sumx/ne) *
              (sumy2 - sumy*sumy/ne));
     }
     *no=ne;
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       yhat = y[i] - *a -*b* x[i];
       sume2  += yhat * yhat ;       
       
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
     *sa= *sb * sqrt(sumx2/ne);
     
     return 0; 
   }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
 void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 {    {  
Line 4869  void prevalence(double ***probs, double Line 5059  void prevalence(double ***probs, double
           } 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 in log file...\n",jk,i,j1,probs[i][jk][j1]);                printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
                 fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
               }else{
                 fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
             }              }
           }            }
         }           } 
Line 4929  void  concatwav(int wav[], int **dh, int Line 5122  void  concatwav(int wav[], int **dh, int
 #else  #else
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
           if(firsthree == 0){            if(firsthree == 0){
             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);              printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
             firsthree=1;              firsthree=1;
           }            }
           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);            fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
           mw[++mi][i]=m;            mw[++mi][i]=m;
           mli=m;            mli=m;
         }          }
Line 4959  void  concatwav(int wav[], int **dh, int Line 5152  void  concatwav(int wav[], int **dh, int
       /* if(mi==0)  never been interviewed correctly before death */        /* if(mi==0)  never been interviewed correctly before death */
       /* Only death is a correct wave */        /* Only death is a correct wave */
       mw[mi][i]=m;        mw[mi][i]=m;
     }      } /* else not in a death state */
 #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */      else if ((int) andc[i] != 9999) {  /* Date of death is known */
       /* m++; */  
       /* mi++; */  
       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */  
       /* mw[mi][i]=m; */  
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
           nbwarn++;            nbwarn++;
Line 4978  void  concatwav(int wav[], int **dh, int Line 5167  void  concatwav(int wav[], int **dh, int
         }else{ /* Death occured afer last wave potential bias */          }else{ /* Death occured afer last wave potential bias */
           nberr++;            nberr++;
           if(firstwo==0){            if(firstwo==0){
             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );              printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
             firstwo=1;              firstwo=1;
           }            }
           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
         }          }
       }else{ /* end date of interview is known */        }else{ /* if date of interview is unknown */
         /* death is known but not confirmed by death status at any wave */          /* death is known but not confirmed by death status at any wave */
         if(firstfour==0){          if(firstfour==0){
           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
Line 5014  void  concatwav(int wav[], int **dh, int Line 5203  void  concatwav(int wav[], int **dh, int
       if (stepm <=0)        if (stepm <=0)
         dh[mi][i]=1;          dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
           if (agedc[i] < 2*AGESUP) {            if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */              if(j==0) j=1;  /* Survives at least one month after exam */
Line 5313  void  concatwav(int wav[], int **dh, int Line 5502  void  concatwav(int wav[], int **dh, int
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.     /* 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        nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin.        nstepm is the number of stepm from age to agelin. 
      Look at hpijx to understand the reason of that which relies in memory size       Look at hpijx to understand the reason which relies in memory size consideration
      and note for a fixed period like estepm months */       and note for a fixed period like estepm months */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* 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       survival function given by stepm (the optimization length). Unfortunately it
Line 5544  void  concatwav(int wav[], int **dh, int Line 5733  void  concatwav(int wav[], int **dh, int
           /* 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]);*/
                                                                                   
         }          }
                   
       /* Standard deviation of expectancies ij */         
     fprintf(ficresstdeij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     for(i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++){
       eip=0.;        eip=0.;
Line 5559  void  concatwav(int wav[], int **dh, int Line 5749  void  concatwav(int wav[], int **dh, int
     }      }
     fprintf(ficresstdeij,"\n");      fprintf(ficresstdeij,"\n");
                                   
       /* Variance of expectancies ij */           
     fprintf(ficrescveij,"%3.0f",age );      fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
Line 5592  void  concatwav(int wav[], int **dh, int Line 5783  void  concatwav(int wav[], int **dh, int
 /************ 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[], int nres)   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
  {   {
    /* Variance of health expectancies */     /** 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;
Line 5603  void  concatwav(int wav[], int **dh, int Line 5795  void  concatwav(int wav[], int **dh, int
    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; */
Line 5668  void  concatwav(int wav[], int **dh, int Line 5860  void  concatwav(int wav[], int **dh, int
    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/     /* 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<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);     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */  
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    pstamp(ficresvij);     pstamp(ficresvij);
    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
Line 5723  void  concatwav(int wav[], int **dh, int Line 5915  void  concatwav(int wav[], int **dh, int
        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
          xp[i] = x[i] + (i==theta ?delti[theta]:0);           xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }         }
                                  /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
           * returns into prlim .
           */              
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                           
          /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
            for(i=1; i<=nlstate;i++)             for(i=1; i<=nlstate;i++)
Line 5735  void  concatwav(int wav[], int **dh, int Line 5930  void  concatwav(int wav[], int **dh, int
              prlim[i][i]=mobaverage[(int)age][i][ij];               prlim[i][i]=mobaverage[(int)age][i][ij];
          }           }
        }         }
                                  /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */          */                      
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
          /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
           * at horizon h in state j including mortality.
           */
        for(j=1; j<= nlstate; j++){         for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }           }
        }         }
        /* Next for computing probability of death (h=1 means         /* Next for computing shifted+ probability of death (h=1 means
           computed over hstepm matrices product = hstepm*stepm months)             computed over hstepm matrices product = hstepm*stepm months) 
           as a weighted average of prlim.            as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
        */         */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){         for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gpp[j]=0.; i<= nlstate; i++)           for(i=1,gpp[j]=0.; i<= nlstate; i++)
            gpp[j] += prlim[i][i]*p3mat[i][j][1];             gpp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }
        /* end probability of death */         
          /* Again with minus shift */
                                                   
        for(i=1; i<=npar; i++) /* Computes gradient x - delta */         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);           xp[i] = x[i] - (i==theta ?delti[theta]:0);
Line 5784  void  concatwav(int wav[], int **dh, int Line 5984  void  concatwav(int wav[], int **dh, int
          for(i=1,gmp[j]=0.; i<= nlstate; i++)           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];             gmp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }    
        /* end probability of death */         /* end shifting computations */
                           
          /**< Computing gradient matrix at horizon h 
           */
        for(j=1; j<= nlstate; j++) /* vareij */         for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }           }
                                  /**< Gradient of overall mortality p.3 (or p.j) 
        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          */
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }         }
                                                   
      } /* End theta */       } /* End theta */
                        
        /* We got the gradient matrix for each theta and state j */                
      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                                   
      for(h=0; h<=nhstepm; h++) /* veij */       for(h=0; h<=nhstepm; h++) /* veij */
Line 5807  void  concatwav(int wav[], int **dh, int Line 6011  void  concatwav(int wav[], int **dh, int
      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
        for(theta=1; theta <=npar; theta++)         for(theta=1; theta <=npar; theta++)
          trgradgp[j][theta]=gradgp[theta][j];           trgradgp[j][theta]=gradgp[theta][j];
                        /**< as well as its transposed matrix 
         */                
                                   
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)       for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)         for(j=1;j<=nlstate;j++)
          vareij[i][j][(int)age] =0.;           vareij[i][j][(int)age] =0.;
                   
        /* Computing trgradg by matcov by gradg at age and summing over h
         * and k (nhstepm) formula 15 of article
         * Lievre-Brouard-Heathcote
         */
        
      for(h=0;h<=nhstepm;h++){       for(h=0;h<=nhstepm;h++){
        for(k=0;k<=nhstepm;k++){         for(k=0;k<=nhstepm;k++){
          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
Line 5824  void  concatwav(int wav[], int **dh, int Line 6034  void  concatwav(int wav[], int **dh, int
        }         }
      }       }
                                   
      /* pptj */       /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
         * p.j overall mortality formula 49 but computed directly because
         * we compute the grad (wix pijx) instead of grad (pijx),even if
         * wix is independent of theta.
         */
      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       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);       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
      for(j=nlstate+1;j<=nlstate+ndeath;j++)       for(j=nlstate+1;j<=nlstate+ndeath;j++)
Line 5912  void  concatwav(int wav[], int **dh, int Line 6126  void  concatwav(int wav[], int **dh, int
  }  /* 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[], int nres)   void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
 {  {
   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
   double **dnewm,**doldm;    double **dnewmpar,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
Line 5936  void  concatwav(int wav[], int **dh, int Line 6150  void  concatwav(int wav[], int **dh, int
   fprintf(ficresvpl,"\n");    fprintf(ficresvpl,"\n");
   
