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Diff for /imach/src/imach.c between versions 1.266 and 1.268

version 1.266, 2017/05/13 07:26:12 version 1.268, 2017/05/18 20:09:32
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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    Revision 1.266  2017/05/13 07:26:12  brouard
   Summary: Version 0.99r13 (improvements and bugs fixed)    Summary: Version 0.99r13 (improvements and bugs fixed)
   
Line 818  Back prevalence and projections: Line 824  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 986  typedef struct { Line 992  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 1079  FILE  *ficresvij; Line 1086  FILE  *ficresvij;
 char fileresv[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvpl;
 char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
   FILE  *ficresvbl;
   char fileresvbl[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 1176  double *agedc; Line 1185  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 2739  Earliest age to start was %d-%d=%d, ncvl Line 2748  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 == 70){ */      /* if((int)age == 86 || (int)age == 87){ */
     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */      /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
     /*   for(i=1; i<=nlstate+ndeath; i++) { */      /*   for(i=1; i<=nlstate+ndeath; i++) { */
     /*  printf("%d newm= ",i); */      /*  printf("%d newm= ",i); */
Line 2750  Earliest age to start was %d-%d=%d, ncvl Line 2759  Earliest age to start was %d-%d=%d, ncvl
     /*  for(j=1;j<=nlstate+ndeath;j++) { */      /*  for(j=1;j<=nlstate+ndeath;j++) { */
     /*    printf("%f ",oldm[i][j]); */      /*    printf("%f ",oldm[i][j]); */
     /*  } */      /*  } */
     /*  printf(" pmmij "); */      /*  printf(" bmmij "); */
     /*  for(j=1;j<=nlstate+ndeath;j++) { */      /*  for(j=1;j<=nlstate+ndeath;j++) { */
     /*    printf("%f ",pmmij[i][j]); */      /*    printf("%f ",pmmij[i][j]); */
     /*  } */      /*  } */
Line 2778  Earliest age to start was %d-%d=%d, ncvl Line 2787  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 2902  double **pmij(double **ps, double *cov, Line 2911  double **pmij(double **ps, double *cov,
   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 2911  double **pmij(double **ps, double *cov, Line 2920  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) at beginning of transition */       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); */
   
     /* P_x */
   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */    pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
   /* outputs pmmij which is a stochastic matrix */    /* outputs pmmij which is a stochastic matrix in row */
   /* We do have the matrix Px in savm  and we need pij */  
     /* 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 */
       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 N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */      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]*prevacurrent[(int)agefin][ii][ij]; /* Yes prevalence at beginning of transition */        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 */
     if(sumnew >= 1.e-10){      for (ii=1;ii<=nlstate+ndeath;ii++){
       for (ii=1;ii<=nlstate+ndeath;ii++){  
         /* 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);
       } /*End ii */      } /*End ii */
     }else{ /* We put the identity matrix */    } /* 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 */
       for (ii=1;ii<=nlstate+ndeath;ii++){  
         doldm[ii][j]=(ii==j ? 1. : 0.0);    ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
       } /*End ii */    /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
       /* printf("Problem internal bmij A: sum_i w_i*p_ij=N.j/N.. <1.e-10 i=%d, j=%d, sumnew=%lf,agefin=%d\n",ii,j,sumnew, (int)agefin); */  
     }  
   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] or identity*/  
   /* left Product of this diag matrix by dsavm=Px (dnewm=dsavm*doldm) */  
   /* bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /\* Bug Valgrind *\/ */  
   bbmij=matprod2(dnewm, pmmij,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */  
   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */  
   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */  
   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */  
   /* left Product of this matrix by diag matrix of prevalences (savm) */  
   for (j=1;j<=nlstate+ndeath;j++){  
     sumnew=0.;  
     for (ii=1;ii<=nlstate+ndeath;ii++){  
       sumnew+=prevacurrent[(int)agefin][ii][ij];  
       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 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); */  
     /* } */  
   } /* End j, At the end dsavm is diag[(w_i)] */  
   /* What if dsavm doesn't sum ii to 1? */  
   /* ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /\* Bug Valgrind *\/ */  
   ps=matprod2(ps, 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; /*pointer is unchanged */    return ps; /*pointer is unchanged */
 }  }
Line 3174  double ***hpxij(double ***po, int nhstep Line 3193  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 )
 {  {
   /* For a combination of dummy covariate ij, 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
Line 3230  double ***hbxij(double ***po, int nhstep Line 3249  double ***hbxij(double ***po, int nhstep
       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */        /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
         /* 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)); */          /* 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)); */
   
       }        }
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */          /* 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<=cptcovprod;k++) /* Useless because included in cptcovn */        }
         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], prevacurrent at beginning of transition. */        /* 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),\ */
Line 3268  double ***hbxij(double ***po, int nhstep Line 3295  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 3727  double funcone( double *x) Line 3755  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 3760  double funcone( double *x) Line 3788  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 4280  void pstamp(FILE *fichier) Line 4308  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 4356  void  freqsummary(char fileres[], double Line 4321  void  freqsummary(char fileres[], double
   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 4795  Title=%s <br>Datafile=%s Firstpass=%d La Line 4760  Title=%s <br>Datafile=%s Firstpass=%d La
                     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, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,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[s1]=b;                    pstart[s1]=b;
                   pstart[s1-1]=a;                    pstart[s1-1]=a;
Line 4898  Title=%s <br>Datafile=%s Firstpass=%d La Line 4865  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 6034  void  concatwav(int wav[], int **dh, int Line 6067  void  concatwav(int wav[], int **dh, int
   /* 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 6053  void  concatwav(int wav[], int **dh, int Line 6086  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 6123  void  concatwav(int wav[], int **dh, int Line 6156  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 6148  void  concatwav(int wav[], int **dh, int Line 6181  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 fileres[], 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 6649  divided by h: <sub>h</sub>P<sub>ij</sub> Line 6807  divided by h: <sub>h</sub>P<sub>ij</sub>
      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 and mobil_average=%d) 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) up 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, mobilavproj, 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, 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) up to stable (mixed) back prevalence in state %d. 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, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
          }
        }
                     
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
Line 6756  true period expectancies (those weighted Line 6921  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[], int offyear){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, 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], gplotlabel[132];    char gplotcondition[132], gplotlabel[132];
Line 6920  true period expectancies (those weighted Line 7085  true period expectancies (those weighted
               }                }
             } /* 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 0,\"%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 1,\"%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 1");
             } /* end if backprojcast */
         } /* end if backcast */          } /* end if backcast */
         fprintf(ficgp,"\nset out ;unset label;\n");          fprintf(ficgp,"\nset out ;unset label;\n");
       } /* nres */        } /* nres */
Line 7213  set ter svg size 640, 480\nunset log y\n Line 7397  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 */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);          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 */
Line 7237  set ter svg size 640, 480\nunset log y\n Line 7421  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 \"Ending alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);          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 7254  set ter svg size 640, 480\nunset log y\n Line 7438  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; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
Line 7325  set ter svg size 640, 480\nunset log y\n Line 7509  set ter svg size 640, 480\nunset log y\n
               fprintf(ficgp," u %d:(",ioffset);                 fprintf(ficgp," u %d:(",ioffset); 
               fprintf(ficgp," (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", \                fprintf(ficgp," (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", \
                      offyear,                           \                       offyear,                           \
                       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 );
             }else              }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 );
Line 7364  set ter svg size 640, 480\nunset log y\n Line 7548  set ter svg size 640, 480\nunset log y\n
               fprintf(ficgp," u %d:(",ioffset);                 fprintf(ficgp," u %d:(",ioffset); 
               fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \                fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \
                      offyear,                           \                       offyear,                           \
                       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 );
 /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/  /*  '' 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, \
Line 7377  set ter svg size 640, 480\nunset log y\n Line 7561  set ter svg size 640, 480\nunset log y\n
     } /* 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)):5 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," (($5-$6) == %d ) ? $%d : 1/0):5 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 */
               if(cptcoveff ==1){
                 ioffset=4; /* Age is in 4 */
               }else{
                 ioffset=6; /* Age is in 6 */
                 /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                 /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               }   
               fprintf(ficgp," u %d:(",ioffset); 
               kl=0;
               strcpy(gplotcondition,"(");
               for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                 kl++;
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                 kl++;
                 if(k <cptcoveff && cptcoveff>1)
                   sprintf(gplotcondition+strlen(gplotcondition)," && ");
               }
               strcpy(gplotcondition+strlen(gplotcondition),")");
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(i==nlstate+1){
                 fprintf(ficgp,"%s ? $%d : 1/0):5 t 'bw%d' with line lc variable", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
                 fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d : 1/0):5 with labels center not ", gplotcondition, \
                        offbyear,                          \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
   /*  '' 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");
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             /* 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(k1,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(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 */                      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(k1,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){
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               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+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);                       if(ij <=cptcovage) { /* Bug valgrind */
                     /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,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+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,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,")");
             }              }
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          sumr+=probs[(int)age][i][cptcod];           sumr+=probs[(int)age][i][cptcod];
        }         }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */         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, bage);           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 */         } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        if(fabs(sumr - 1.) > 1.e-3) { /* bad */         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, bage);           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 */
   