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,nlstate,1,npar);    dnewmpar=matrix(1,nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    doldm=matrix(1,nlstate,1,nlstate);
       
   hstepm=1*YEARM; /* Every year of age */    hstepm=1*YEARM; /* Every year of age */
Line 6006  void  concatwav(int wav[], int **dh, int Line 6220  void  concatwav(int wav[], int **dh, int
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] =0.;        varpl[i][(int)age] =0.;
     if((int)age==79 ||(int)age== 80  ||(int)age== 81){      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
     }else{      }else{
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
     }      }
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
Line 6031  void  concatwav(int wav[], int **dh, int Line 6245  void  concatwav(int wav[], int **dh, int
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(doldm,1,nlstate,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
   }
   
   
   /************ Variance of backprevalence limit ******************/
    void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
   {
     /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewmpar,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mgm, **mgp;
     double age,agelim;
     int theta;
     
     pstamp(ficresvbl);
     fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
     fprintf(ficresvbl,"# Age ");
     if(nresult >=1)
       fprintf(ficresvbl," Result# ");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvbl," %1d-%1d",i,i);
     fprintf(ficresvbl,"\n");
   
     xp=vector(1,npar);
     dnewmpar=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGEINF;
     for (age=fage; age>=bage; age --){ /* If stepm=6 months */
       nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gp[i] = bprlim[i][i];
           mgp[theta][i] = bprlim[i][i];
         }
        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
          if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
          else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gm[i] = bprlim[i][i];
           mgm[theta][i] = bprlim[i][i];
         }
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
       for(i=1;i<=nlstate;i++)
         varbpl[i][(int)age] =0.;
       if((int)age==79 ||(int)age== 80  ||(int)age== 81){
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }else{
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }
       for(i=1;i<=nlstate;i++)
         varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvbl,"%.0f ",age );
       if(nresult >=1)
         fprintf(ficresvbl,"%d ",nres );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
       fprintf(ficresvbl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
 }  }
   
Line 6111  void varprob(char optionfilefiname[], do Line 6450  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");     fprintf(fichtm,"\n");
   
    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s</li>\n",optionfilehtmcov,optionfilehtmcov);
    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
Line 6308  To be simple, these graphs help to under Line 6647  To be simple, these graphs help to under
                  }                   }
                                                                                                                                   
                  /* Eigen vectors */                   /* Eigen vectors */
                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                   if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
                      printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
                    }else
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                  /*v21=sqrt(1.-v11*v11); *//* error */                   /*v21=sqrt(1.-v11*v11); *//* error */
                  v21=(lc1-v1)/cv12*v11;                   v21=(lc1-v1)/cv12*v11;
                  v12=-v21;                   v12=-v21;
Line 6328  To be simple, these graphs help to under Line 6672  To be simple, these graphs help to under
                    fprintf(ficgp,"\nset parametric;unset label");                     fprintf(ficgp,"\nset parametric;unset label");
                    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                    fprintf(ficgp,"\nset ter svg size 640, 480");                     fprintf(ficgp,"\nset ter svg size 640, 480");
                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\                     fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
 %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
Line 6339  To be simple, these graphs help to under Line 6683  To be simple, these graphs help to under
                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \                             mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
                  }else{                   }else{
                    first=0;                     first=0;
                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                    fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \                             mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
                  }/* if first */                   }/* if first */
                } /* age mod 5 */                 } /* age mod 5 */
              } /* end loop age */               } /* end loop age */
Line 6376  To be simple, these graphs help to under Line 6720  To be simple, these graphs help to under
 void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int prevfcast, int backcast, int estepm , \                    int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, double dateprev1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2){                    double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
   int jj1, k1, i1, cpt, k4, nres;    int jj1, k1, i1, cpt, k4, nres;
   
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
Line 6414  void printinghtml(char fileresu[], char Line 6758  void printinghtml(char fileresu[], char
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
    }     }
   
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  
   
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
      jj1=0;
   
      fprintf(fichtm," \n<ul>");
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\">");
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          fprintf(fichtm,"************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          if(invalidvarcomb[k1]){
            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
            continue;
          }
          fprintf(fichtm,"</a></li>");
        } /* cptcovn >0 */
      }
        fprintf(fichtm," \n</ul>");
   
    jj1=0;     jj1=0;
   
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++) /* For each resultline */
Line 6429  void printinghtml(char fileresu[], char Line 6809  void printinghtml(char fileresu[], char
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
          fprintf(fichtm,"\n<p><a name=\"rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\"</a>");
    
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
Line 6450  void printinghtml(char fileresu[], char Line 6839  void printinghtml(char fileresu[], char
        }         }
      }       }
      /* aij, bij */       /* aij, bij */
      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \       fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
 <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);  <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \       fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
Line 6474  divided by h: <sub>h</sub>P<sub>ij</sub> Line 6863  divided by h: <sub>h</sub>P<sub>ij</sub>
      }       }
      /* Period (stable) prevalence in each health state */       /* Period (stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d some years earlier, knowing that we will be in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(backcast==1){       if(backcast==1){
        /* Period (stable) back prevalence in each health state */         /* Period (stable) back prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability to be in state %d at a younger age, knowing that we will be in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
        }         }
      }       }
      if(prevfcast==1){       if(prevfcast==1){
        /* Projection of prevalence up to period (stable) prevalence in each health state */         /* Projection of prevalence up to period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
          }
        }
        if(backcast==1){
         /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
    from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
    account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
   with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
    <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
        }         }
      }       }
                     
Line 6576  See page 'Matrix of variance-covariance Line 6975  See page 'Matrix of variance-covariance
        }         }
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
 <img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);    <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       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) \
Line 6594  true period expectancies (those weighted Line 6993  true period expectancies (those weighted
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   char gplotcondition[132];    char gplotcondition[132], gplotlabel[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
   int lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
   int ioffset; /* variable offset for columns */    int ioffset; /* variable offset for columns */
     int iyearc=1; /* variable column for year of projection  */
     int iagec=1; /* variable column for age of projection  */
   int nres=0; /* Index of resultline */    int nres=0; /* Index of resultline */
     int istart=1; /* For starting graphs in projections */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 6615  void printinggnuplot(char fileresu[], ch Line 7017  void printinggnuplot(char fileresu[], ch
   /*#endif */    /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
   
     /* diagram of the model */
     fprintf(ficgp,"\n#Diagram of the model \n");
     fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
     fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
     fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
   
     fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
     fprintf(ficgp,"\n#show arrow\nunset label\n");
     fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
     fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
     fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
     fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
     fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
   
   /* Contribution to likelihood */    /* Contribution to likelihood */
   /* Plot the probability implied in the likelihood */    /* Plot the probability implied in the likelihood */
   fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");    fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
Line 6656  void printinggnuplot(char fileresu[], ch Line 7072  void printinggnuplot(char fileresu[], ch
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
           strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */            lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate 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 */
Line 6665  void printinggnuplot(char fileresu[], ch Line 7082  void printinggnuplot(char fileresu[], ch
           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */            /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
           /* printf(" V%d=%d ",Tvaraff[k],vlv); */            /* printf(" V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */            /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }
           strcpy(gplotlabel+strlen(gplotlabel),")");
         /* printf("\n#\n"); */          /* printf("\n#\n"); */
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
             /*k1=k1-1;*/ /* To be checked */
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;            continue;
         }          }
               
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);          fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);          /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
                 fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
           /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
         /* k1-1 error should be nres-1*/
         for (i=1; i<= nlstate ; i ++) {          for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else        fprintf(ficgp," %%*lf (%%*lf)");            else        fprintf(ficgp," %%*lf (%%*lf)");
         }          }
         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);          fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         for (i=1; i<= nlstate ; i ++) {          for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
         }           } 
         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);           fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); 
         for (i=1; i<= nlstate ; i ++) {          for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
         }            }  
         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));          /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
           
           fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
           if(cptcoveff ==0){
             fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
           }else{
             kl=0;
             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv];
               kl++;
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(k==cptcoveff){
                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         2+cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
               }else{
                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                 kl++;
               }
             } /* end covariate */
           } /* end if no covariate */
   
         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */          if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
           /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */            /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
           fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */            fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
Line 6723  void printinggnuplot(char fileresu[], ch Line 7174  void printinggnuplot(char fileresu[], ch
               }                }
             } /* end covariate */              } /* end covariate */
           } /* end if no covariate */            } /* end if no covariate */
             if(backcast == 1){
               fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
               /* k1-1 error should be nres-1*/
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else        fprintf(ficgp," %%*lf (%%*lf)");
               }
               fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else fprintf(ficgp," %%*lf (%%*lf)");
               } 
               fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else fprintf(ficgp," %%*lf (%%*lf)");
               } 
               fprintf(ficgp,"\" t\"\" w l lt 4");
             } /* end if backprojcast */
         } /* end if backcast */          } /* end if backcast */
         fprintf(ficgp,"\nset out \n");          /* fprintf(ficgp,"\nset out ;unset label;\n"); */
           fprintf(ficgp,"\nset out ;unset title;\n");
       } /* nres */        } /* nres */
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
Line 6736  void printinggnuplot(char fileresu[], ch Line 7207  void printinggnuplot(char fileresu[], ch
       if(m != 1 && TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
         strcpy(gplotlabel,"(");
       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 */
Line 6743  void printinggnuplot(char fileresu[], ch Line 7215  void printinggnuplot(char fileresu[], ch
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
       }        }
       /* for(k=1; k <= ncovds; k++){ */        /* for(k=1; k <= ncovds; k++){ */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }        }
         strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 6757  void printinggnuplot(char fileresu[], ch Line 7232  void printinggnuplot(char fileresu[], ch
                                                   
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
       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*/
         if(vpopbased==0)          fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
           if(vpopbased==0){
           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);            fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
         else          }else
           fprintf(ficgp,"\nreplot ");            fprintf(ficgp,"\nreplot ");
         for (i=1; i<= nlstate+1 ; i ++) {          for (i=1; i<= nlstate+1 ; i ++) {
           k=2*i;            k=2*i;
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {            for (j=1; j<= nlstate+1 ; j ++) {
             if (j==i) fprintf(ficgp," %%lf (%%lf)");              if (j==i) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");              else fprintf(ficgp," %%*lf (%%*lf)");
           }               }   
           if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);            if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);            else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {            for (j=1; j<= nlstate+1 ; j ++) {
             if (j==i) fprintf(ficgp," %%lf (%%lf)");              if (j==i) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");              else fprintf(ficgp," %%*lf (%%*lf)");
           }               }   
           fprintf(ficgp,"\" t\"\" w l lt 0,");            fprintf(ficgp,"\" t\"\" w l lt 0,");
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {            for (j=1; j<= nlstate+1 ; j ++) {
             if (j==i) fprintf(ficgp," %%lf (%%lf)");              if (j==i) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");              else fprintf(ficgp," %%*lf (%%*lf)");
Line 6785  void printinggnuplot(char fileresu[], ch Line 7261  void printinggnuplot(char fileresu[], ch
           else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");            else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
         } /* state */          } /* state */
       } /* vpopbased */        } /* vpopbased */
       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */        fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
     } /* end nres */      } /* end nres */
   } /* k1 end 2 eme*/    } /* k1 end 2 eme*/
                   
Line 6797  void printinggnuplot(char fileresu[], ch Line 7273  void printinggnuplot(char fileresu[], ch
         continue;          continue;
   
       for (cpt=1; cpt<= nlstate ; cpt ++) {        for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);          fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
           strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          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 */
Line 6805  void printinggnuplot(char fileresu[], ch Line 7282  void printinggnuplot(char fileresu[], ch
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                 }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 6818  void printinggnuplot(char fileresu[], ch Line 7298  void printinggnuplot(char fileresu[], ch
         /*       k=2+nlstate*(2*cpt-2); */          /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);          k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
         fprintf(ficgp,"set ter svg size 640, 480\n\          fprintf(ficgp,"set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 6829  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 7310  plot [%.f:%.f] \"%s\" every :::%d::%d u
                                                                   
         */          */
         for (i=1; i< nlstate ; i ++) {          for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);            fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
           /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/            /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                                                                   
         }           } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
       }        }
         fprintf(ficgp,"\nunset label;\n");
     } /* end nres */      } /* end nres */
   } /* end kl 3eme */    } /* end kl 3eme */
       
Line 6845  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 7327  plot [%.f:%.f] \"%s\" every :::%d::%d u
       if(m != 1 && TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
           strcpy(gplotlabel,"(");
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          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 */
Line 6853  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 7336  plot [%.f:%.f] \"%s\" every :::%d::%d u
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                 }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 6864  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 7350  plot [%.f:%.f] \"%s\" every :::%d::%d u
         }          }
               
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3;          k=3;
Line 6879  set ter svg size 640, 480\nunset log y\n Line 7366  set ter svg size 640, 480\nunset log y\n
             fprintf(ficgp,"+$%d",k+l+j-1);              fprintf(ficgp,"+$%d",k+l+j-1);
           fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);            fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
         } /* nlstate */          } /* nlstate */
         fprintf(ficgp,"\nset out\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end nres */      } /* end nres */
   } /* end covariate k1 */      } /* end covariate k1 */  
Line 6891  set ter svg size 640, 480\nunset log y\n Line 7378  set ter svg size 640, 480\nunset log y\n
       if(m != 1 && TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
           strcpy(gplotlabel,"(");
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          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 */
Line 6899  set ter svg size 640, 480\nunset log y\n Line 7387  set ter svg size 640, 480\nunset log y\n
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                 }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 6910  set ter svg size 640, 480\nunset log y\n Line 7401  set ter svg size 640, 480\nunset log y\n
         }          }
               
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3;          k=3;
Line 6933  set ter svg size 640, 480\nunset log y\n Line 7425  set ter svg size 640, 480\nunset log y\n
           else            else
             fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);              fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
         }          }
         fprintf(ficgp,"\nset out\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* end nres */    } /* end nres */
Line 6945  set ter svg size 640, 480\nunset log y\n Line 7437  set ter svg size 640, 480\nunset log y\n
     if(m != 1 && TKresult[nres]!= k1)      if(m != 1 && TKresult[nres]!= k1)
       continue;        continue;
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
               strcpy(gplotlabel,"(");      
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        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 */
Line 6954  set ter svg size 640, 480\nunset log y\n Line 7446  set ter svg size 640, 480\nunset log y\n
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
       }        }
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }         } 
         strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 6965  set ter svg size 640, 480\nunset log y\n Line 7460  set ter svg size 640, 480\nunset log y\n
       }        }
               
       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
         fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
       k=3; /* Offset */        k=3; /* Offset */
Line 6979  set ter svg size 640, 480\nunset log y\n Line 7475  set ter svg size 640, 480\nunset log y\n
           fprintf(ficgp,"+$%d",k+l+j-1);            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out; unset label;\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
       
Line 6991  set ter svg size 640, 480\nunset log y\n Line 7487  set ter svg size 640, 480\nunset log y\n
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);          strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          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 */
Line 7000  set ter svg size 640, 480\nunset log y\n Line 7497  set ter svg size 640, 480\nunset log y\n
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                 }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 7011  set ter svg size 640, 480\nunset log y\n Line 7511  set ter svg size 640, 480\nunset log y\n
         }          }
                   
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */          k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){ /* State of origin */          for (i=1; i<= nlstate ; i ++){ /* State of arrival */
           if(i==1)            if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
           else            else
Line 7027  set ter svg size 640, 480\nunset log y\n Line 7528  set ter svg size 640, 480\nunset log y\n
           /* for (j=2; j<= nlstate ; j ++) */            /* for (j=2; j<= nlstate ; j ++) */
           /*    fprintf(ficgp,"+$%d",k+l+j-1); */            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);            fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
         } /* nlstate */          } /* nlstate */
         fprintf(ficgp,"\nset out\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if backcast */
Line 7043  set ter svg size 640, 480\nunset log y\n Line 7544  set ter svg size 640, 480\nunset log y\n
       if(m != 1 && TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
Line 7051  set ter svg size 640, 480\nunset log y\n Line 7553  set ter svg size 640, 480\nunset log y\n
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                 }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 7063  set ter svg size 640, 480\nunset log y\n Line 7568  set ter svg size 640, 480\nunset log y\n
                   
         fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");          fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */  
           /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
           istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
           /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
           for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
           /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/            /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
           /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
           /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/            /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
           /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */               /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
           if(i==1){            if(i==istart){
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
           }else{            }else{
             fprintf(ficgp,",\\\n '' ");              fprintf(ficgp,",\\\n '' ");
Line 7082  set ter svg size 640, 480\nunset log y\n Line 7592  set ter svg size 640, 480\nunset log y\n
             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/              /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
             /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */              /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
             fprintf(ficgp," u %d:(", ioffset);               fprintf(ficgp," u %d:(", ioffset); 
             if(i==nlstate+1)              if(i==nlstate+1){
               fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ",      \                fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
             else                fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
                        offyear,                           \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
               }else
               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \                fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
           }else{ /* more than 2 covariates */            }else{ /* more than 2 covariates */
             if(cptcoveff ==1){              ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
               ioffset=4; /* Age is in 4 */              /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             }else{              /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               ioffset=6; /* Age is in 6 */              iyearc=ioffset-1;
               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/              iagec=ioffset;
               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */  
             }     
             fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
             kl=0;              kl=0;
             strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
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             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
             if(i==nlstate+1){              if(i==nlstate+1){
               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",iagec); 
                 fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
                         iyearc, iagec, offyear,                           \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
   /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
             }else{              }else{
               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
             }              }
           } /* end if covariate */            } /* end if covariate */
         } /* nlstate */          } /* nlstate */
         fprintf(ficgp,"\nset out\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/        } /* end cpt state*/
     } /* end covariate */      } /* end covariate */
   } /* End if prevfcast */    } /* End if prevfcast */
       
     if(backcast==1){
       /* Back projection from cross-sectional to stable (mixed) for each covariate */
       
       for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
           for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
             vlv= nbcode[Tvaraff[k]][lv];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
   