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          sumr+=mobaverage[(int)age][i][cptcod];           sumr+=mobaverage[(int)age][i][cptcod];
        }         }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */         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, fage);           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 */         } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        if(fabs(sumr - 1.) > 1.e-3) { /* bad */         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, fage);           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 */         } /* end bad */
      }/* age */       }/* age */
   
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 /************** Forecasting ******************/  /************** Forecasting ******************/
  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   /* 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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         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 { */ /* even if mobilav==-1 we use mobaverage */            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]*mobaverage[(int)agec][i][k];
               if (h*hstepm/YEARM*stepm== yearp) {              /* else { */ /* even if mobilav==-1 we use mobaverage */
                 fprintf(ficresf," %.3f", p3mat[i][j][h]);              /*  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
               }              /* } */
             } /* end i */              fprintf(ficresf," %.3f", p3mat[i][j][h]);
             if (h*hstepm/YEARM*stepm==yearp) {            } /* end i */
               fprintf(ficresf," %.3f", ppij);            fprintf(ficresf," %.3f", ppij);
             }          }/* end j */
           }/* end j */  
         } /* end h */  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       } /* end agec */        } /* end agec */
       /* diffyear=(int) anproj1+yearp-ageminpar-1; */        /* diffyear=(int) anproj1+yearp-ageminpar-1; */
Line 7935  set ter svg size 640, 480\nunset log y\n Line 8240  set ter svg size 640, 480\nunset log y\n
 }  }
   
 /* /\************** Back Forecasting ******************\/ */  /* /\************** Back Forecasting ******************\/ */
 /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */  void prevbackforecast(char fileres[], double ***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 en of backection (same day and month as back1).
 /*   *\/ */    */
 /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
 /*   double agec; /\* generic age *\/ */    double agec; /* generic age */
 /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */    double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 /*   double *popeffectif,*popcount; */    double *popeffectif,*popcount;
 /*   double ***p3mat; */    double ***p3mat;
 /*   /\* double ***mobaverage; *\/ */    /* double ***mobaverage; */
 /*   char fileresfb[FILENAMELENGTH]; */    char fileresfb[FILENAMELENGTH];
            
 /*   agelim=AGESUP; */    agelim=AGEINF;
 /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */       in each health status at the date of interview (if between dateprev1 and dateprev2).
 /*      We still use firstpass and lastpass as another selection. */       We still use firstpass and lastpass as another selection.
 /*   *\/ */    */
 /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */    /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
 /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */    /*          firstpass, lastpass,  stepm,  weightopt, model); */
 /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */  
             /*Do we need to compute prevalence again?*/
 /*   strcpy(fileresfb,"FB_");  */  
 /*   strcat(fileresfb,fileresu); */    /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
 /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */  
 /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */  
 /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */  
 /*   } */  
 /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */  
 /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */  
           