           /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
           istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
           /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
           for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             if(i==istart){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
             }else{
               fprintf(ficgp,",\\\n '' ");
             }
             if(cptcoveff ==0){ /* No covariate */
               ioffset=2; /* Age is in 2 */
               /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
               /*#  1    2        3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               fprintf(ficgp," u %d:(", ioffset); 
               if(i==nlstate+1){
                 fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
                        offbyear,                          \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
               }else
                 fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
             }else{ /* more than 2 covariates */
               ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               iyearc=ioffset-1;
               iagec=ioffset;
               fprintf(ficgp," u %d:(",ioffset); 
               kl=0;
               strcpy(gplotcondition,"(");
               for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                 kl++;
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                 kl++;
                 if(k <cptcoveff && cptcoveff>1)
                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
               }
               strcpy(gplotcondition+strlen(gplotcondition),")");
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(i==nlstate+1){
                 fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",iagec); 
                 /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
                 fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
                         iyearc,iagec,offbyear,                            \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
   /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
               }else{
                 /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
                 fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
               }
             } /* end if covariate */
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if backcast */
     
       
   /* 9eme writing MLE parameters */    /* 9eme writing MLE parameters */
   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
Line 7168  set ter svg size 640, 480\nunset log y\n Line 7802  set ter svg size 640, 480\nunset log y\n
     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
     fprintf(ficgp,"#model=%s \n",model);      fprintf(ficgp,"#model=%s \n",model);
     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */      fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
     for(jk=1; jk <=m; jk++)  /* For each combination of covariate */      for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= jk)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);        fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
         strcpy(gplotlabel,"(");
         /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
       }         } 
         strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
         fprintf(ficgp,"\nset key outside ");
         /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
         fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
       fprintf(ficgp,"\nset ter svg size 640, 480 ");        fprintf(ficgp,"\nset ter svg size 640, 480 ");
       if (ng==1){        if (ng==1){
         fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
Line 7222  set ter svg size 640, 480\nunset log y\n Line 7872  set ter svg size 640, 480\nunset log y\n
             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */              /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */              for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
               if(j==Tage[ij]) { /* Product by age */                if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                 if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */                  if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
                   if(DummyV[j]==0){                    if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                     fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;                      if(DummyV[j]==0){
                   }else{ /* quantitative */                        fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                     fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */                      }else{ /* quantitative */
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                        fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                   }                        /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   ij++;  
                 }  
               }else if(j==Tprod[ijp]) { /* */   
                 /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */  
                 if(ijp <=cptcovprod) { /* Product */  
                   if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */  
                     if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */  
                       /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */  
                       fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);  
                     }else{ /* Vn is dummy and Vm is quanti */  
                       /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */  
                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);  
                     }                      }
                   }else{ /* Vn*Vm Vn is quanti */                      ij++;
                     if(DummyV[Tvard[ijp][2]]==0){                    }
                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);                  } 
                     }else{ /* Both quanti */                }else if(cptcovprod >0){
                       fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);                  if(j==Tprod[ijp]) { /* */ 
                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                     if(ijp <=cptcovprod) { /* Product */
                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                           /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                           fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                         }else{ /* Vn is dummy and Vm is quanti */
                           /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                       }else{ /* Vn*Vm Vn is quanti */
                         if(DummyV[Tvard[ijp][2]]==0){
                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                         }else{ /* Both quanti */
                           fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                     }                      }
                       ijp++;
                   }                    }
                   ijp++;                  } /* end Tprod */
                 }  
               } else{  /* simple covariate */                } else{  /* simple covariate */
                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */                  /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                 if(Dummy[j]==0){                  if(Dummy[j]==0){
                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */                    fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
                 }else{ /* quantitative */                  }else{ /* quantitative */
                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */                    fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                 }                  }
               } /* end simple */                } /* end simple */
             } /* end j */              } /* end j */
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           if(ng != 1){            if(ng != 1){
             fprintf(ficgp,")/(1");              fprintf(ficgp,")/(1");
                           
             for(k1=1; k1 <=nlstate; k1++){               for(cpt=1; cpt <=nlstate; cpt++){ 
               if(nagesqr==0)                if(nagesqr==0)
                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
               else /* nagesqr =1 */                else /* nagesqr =1 */
                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                                 
               ij=1;                ij=1;
               for(j=3; j <=ncovmodel-nagesqr; j++){                for(j=3; j <=ncovmodel-nagesqr; j++){
                 if((j-2)==Tage[ij]) { /* Bug valgrind */                   if(cptcovage >0){ 
                   if(ij <=cptcovage) { /* Bug valgrind */                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                       if(ij <=cptcovage) { /* Bug valgrind */
                     /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                         fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
                     ij++;                         /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   }                         ij++;
                 }                       }
                 else                     }
                   fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */                   }else
                      fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
               }                }
               fprintf(ficgp,")");                fprintf(ficgp,")");
             }              }
             fprintf(ficgp,")");              fprintf(ficgp,")");
             if(ng ==2)              if(ng ==2)
               fprintf(ficgp," t \"p%d%d\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
             else /* ng= 3 */              else /* ng= 3 */
               fprintf(ficgp," t \"i%d%d\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }else{ /* end ng <> 1 */            }else{ /* end ng <> 1 */
             if( k !=k2) /* logit p11 is hard to draw */              if( k !=k2) /* logit p11 is hard to draw */
               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }            }
           if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
             fprintf(ficgp,",");              fprintf(ficgp,",");
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           i=i+ncovmodel;            i=i+ncovmodel;
         } /* end k */          } /* end k */
       } /* end k2 */        } /* end k2 */
       fprintf(ficgp,"\n set out\n");        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
     } /* end jk */        fprintf(ficgp,"\n set out; unset title;set key default;\n");
       } /* end k1 */
   } /* end ng */    } /* end ng */
   /* avoid: */    /* avoid: */
   fflush(ficgp);     fflush(ficgp); 
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    int mobilavrange, mob;     int mobilavrange, mob;
    int iage=0;     int iage=0;
   
    double sum=0.;     double sum=0., sumr=0.;
    double age;     double age;
    double *sumnewp, *sumnewm;     double *sumnewp, *sumnewm, *sumnewmr;
    double *agemingood, *agemaxgood; /* Currently identical for all covariates */     double *agemingood, *agemaxgood; 
      double *agemingoodr, *agemaxgoodr; 
       
       
    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */     /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */     /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
   
    sumnewp = vector(1,ncovcombmax);     sumnewp = vector(1,ncovcombmax);
    sumnewm = vector(1,ncovcombmax);     sumnewm = vector(1,ncovcombmax);
      sumnewmr = vector(1,ncovcombmax);
    agemingood = vector(1,ncovcombmax);       agemingood = vector(1,ncovcombmax);  
      agemingoodr = vector(1,ncovcombmax); 
    agemaxgood = vector(1,ncovcombmax);     agemaxgood = vector(1,ncovcombmax);
      agemaxgoodr = vector(1,ncovcombmax);
   
    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
      sumnewm[cptcod]=0.;       sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
      sumnewp[cptcod]=0.;       sumnewp[cptcod]=0.;
      agemingood[cptcod]=0;       agemingood[cptcod]=0, agemingoodr[cptcod]=0;
      agemaxgood[cptcod]=0;       agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
    }     }
    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
       
    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){     if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
      if(mobilav==1) mobilavrange=5; /* default */       if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
      else mobilavrange=mobilav;       else mobilavrange=mobilav;
      for (age=bage; age<=fage; age++)       for (age=bage; age<=fage; age++)
        for (i=1; i<=nlstate;i++)         for (i=1; i<=nlstate;i++)
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      */        */ 
      for (mob=3;mob <=mobilavrange;mob=mob+2){       for (mob=3;mob <=mobilavrange;mob=mob+2){
        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
          for (i=1; i<=nlstate;i++){           for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){             sumnewm[cptcod]=0.;
              for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];               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;
            }               sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }             } /* end i */
              if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
            } /* end cptcod */
        }/* end age */         }/* end age */
      }/* end mob */       }/* end mob */
    }else     }else{
        printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
      return -1;       return -1;
    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     }
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
      if(invalidvarcomb[cptcod]){       if(invalidvarcomb[cptcod]){
        printf("\nCombination (%d) ignored because no cases \n",cptcod);          printf("\nCombination (%d) ignored because no cases \n",cptcod); 
        continue;         continue;
      }       }
   
      agemingood[cptcod]=fage-(mob-1)/2;       for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */  
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
        for (i=1; i<=nlstate;i++){         for (i=1; i<=nlstate;i++){
          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemingoodr[cptcod]=age;
        }         }
        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
          agemingood[cptcod]=age;             agemingood[cptcod]=age;
        }else{ /* bad */         }
          for (i=1; i<=nlstate;i++){       } /* age */
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
          } /* i */  
        } /* end bad */  
      }/* age */  
      sum=0.;  
      for (i=1; i<=nlstate;i++){  
        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];  
      }  
      if(fabs(sum - 1.) > 1.e-3) { /* bad */  
        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);  
        /* for (i=1; i<=nlstate;i++){ */  
        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */  
        /* } /\* i *\/ */  
      } /* end bad */  
      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */  
      /* From youngest, finding the oldest wrong */  
      agemaxgood[cptcod]=bage+(mob-1)/2;  
      for (age=bage+(mob-1)/2; age<=fage; age++){  
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
        for (i=1; i<=nlstate;i++){         for (i=1; i<=nlstate;i++){
          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemaxgoodr[cptcod]=age;
        }         }
        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
          agemaxgood[cptcod]=age;           agemaxgood[cptcod]=age;
        }else{ /* bad */         }
          for (i=1; i<=nlstate;i++){       } /* age */
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];       /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
          } /* i */       /* but they will change */
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
            if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
              agemaxgoodr[cptcod]=age;  /* age min */
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemaxgood[cptcod]=age;
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=probs[(int)age][i][cptcod];
          }
          if(fabs(sum - 1.) > 1.e-3) { /* bad */
            printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          if(fabs(sumr - 1.) > 1.e-3) { /* bad */
            printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
        } /* end bad */         } /* end bad */
      }/* age */       }/* age */
      sum=0.;  
      for (i=1; i<=nlstate;i++){       for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];         sumnewm[cptcod]=0.;
      }         sumnewmr[cptcod]=0.;
      if(fabs(sum - 1.) > 1.e-3) { /* bad */         for (i=1; i<=nlstate;i++){
        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
        /* for (i=1; i<=nlstate;i++){ */           sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */         } 
        /* } /\* i *\/ */         if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
      } /* end bad */           if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingoodr[cptcod]=age;
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingood[cptcod]=age;
            }else{ /* bad */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=mobaverage[(int)age][i][cptcod];
          }
          if(fabs(sum - 1.) > 1.e-3) { /* bad */
            printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          if(fabs(sumr - 1.) > 1.e-3) { /* bad */
            printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
          } /* end bad */
        }/* age */
   
                                   
      for (age=bage; age<=fage; age++){       for (age=bage; age<=fage; age++){
        /* printf("%d %d ", cptcod, (int)age); */         /* printf("%d %d ", cptcod, (int)age); */
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      }       }
      /* printf("\n"); */       /* printf("\n"); */
      /* } */       /* } */
   
      /* brutal averaging */       /* brutal averaging */
      for (i=1; i<=nlstate;i++){       /* for (i=1; i<=nlstate;i++){ */
        for (age=1; age<=bage; age++){       /*   for (age=1; age<=bage; age++){ */
          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];       /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
        }               /*   }      */
        for (age=fage; age<=AGESUP; age++){       /*   for (age=fage; age<=AGESUP; age++){ */
          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];       /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
        }       /*   } */
      } /* end i status */       /* } /\* end i status *\/ */
      for (i=nlstate+1; i<=nlstate+ndeath;i++){       /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
        for (age=1; age<=AGESUP; age++){       /*   for (age=1; age<=AGESUP; age++){ */
          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/       /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
          mobaverage[(int)age][i][cptcod]=0.;       /*          mobaverage[(int)age][i][cptcod]=0.; */
        }       /*   } */
      }       /* } */
    }/* end cptcod */     }/* end cptcod */
    free_vector(sumnewm,1, ncovcombmax);     free_vector(agemaxgoodr,1, ncovcombmax);
    free_vector(sumnewp,1, ncovcombmax);  
    free_vector(agemaxgood,1, ncovcombmax);     free_vector(agemaxgood,1, ncovcombmax);
    free_vector(agemingood,1, ncovcombmax);     free_vector(agemingood,1, ncovcombmax);
      free_vector(agemingoodr,1, ncovcombmax);
      free_vector(sumnewmr,1, ncovcombmax);
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
    return 0;     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 ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   /* proj1, year, month, day of starting projection     /* proj1, year, month, day of starting projection 
      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
      anproj2 year of en of projection (same day and month as proj1).       anproj2 year of en of projection (same day and month as proj1).
   */    */
    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
   double agec; /* generic age */    double 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;
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   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;   
     }
     if(estepm > stepm){ /* Yes every two year */
       stepsize=2;
     }
   
   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
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     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {      for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
       fprintf(ficresf,"\n");        fprintf(ficresf,"\n");
       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       for (agec=fage; agec>=(ageminpar-1); agec--){         /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
         for (agec=fage; agec>=(bage); agec--){ 
         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
         nhstepm = nhstepm/hstepm;           nhstepm = nhstepm/hstepm; 
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
           /* We compute pii at age agec over nhstepm);*/
         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
                   /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
         for (h=0; h<=nhstepm; h++){          for (h=0; h<=nhstepm; h++){
           if (h*hstepm/YEARM*stepm ==yearp) {            if (h*hstepm/YEARM*stepm ==yearp) {
             fprintf(ficresf,"\n");              break;
             for(j=1;j<=cptcoveff;j++)             }
               fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          }
             fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);          fprintf(ficresf,"\n");
           }           for(j=1;j<=cptcoveff;j++) 
           for(j=1; j<=nlstate+ndeath;j++) {            fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
             ppij=0.;          fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             for(i=1; i<=nlstate;i++) {          
               if (mobilav==1)           for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];            ppij=0.;
               else {            for(i=1; i<=nlstate;i++) {
                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];              if (mobilav>=1)
               }               ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
               if (h*hstepm/YEARM*stepm== yearp) {              else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
                 fprintf(ficresf," %.3f", p3mat[i][j][h]);                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
               }  
             } /* end i */  
             if (h*hstepm/YEARM*stepm==yearp) {  
               fprintf(ficresf," %.3f", ppij);  
             }              }
           }/* end j */              fprintf(ficresf," %.3f", p3mat[i][j][h]);
         } /* end h */            } /* end i */
             fprintf(ficresf," %.3f", ppij);
           }/* end j */
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       } /* end agec */        } /* end agec */
         /* diffyear=(int) anproj1+yearp-ageminpar-1; */
         /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
     } /* end yearp */      } /* end yearp */
   } /* end  k */    } /* end  k */
                   
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 }  }
   
 /* /\************** 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 ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
 /*   /\* back1, year, month, day of starting backection  */    /* back1, year, month, day of starting backection
 /*      agemin, agemax range of age */       agemin, agemax range of age
 /*      dateprev1 dateprev2 range of dates during which prevalence is computed */       dateprev1 dateprev2 range of dates during which prevalence is computed
 /*      anback2 year of en of backection (same day and month as back1). */       anback2 year of end of backprojection (same day and month as back1).
 /*   *\/ */       prevacurrent and prev are prevalences.
 /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */    */
 /*   double agec; /\* generic age *\/ */    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
 /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */    double agec; /* generic age */
 /*   double *popeffectif,*popcount; */    double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 /*   double ***p3mat; */    double *popeffectif,*popcount;
 /*   /\* double ***mobaverage; *\/ */    double ***p3mat;
 /*   char fileresfb[FILENAMELENGTH]; */    /* double ***mobaverage; */
             char fileresfb[FILENAMELENGTH];
 /*   agelim=AGESUP; */   
 /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */    agelim=AGEINF;
 /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 /*      We still use firstpass and lastpass as another selection. */       in each health status at the date of interview (if between dateprev1 and dateprev2).
 /*   *\/ */       We still use firstpass and lastpass as another selection.
 /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */    */
 /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */    /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
 /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */    /*          firstpass, lastpass,  stepm,  weightopt, model); */
           