 /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */  
           
 /*   /\* if (mobilav!=0) { *\/ */  
 /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */  
 /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */  
 /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */  
 /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */  
 /*   /\*   } *\/ */  
 /*   /\* } *\/ */  
           
 /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */  
 /*   if (stepm<=12) stepsize=1; */  
 /*   if(estepm < stepm){ */  
 /*     printf ("Problem %d lower than %d\n",estepm, stepm); */  
 /*   } */  
 /*   else  hstepm=estepm;    */  
           
 /*   hstepm=hstepm/stepm;  */  
 /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */  
 /*                                fractional in yp1 *\/ */  
 /*   anprojmean=yp; */  
 /*   yp2=modf((yp1*12),&yp); */  
 /*   mprojmean=yp; */  
 /*   yp1=modf((yp2*30.5),&yp); */  
 /*   jprojmean=yp; */  
 /*   if(jprojmean==0) jprojmean=1; */  
 /*   if(mprojmean==0) jprojmean=1; */  
           
 /*   i1=cptcoveff; */  
 /*   if (cptcovn < 1){i1=1;} */  
       
 /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */    strcpy(fileresfb,"FB_");
     strcat(fileresfb,fileresu);
     if((ficresfb=fopen(fileresfb,"w"))==NULL) {
       printf("Problem with back forecast resultfile: %s\n", fileresfb);
       fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
     }
     printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
     fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
       
 /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             
 /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */     
 /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */    stepsize=(int) (stepm+YEARM-1)/YEARM;
 /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */    if (stepm<=12) stepsize=1;
 /*       k=k+1; */    if(estepm < stepm){
 /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */      printf ("Problem %d lower than %d\n",estepm, stepm);
 /*       for(j=1;j<=cptcoveff;j++) { */    }
 /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */    else  hstepm=estepm;
 /*       } */    
 /*       fprintf(ficresfb," yearbproj age"); */    hstepm=hstepm/stepm;
 /*       for(j=1; j<=nlstate+ndeath;j++){  */    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
 /*                              for(i=1; i<=nlstate;i++)               */                                 fractional in yp1 */
 /*           fprintf(ficresfb," p%d%d",i,j); */    anprojmean=yp;
 /*                              fprintf(ficresfb," p.%d",j); */    yp2=modf((yp1*12),&yp);
 /*       } */    mprojmean=yp;
 /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */    yp1=modf((yp2*30.5),&yp);
 /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */    jprojmean=yp;
 /*                              fprintf(ficresfb,"\n"); */    if(jprojmean==0) jprojmean=1;
 /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */    if(mprojmean==0) jprojmean=1;
 /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */    
 /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */    i1=pow(2,cptcoveff);
 /*                                      nhstepm = nhstepm/hstepm;  */    if (cptcovn < 1){i1=1;}
 /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */    
 /*                                      oldm=oldms;savm=savms; */    fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
 /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */    printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
 /*                                      for (h=0; h<=nhstepm; h++){ */    
 /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
 /*               fprintf(ficresfb,"\n"); */    
 /*               for(j=1;j<=cptcoveff;j++)  */    /*          if (h==(int)(YEARM*yearp)){ */
 /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */    /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
 /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */    /*   for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
 /*                                              }  */    /*     k=k+1; */
 /*                                              for(j=1; j<=nlstate+ndeath;j++) { */    for(nres=1; nres <= nresult; nres++) /* For each resultline */
 /*                                                      ppij=0.; */    for(k=1; k<=i1;k++){
 /*                                                      for(i=1; i<=nlstate;i++) { */      if(i1 != 1 && TKresult[nres]!= k)
 /*                                                              if (mobilav==1)  */        continue;
 /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */      if(invalidvarcomb[k]){
 /*                                                              else { */        printf("\nCombination (%d) projection ignored because no cases \n",k); 
 /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */        continue;
 /*                                                              } */      }
 /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
 /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */      for(j=1;j<=cptcoveff;j++) {
 /*                                                              } */        fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 /*                                                      } /\* end i *\/ */      }
 /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
 /*                                                              fprintf(ficresfb," %.3f", ppij); */        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
 /*                                                      } */      }
 /*                                              }/\* end j *\/ */      fprintf(ficresfb," yearbproj age");
 /*                                      } /\* end h *\/ */      for(j=1; j<=nlstate+ndeath;j++){
 /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */        for(i=1; i<=nlstate;i++)
 /*                              } /\* end agec *\/ */          fprintf(ficresfb," b%d%d",i,j);
 /*       } /\* end yearp *\/ */        fprintf(ficresfb," b.%d",j);
 /*     } /\* end cptcod *\/ */      }
 /*   } /\* end  cptcov *\/ */      for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
                 /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
 /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */        fprintf(ficresfb,"\n");
                 fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
 /*   fclose(ficresfb); */        printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
 /*   printf("End of Computing Back forecasting \n"); */        /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
 /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */        /*        nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
         for (agec=bage; agec<=agemax-1; agec++){  /* testing */
           /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
           nhstepm=(int) rint((agec-agelim)*YEARM/stepm);
           nhstepm = nhstepm/hstepm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           /* computes hbxij at age agec over 1 to nhstepm */
           hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, 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 */
           /* printf(" agec=%.2f\n",agec);fflush(stdout); */
           for (h=0; h<=nhstepm; h++){
             if (h*hstepm/YEARM*stepm ==-yearp) {
               break;
             }
           }
           fprintf(ficresfb,"\n");
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
           for(i=1; i<=nlstate+ndeath;i++) {
             ppij=0.;ppi=0.;
             for(j=1; j<=nlstate;j++) {
               /* if (mobilav==1) */
               ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k];
               ppi=ppi+mobaverage[(int)agec][j][k];
                 /* else { */
                 /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
                 /* } */
               fprintf(ficresfb," %.3f", p3mat[i][j][h]);
             } /* 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");
                   