 /*   strcpy(fileresfb,"FB_");  */    /*Do we need to compute prevalence again?*/
 /*   strcat(fileresfb,fileresu); */  
 /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */    /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
 /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */    
 /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */    strcpy(fileresfb,"FB_");
 /*   } */    strcat(fileresfb,fileresu);
 /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */    if((ficresfb=fopen(fileresfb,"w"))==NULL) {
 /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */      printf("Problem with back forecast resultfile: %s\n", fileresfb);
               fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
 /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */    }
             printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
 /*   /\* if (mobilav!=0) { *\/ */    fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
 /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */    
 /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
 /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */    
 /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */     
 /*   /\*   } *\/ */    stepsize=(int) (stepm+YEARM-1)/YEARM;
 /*   /\* } *\/ */    if (stepm<=12) stepsize=1;
             if(estepm < stepm){
 /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */      printf ("Problem %d lower than %d\n",estepm, stepm);
 /*   if (stepm<=12) stepsize=1; */    }
 /*   if(estepm < stepm){ */    else{
 /*     printf ("Problem %d lower than %d\n",estepm, stepm); */      hstepm=estepm;   
 /*   } */    }
 /*   else  hstepm=estepm;    */    if(estepm >= stepm){ /* Yes every two year */
               stepsize=2;
 /*   hstepm=hstepm/stepm;  */    }
 /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */    
 /*                                fractional in yp1 *\/ */    hstepm=hstepm/stepm;
 /*   anprojmean=yp; */    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
 /*   yp2=modf((yp1*12),&yp); */                                 fractional in yp1 */
 /*   mprojmean=yp; */    anprojmean=yp;
 /*   yp1=modf((yp2*30.5),&yp); */    yp2=modf((yp1*12),&yp);
 /*   jprojmean=yp; */    mprojmean=yp;
 /*   if(jprojmean==0) jprojmean=1; */    yp1=modf((yp2*30.5),&yp);
 /*   if(mprojmean==0) jprojmean=1; */    jprojmean=yp;
             if(jprojmean==0) jprojmean=1;
 /*   i1=cptcoveff; */    if(mprojmean==0) jprojmean=1;
 /*   if (cptcovn < 1){i1=1;} */    
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
     printf("# 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"); */    for(nres=1; nres <= nresult; nres++) /* For each resultline */
             for(k=1; k<=i1;k++){
 /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */      if(i1 != 1 && TKresult[nres]!= k)
 /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */        continue;
 /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */      if(invalidvarcomb[k]){
 /*       k=k+1; */        printf("\nCombination (%d) projection ignored because no cases \n",k); 
 /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */        continue;
 /*       for(j=1;j<=cptcoveff;j++) { */      }
 /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
 /*       } */      for(j=1;j<=cptcoveff;j++) {
 /*       fprintf(ficresfb," yearbproj age"); */        fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 /*       for(j=1; j<=nlstate+ndeath;j++){  */      }
 /*                              for(i=1; i<=nlstate;i++)               */      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
 /*           fprintf(ficresfb," p%d%d",i,j); */        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
 /*                              fprintf(ficresfb," p.%d",j); */      }
 /*       } */      fprintf(ficresfb," yearbproj age");
 /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */      for(j=1; j<=nlstate+ndeath;j++){
 /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */        for(i=1; i<=nlstate;i++)
 /*                              fprintf(ficresfb,"\n"); */          fprintf(ficresfb," b%d%d",i,j);
 /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */        fprintf(ficresfb," b.%d",j);
 /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */      }
 /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */      for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
 /*                                      nhstepm = nhstepm/hstepm;  */        /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
 /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */        fprintf(ficresfb,"\n");
 /*                                      oldm=oldms;savm=savms; */        fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
 /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */        /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
 /*                                      for (h=0; h<=nhstepm; h++){ */        /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
 /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */        for (agec=bage; agec<=fage; agec++){  /* testing */
 /*               fprintf(ficresfb,"\n"); */          /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
 /*               for(j=1;j<=cptcoveff;j++)  */          nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
 /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */          nhstepm = nhstepm/hstepm;
 /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /*                                              }  */          oldm=oldms;savm=savms;
 /*                                              for(j=1; j<=nlstate+ndeath;j++) { */          /* computes hbxij at age agec over 1 to nhstepm */
 /*                                                      ppij=0.; */          /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
 /*                                                      for(i=1; i<=nlstate;i++) { */          hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
 /*                                                              if (mobilav==1)  */          /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
 /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */          /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
 /*                                                              else { */          /* printf(" agec=%.2f\n",agec);fflush(stdout); */
 /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */          for (h=0; h<=nhstepm; h++){
 /*                                                              } */            if (h*hstepm/YEARM*stepm ==-yearp) {
 /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */              break;
 /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */            }
 /*                                                              } */          }
 /*                                                      } /\* end i *\/ */          fprintf(ficresfb,"\n");
 /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */          for(j=1;j<=cptcoveff;j++)
 /*                                                              fprintf(ficresfb," %.3f", ppij); */            fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 /*                                                      } */          fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
 /*                                              }/\* end j *\/ */          for(i=1; i<=nlstate+ndeath;i++) {
 /*                                      } /\* end h *\/ */            ppij=0.;ppi=0.;
 /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */            for(j=1; j<=nlstate;j++) {
 /*                              } /\* end agec *\/ */              /* if (mobilav==1) */
 /*       } /\* end yearp *\/ */              ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
 /*     } /\* end cptcod *\/ */              ppi=ppi+prevacurrent[(int)agec][j][k];
 /*   } /\* end  cptcov *\/ */              /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
                       /* ppi=ppi+mobaverage[(int)agec][j][k]; */
 /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */                /* else { */
                         /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
 /*   fclose(ficresfb); */                /* } */
 /*   printf("End of Computing Back forecasting \n"); */              fprintf(ficresfb," %.3f", p3mat[i][j][h]);
 /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */            } /* end j */
             if(ppi <0.99){
               printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
               fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
             }
             fprintf(ficresfb," %.3f", ppij);
           }/* end j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
       } /* end yearp */
     } /* end k */
     
     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     
     fclose(ficresfb);
     printf("End of Computing Back forecasting \n");
     fprintf(ficlog,"End of Computing Back forecasting\n");
                   
 /* } */  }
   
   /* Variance of prevalence limit: varprlim */
    void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
       /*------- Variance of period (stable) prevalence------*/   
    
      char fileresvpl[FILENAMELENGTH];  
      FILE *ficresvpl;
      double **oldm, **savm;
      double **varpl; /* Variances of prevalence limits by age */   
      int i1, k, nres, j ;
      
       strcpy(fileresvpl,"VPL_");
       strcat(fileresvpl,fileresu);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
       fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
       
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
       
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         fprintf(ficresvpl,"\n#****** ");
         printf("\n#****** ");
         fprintf(ficlog,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficresvpl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       
       fclose(ficresvpl);
       printf("done variance-covariance of period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
   
    }
   /* Variance of back prevalence: varbprlim */
    void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
         /*------- Variance of back (stable) prevalence------*/
   
      char fileresvbl[FILENAMELENGTH];  
      FILE  *ficresvbl;
   
      double **oldm, **savm;
      double **varbpl; /* Variances of back prevalence limits by age */   
      int i1, k, nres, j ;
   
      strcpy(fileresvbl,"VBL_");
      strcat(fileresvbl,fileresu);
      if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
        printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
        exit(0);
      }
      printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
      fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
      
      
      i1=pow(2,cptcoveff);
      if (cptcovn < 1){i1=1;}
      
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
        for(k=1; k<=i1;k++){
          if(i1 != 1 && TKresult[nres]!= k)
            continue;
          fprintf(ficresvbl,"\n#****** ");
          printf("\n#****** ");
          fprintf(ficlog,"\n#****** ");
          for(j=1;j<=cptcoveff;j++) {
            fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          }
          for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
            printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
          }
          fprintf(ficresvbl,"******\n");
          printf("******\n");
          fprintf(ficlog,"******\n");
          
          varbpl=matrix(1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
          
          varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
          free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
          /*}*/
        }
      
      fclose(ficresvbl);
      printf("done variance-covariance of back prevalence\n");fflush(stdout);
      fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
   
    } /* End of varbprlim */
   
 /************** 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 dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */  /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
Line 9103  int calandcheckages(int imx, int maxwav, Line 9978  int calandcheckages(int imx, int maxwav,
         *nberr = *nberr + 1;          *nberr = *nberr + 1;
         if(firstone == 0){          if(firstone == 0){
           firstone=1;            firstone=1;
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);          printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
         }          }
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);          fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
         s[m][i]=-1;          s[m][i]=-1;  /* Droping the death status */
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
         (*nberr)++;          (*nberr)++;
         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);           printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);           fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */          s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
       }        }
     }      }
   }    }
Line 9569  int back_prevalence_limit(double *p, dou Line 10444  int back_prevalence_limit(double *p, dou
         }else{          }else{
           /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */            /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
           bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);            bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
             /* printf("TOTOT\n"); */
             /* exit(1); */
         }          }
         fprintf(ficresplb,"%.0f ",age );          fprintf(ficresplb,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcoveff;j++)
Line 9714  int hPijx(double *p, int bage, int fage) Line 10591  int hPijx(double *p, int bage, int fage)
         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       }        }
       fprintf(ficrespijb,"******\n");        fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){        if(invalidvarcomb[k]){  /* Is it necessary here? */
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);           fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;          continue;
       }        }
Line 9727  int hPijx(double *p, int bage, int fage) Line 10604  int hPijx(double *p, int bage, int fage)
                   
         /*        nhstepm=nhstepm*YEARM; aff par mois*/          /*        nhstepm=nhstepm*YEARM; aff par mois*/
                   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
           /* and memory limitations if stepm is small */
   
         /* oldm=oldms;savm=savms; */          /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);          hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");          fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
Line 9778  int main(int argc, char *argv[]) Line 10657  int main(int argc, char *argv[])
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
   int nres=0;    int nres=0;
     int endishere=0;
     int noffset=0;
     int ncurrv=0; /* Temporary variable */
     
   char ca[32], cb[32];    char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
Line 9830  int main(int argc, char *argv[]) Line 10712  int main(int argc, char *argv[])
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2;
   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;    double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
   
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
Line 10000  int main(int argc, char *argv[]) Line 10884  int main(int argc, char *argv[])
     fflush(ficlog);      fflush(ficlog);
     goto end;      goto end;
   }    }
         /*-------- Rewriting parameter file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name */
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
       fflush(ficlog);
       goto end;
     }
     fprintf(ficres,"#IMaCh %s\n",version);
   
                                         
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
     /* Is it a BOM UTF-8 Windows file? */
     /* First parameter line */    /* First parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# File is an UTF8 Bom.\n"); // 0xBF
       }
       else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
       {
         noffset=noffset+2;
         printf("# File is an UTF16BE BOM file\n");
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# File is an UTF16BE BOM file\n");
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
     
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
     if (line[0] == '#') {      if (line[noffset] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
         fputs(line,ficres);
       fputs(line,ficlog);        fputs(line,ficlog);
       continue;        continue;
     }else      }else
Line 10031  int main(int argc, char *argv[]) Line 10950  int main(int argc, char *argv[])
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
         fputs(line,ficres);
       fputs(line,ficlog);        fputs(line,ficlog);
       continue;        continue;
     }else      }else
Line 10053  int main(int argc, char *argv[]) Line 10973  int main(int argc, char *argv[])
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
         fputs(line,ficres);
       fputs(line,ficlog);        fputs(line,ficlog);
       continue;        continue;
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
     if (num_filled == 0)      if (num_filled != 1){
             model[0]='\0';        printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
     else if (num_filled != 1){        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);  
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);  
       model[0]='\0';        model[0]='\0';
       goto end;        goto end;
     }      }
Line 10085  int main(int argc, char *argv[]) Line 11004  int main(int argc, char *argv[])
   fflush(ficlog);    fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */    /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \      printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \   'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \   'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
     if(mle != -1){      if(mle != -1){
       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");        printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
       exit(1);        exit(1);
     }      }
   }    }
Line 10110  int main(int argc, char *argv[]) Line 11029  int main(int argc, char *argv[])
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */    if(nqv>=1)coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/    if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */
   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */    if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
      v1+v2*age+v2*v3 makes cptcovn = 3       v1+v2*age+v2*v3 makes cptcovn = 3
Line 10311  Please run with mle=-1 to get a correct Line 11230  Please run with mle=-1 to get a correct
           
     fflush(ficlog);      fflush(ficlog);
           
     /*-------- Rewriting parameter file ----------*/  
     strcpy(rfileres,"r");    /* "Rparameterfile */  
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
     strcat(rfileres,".");    /* */  
     strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {  
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;  
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;  
     }  
     fprintf(ficres,"#%s\n",version);  
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
       
   /*  Main data    /*  Main data
Line 10658  Title=%s <br>Datafile=%s Firstpass=%d La Line 11567  Title=%s <br>Datafile=%s Firstpass=%d La
               firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\
             ftol, stepm);
     fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
     ncurrv=1;
     for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); 
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
              nlstate, ndeath, maxwav, mle, weightopt);
   
     fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
   <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
   
     
     fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);    imx,agemin,agemax,jmin,jmax,jmean);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   
   /* For Powell, parameters are in a vector p[] starting at p[1]    /* For Powell, parameters are in a vector p[] starting at p[1]
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
Line 11152  Please run with mle=-1 to get a correct Line 12082  Please run with mle=-1 to get a correct
         fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);          fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
         goto end;          goto end;
       }        }
     /* fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); */  
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     }      }
   
Line 11188  Please run with mle=-1 to get a correct Line 12116  Please run with mle=-1 to get a correct
       fprintf(ficres,"pop_based=%d\n",popbased);           fprintf(ficres,"pop_based=%d\n",popbased);   
     }      }
             
     while(fgets(line, MAXLINE, ficpar)) {  
       /* If line starts with a # it is a comment */  
       if (line[0] == '#') {  
         numlinepar++;  
         fputs(line,stdout);  
         fputs(line,ficparo);  
         fputs(line,ficlog);  
         continue;  
       }else  
         break;  
     }  
    /* while((c=getc(ficpar))=='#' && c!= EOF){ */  
    /*    ungetc(c,ficpar); */  
    /*    fgets(line, MAXLINE, ficpar); */  
    /*    fputs(line,stdout); */  
    /*    fputs(line,ficres); */  
    /*    fputs(line,ficparo); */  
    /*  } */  
    /*  ungetc(c,ficpar); */  
       
     /* fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj); */  
     if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){  
       if (num_filled != 8) {  
         printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
         fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
         goto end;  
       }  
      fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
      printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
      fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
      fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);  
     /* day and month of proj2 are not used but only year anproj2.*/  
     }  
      while(fgets(line, MAXLINE, ficpar)) {  
       /* If line starts with a # it is a comment */  
       if (line[0] == '#') {  
         numlinepar++;  
         fputs(line,stdout);  
         fputs(line,ficparo);  
         fputs(line,ficlog);  
         continue;  
       }else  
         break;  
     }  
     /* while((c=getc(ficpar))=='#' && c!= EOF){ */  
     /*   ungetc(c,ficpar); */  
     /*   fgets(line, MAXLINE, ficpar); */  
     /*   fputs(line,stdout); */  
     /*   fputs(line,ficparo); */  
     /*   fputs(line,ficres); */  
     /* } */  
     /* ungetc(c,ficpar); */  
       
     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);  
     if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){  
       if (num_filled != 8) {  
         printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
         fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);  
         goto end;  
       }  
       printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
       fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
       fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
       fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);  
     /* day and month of proj2 are not used but only year anproj2.*/  
     }  
     /* Results */      /* Results */
     nresult=0;      nresult=0;
     while(fgets(line, MAXLINE, ficpar)) {      do{
       /* If line starts with a # it is a comment */        if(!fgets(line, MAXLINE, ficpar)){
       if (line[0] == '#') {          endishere=1;
           parameterline=14;
         }else if (line[0] == '#') {
           /* If line starts with a # it is a comment */
         numlinepar++;          numlinepar++;
         fputs(line,stdout);          fputs(line,stdout);
         fputs(line,ficparo);          fputs(line,ficparo);
         fputs(line,ficlog);          fputs(line,ficlog);
         fputs(line,ficres);  
         continue;          continue;
       }else        }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
         break;          parameterline=11;
     }        else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
     if (!feof(ficpar))          parameterline=12;
     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){        else if(sscanf(line,"result:%[^\n]\n",modeltemp))
       if (num_filled == 0){          parameterline=13;
         resultline[0]='\0';        else{
         printf("Warning %d: no result line should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);          parameterline=14;
       break;  
       } else if (num_filled != 1){  
         printf("ERROR %d: result line should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);  
       }  
       nresult++; /* Sum of resultlines */  
       printf("Result %d: result=%s\n",nresult, resultline);  
       if(nresult > MAXRESULTLINES){  
         printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);  
         fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);  
         goto end;  
       }  
       decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */  
       fprintf(ficparo,"result: %s\n",resultline);  
       fprintf(ficres,"result: %s\n",resultline);  
       fprintf(ficlog,"result: %s\n",resultline);  
       while(fgets(line, MAXLINE, ficpar)) {  
         /* If line starts with a # it is a comment */  
         if (line[0] == '#') {  
           numlinepar++;  
           fputs(line,stdout);  
           fputs(line,ficparo);  
           fputs(line,ficres);  
           fputs(line,ficlog);  
           continue;  
         }else  
           break;  
       }        }
       if (feof(ficpar))        switch (parameterline){ 
         break;        case 11:
       else{ /* Processess output results for this combination of covariate values */          if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){
       }                                        if (num_filled != 8) {
     } /* end while */              printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
             }
             fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
             /* day and month of proj2 are not used but only year anproj2.*/
             dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
             dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
   