 /* } */  }
   
 /************** 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 10071  int hPijx(double *p, int bage, int fage) Line 10393  int hPijx(double *p, int bage, int fage)
   
         /* 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 10172  int main(int argc, char *argv[]) Line 10494  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 **varbpl; /* Variances of back 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,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
Line 10455  int main(int argc, char *argv[]) Line 10778  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 11008  Youngest age at first (selected) pass %. Line 11331  Youngest age at first (selected) pass %.
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);            imx,agemin,agemax,jmin,jmax,jmean);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   
   /* For Powell, parameters are in a vector p[] starting at p[1]    /* For Powell, parameters are in a vector p[] starting at p[1]
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
Line 11631  Please run with mle=-1 to get a correct Line 11954  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, (int)anproj1-(int)ageminpar);        printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1);
     }      }
     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \                   model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
Line 11681  Please run with mle=-1 to get a correct Line 12004  Please run with mle=-1 to get a correct
     if (mobilav!=0 ||mobilavproj !=0 ) {      if (mobilav!=0 ||mobilavproj !=0 ) {
       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);        mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
       for(i=1;i<=AGESUP;i++)        for(i=1;i<=AGESUP;i++)
         for(j=1;j<=nlstate;j++)          for(j=1;j<=nlstate+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;
Line 11730  Please run with mle=-1 to get a correct Line 12053  Please run with mle=-1 to get a correct
   
       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 ? */        /* free_matrix(bprlim,1,nlstate,1,nlstate); /\*here or after loop ? *\/ */
   
         prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
            bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
   
         /*------- Variance of back (stable) prevalence------*/   
         
         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);
         
         /*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(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(fileres, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, &ncvyear, 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);
   
       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,  
          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */  
       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(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);
     }      }
           free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
    
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
   
Line 12009  Please run with mle=-1 to get a correct Line 12384  Please run with mle=-1 to get a correct
     fclose(ficresvpl);      fclose(ficresvpl);
     printf("done variance-covariance of period prevalence\n");fflush(stdout);      printf("done variance-covariance of period prevalence\n");fflush(stdout);
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);      fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
   
           
     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 12035  Please run with mle=-1 to get a correct Line 12411  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);
Removed from v.1.266  
changed lines
  Added in v.1.268

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