           }
           break;
         case 12:
           /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/
           if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
             if (num_filled != 8) {
               printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
             }
             printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
             /* day and month of proj2 are not used but only year anproj2.*/
             dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
             dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
           }
           break;
         case 13:
           if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
             if (num_filled == 0){
               resultline[0]='\0';
               printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
               fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
               break;
             } else if (num_filled != 1){
               printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
               fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
             }
             nresult++; /* Sum of resultlines */
             printf("Result %d: result=%s\n",nresult, resultline);
             if(nresult > MAXRESULTLINES){
               printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
               fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
               goto end;
             }
             decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
             fprintf(ficparo,"result: %s\n",resultline);
             fprintf(ficres,"result: %s\n",resultline);
             fprintf(ficlog,"result: %s\n",resultline);
             break;
           case 14: 
             if(ncovmodel >2 && nresult==0 ){
               printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
               goto end;
             }
             break;
           default:
             nresult=1;
             decoderesult(".",nresult ); /* No covariate */
           }
         } /* End switch parameterline */
       }while(endishere==0); /* End do */
           
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
Line 11320  Please run with mle=-1 to get a correct Line 12221  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, backcast, pathc,p);        /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
         printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
     }      }
     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,mobilav,prevfcast,mobilavproj,backcast, estepm, \
                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);                   jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
                                   
     /*------------ free_vector  -------------*/      /*------------ free_vector  -------------*/
     /*  chdir(path); */      /*  chdir(path); */
Line 11360  Please run with mle=-1 to get a correct Line 12262  Please run with mle=-1 to get a correct
     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] */      /* Prevalence for each covariate combination in probs[age][status][cov] */
     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=AGEINF;i<=AGESUP;i++)
       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
         for(k=1;k<=ncovcombmax;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);      prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, 
                  ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     if (mobilav!=0 ||mobilavproj !=0 ) {      if (mobilav!=0 ||mobilavproj !=0 ) {
       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);        mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
       for(i=1;i<=AGESUP;i++)        for(i=AGEINF;i<=AGESUP;i++)
         for(j=1;j<=nlstate;j++)          for(j=1;j<=nlstate+ndeath;j++)
           for(k=1;k<=ncovcombmax;k++)            for(k=1;k<=ncovcombmax;k++)
             mobaverages[i][j][k]=0.;              mobaverages[i][j][k]=0.;
       mobaverage=mobaverages;        mobaverage=mobaverages;
       if (mobilav!=0) {        if (mobilav!=0) {
         printf("Movingaveraging observed prevalence\n");          printf("Movingaveraging observed prevalence\n");
           fprintf(ficlog,"Movingaveraging observed prevalence\n");
         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){          if (movingaverage(probs, ageminpar, agemaxpar, 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);
         }          }
       }        } else if (mobilavproj !=0) {
       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */  
       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */  
       else if (mobilavproj !=0) {  
         printf("Movingaveraging projected observed prevalence\n");          printf("Movingaveraging projected observed prevalence\n");
           fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
           printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
         }          }
         }else{
           printf("Internal error moving average\n");
           fflush(stdout);
           exit(1);
       }        }
     }/* end if moving average */      }/* end if moving average */
           
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/  
     if(prevfcast==1){      if(prevfcast==1){
       /*    if(stepm ==1){*/        /*    if(stepm ==1){*/
       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
     }      }
   
       /* Backcasting */
     if(backcast==1){      if(backcast==1){
       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
Line 11406  Please run with mle=-1 to get a correct Line 12313  Please run with mle=-1 to get a correct
       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/        /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
   
       bprlim=matrix(1,nlstate,1,nlstate);        bprlim=matrix(1,nlstate,1,nlstate);
   
       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);        back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
       fclose(ficresplb);        fclose(ficresplb);
   
       hBijx(p, bage, fage, mobaverage);        hBijx(p, bage, fage, mobaverage);
       fclose(ficrespijb);        fclose(ficrespijb);
       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */  
   
       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,        prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */                         mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
         varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
         
         free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
     }      }    /* end  Backcasting */
        
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
   
Line 11471  Please run with mle=-1 to get a correct Line 12382  Please run with mle=-1 to get a correct
     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);
   
                                   
     /*---------- State-specific expectancies and variances ------------*/      /*---------- State-specific 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 11483  Please run with mle=-1 to get a correct Line 12394  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);
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
Line 11512  Please run with mle=-1 to get a correct Line 12421  Please run with mle=-1 to get a correct
     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/  
             
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
     if (cptcovn < 1){i1=1;}      if (cptcovn < 1){i1=1;}
           
Line 11576  Please run with mle=-1 to get a correct Line 12482  Please run with mle=-1 to get a correct
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       pstamp(ficrest);        pstamp(ficrest);
               
               epj=vector(1,nlstate+1);
       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 */
Line 11592  Please run with mle=-1 to get a correct Line 12498  Please run with mle=-1 to get a correct
         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);  
         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++){
Line 11630  Please run with mle=-1 to get a correct Line 12535  Please run with mle=-1 to get a correct
           fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
         }          }
       } /* End vpopbased */        } /* End vpopbased */
         free_vector(epj,1,nlstate+1);
       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);
       free_vector(epj,1,nlstate+1);  
       printf("done selection\n");fflush(stdout);        printf("done selection\n");fflush(stdout);
       fprintf(ficlog,"done selection\n");fflush(ficlog);        fprintf(ficlog,"done selection\n");fflush(ficlog);
               
       /*}*/  
     } /* End k selection */      } /* End k selection */
   
     printf("done State-specific expectancies\n");fflush(stdout);      printf("done State-specific expectancies\n");fflush(stdout);
     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
     /*------- Variance of period (stable) prevalence------*/         /* variance-covariance of period prevalence*/
           varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
     strcpy(fileresvpl,"VPL_");  
     strcat(fileresvpl,fileresu);  
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);  
       exit(0);  
     }  
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);  
     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);  
       
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/  
       
     i1=pow(2,cptcoveff);  
     if (cptcovn < 1){i1=1;}  
   
     for(nres=1; nres <= nresult; nres++) /* For each resultline */  
     for(k=1; k<=i1;k++){  
       if(i1 != 1 && TKresult[nres]!= k)  
         continue;  
       fprintf(ficresvpl,"\n#****** ");  
       printf("\n#****** ");  
       fprintf(ficlog,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
       }  
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */  
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);  
         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);  
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);  
       }   
       fprintf(ficresvpl,"******\n");  
       printf("******\n");  
       fprintf(ficlog,"******\n");  
         
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  
       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);  
       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
       /*}*/  
     }  
       
     fclose(ficresvpl);  
     printf("done variance-covariance of period prevalence\n");fflush(stdout);  
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);  
           
     free_vector(weight,1,n);      free_vector(weight,1,n);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
Line 11707  Please run with mle=-1 to get a correct Line 12566  Please run with mle=-1 to get a correct
           
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0 ||mobilavproj !=0)      if (mobilav!=0 ||mobilavproj !=0)
       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */        free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
Line 11716  Please run with mle=-1 to get a correct Line 12575  Please run with mle=-1 to get a correct
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);    if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);    if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
   free_matrix(coqvar,1,maxwav,1,n);    if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
   free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(covar,0,NCOVMAX,1,n);
   free_matrix(matcov,1,npar,1,npar);    free_matrix(matcov,1,npar,1,npar);
   free_matrix(hess,1,npar,1,npar);    free_matrix(hess,1,npar,1,npar);
   /*free_vector(delti,1,npar);*/    /*free_vector(delti,1,npar);*/
   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
   free_matrix(agev,1,maxwav,1,imx);    free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
       
   free_ivector(ncodemax,1,NCOVMAX);    free_ivector(ncodemax,1,NCOVMAX);

Removed from v.1.256  
changed lines
  Added in v.1.280


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