Diff for /imach/src/imach.c between versions 1.221 and 1.223

version 1.221, 2016/02/15 23:35:36 version 1.223, 2016/02/19 09:23:35
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.223  2016/02/19 09:23:35  brouard
     Summary: temporary
   
     Revision 1.222  2016/02/17 08:14:50  brouard
     Summary: Probably last 0.98 stable version 0.98r6
   
   Revision 1.221  2016/02/15 23:35:36  brouard    Revision 1.221  2016/02/15 23:35:36  brouard
   Summary: minor bug    Summary: minor bug
   
Line 739  Back prevalence and projections: Line 745  Back prevalence and projections:
 /* #define DEBUGLINMIN */  /* #define DEBUGLINMIN */
 /* #define DEBUGHESS */  /* #define DEBUGHESS */
 #define DEBUGHESSIJ  #define DEBUGHESSIJ
 #define LINMINORIGINAL  /* Don't use loop on scale in linmin (accepting nan)*/  /* #define LINMINORIGINAL  /\* Don't use loop on scale in linmin (accepting nan)*\/ */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
 #define POWELLF1F3 /* Skip test */  #define POWELLF1F3 /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
Line 854  int npar=NPARMAX; Line 860  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ 
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
Line 992  double *agedc; Line 999  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 ***cotvar; /* Time varying covariate */
   double ***cotqvar; /* Time varying quantitative covariate */
   double **coqvar; /* Fixed quantitative covariate */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 int *Tage;  int *Tage;
Line 2331  double **pmij(double **ps, double *cov, Line 2341  double **pmij(double **ps, double *cov,
   /*double t34;*/    /*double t34;*/
   int i,j, nc, ii, jj;    int i,j, nc, ii, jj;
   
         for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
                 for(j=1; j<i;j++){      for(j=1; j<i;j++){
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/          /*lnpijopii += param[i][j][nc]*cov[nc];*/
                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                         }        }
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                 }      }
                 for(j=i+1; j<=nlstate+ndeath;j++){      for(j=i+1; j<=nlstate+ndeath;j++){
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/          /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];          lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                         }        }
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                 }      }
         }    }
       
         for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
                 s1=0;      s1=0;
                 for(j=1; j<i; j++){      for(j=1; j<i; j++){
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                 }      }
                 for(j=i+1; j<=nlstate+ndeath; j++){      for(j=i+1; j<=nlstate+ndeath; j++){
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
                 }      }
                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
                 ps[i][i]=1./(s1+1.);      ps[i][i]=1./(s1+1.);
                 /* Computing other pijs */      /* Computing other pijs */
                 for(j=1; j<i; j++)      for(j=1; j<i; j++)
                         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
                 for(j=i+1; j<=nlstate+ndeath; j++)      for(j=i+1; j<=nlstate+ndeath; j++)
                         ps[i][j]= exp(ps[i][j])*ps[i][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         } /* end i */    } /* end i */
       
         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                 for(jj=1; jj<= nlstate+ndeath; jj++){      for(jj=1; jj<= nlstate+ndeath; jj++){
                         ps[ii][jj]=0;        ps[ii][jj]=0;
                         ps[ii][ii]=1;        ps[ii][ii]=1;
                 }      }
         }    }
       
       
         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         /*   } */    /*   } */
         /*   printf("\n "); */    /*   printf("\n "); */
         /* } */    /* } */
         /* printf("\n ");printf("%lf ",cov[2]);*/    /* printf("\n ");printf("%lf ",cov[2]);*/
         /*    /*
                 for(i=1; i<= npar; i++) printf("%f ",x[i]);      for(i=1; i<= npar; i++) printf("%f ",x[i]);
                 goto end;*/                  goto end;*/
         return ps;    return ps;
 }  }
   
 /*************** backward transition probabilities ***************/   /*************** backward transition probabilities ***************/ 
Line 2398  double **pmij(double **ps, double *cov, Line 2408  double **pmij(double **ps, double *cov,
 /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
 {  {
         /* Computes the backward probability at age agefin and covariate ij    /* Computes the backward probability at age agefin and covariate ij
          * and returns in **ps as well as **bmij.     * and returns in **ps as well as **bmij.
          */     */
   int i, ii, j,k;    int i, ii, j,k;
     
         double **out, **pmij();    double **out, **pmij();
         double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
     
         double **dnewm, **dsavm, **doldm;    double **dnewm, **dsavm, **doldm;
         double **bbmij;    double **bbmij;
     
   doldm=ddoldms; /* global pointers */    doldm=ddoldms; /* global pointers */
         dnewm=ddnewms;    dnewm=ddnewms;
         dsavm=ddsavms;    dsavm=ddsavms;
     
         agefin=cov[2];    agefin=cov[2];
         /* bmij *//* age is cov[2], ij is included in cov, but we need for    /* bmij *//* age is cov[2], ij is included in cov, but we need for
                  the observed prevalence (with this covariate ij) */       the observed prevalence (with this covariate ij) */
         dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);    dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
         /* We do have the matrix Px in savm  and we need pij */    /* We do have the matrix Px in savm  and we need pij */
         for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
                 sumnew=0.; /* w1 p11 + w2 p21 only on live states */      sumnew=0.; /* w1 p11 + w2 p21 only on live states */
                 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 is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */      } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
                 for (ii=1;ii<=nlstate+ndeath;ii++){      for (ii=1;ii<=nlstate+ndeath;ii++){
                         if(sumnew >= 1.e-10){        if(sumnew >= 1.e-10){
                                 /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
                                 /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */          /*      doldm[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); */          /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
                                 /* }else */          /* }else */
                                         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);          doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
                         }else{        }else{
                                 printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);          printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);
                         }        }
                 } /*End ii */      } /*End ii */
         } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */    } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
                 /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */    /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
         bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */    bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
         /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */    /* 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)] *\/ */    /* 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)] *\/ */    /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
         /* left Product of this matrix by diag matrix of prevalences (savm) */    /* left Product of this matrix by diag matrix of prevalences (savm) */
         for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
                 for (ii=1;ii<=nlstate+ndeath;ii++){      for (ii=1;ii<=nlstate+ndeath;ii++){
                         dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);        dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
                 }      }
         } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */    } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
         ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */    ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
         /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */    /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
         /* end bmij */    /* end bmij */
         return ps;     return ps; 
 }  }
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
Line 2657  double ***hpxij(double ***po, int nhstep Line 2667  double ***hpxij(double ***po, int nhstep
   
 /************* 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 )
 {  {
   /* 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
Line 2669  double ***hpxij(double ***po, int nhstep Line 2679  double ***hpxij(double ***po, int nhstep
      Model is determined by parameters x and covariates have to be       Model is determined by parameters x and covariates have to be
      included manually here.       included manually here.
   
      */    */
   
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
         double **oldm, **savm;    double **oldm, **savm;
   
         oldm=oldms;savm=savms;    oldm=oldms;savm=savms;
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
Line 2695  double ***hpxij(double ***po, int nhstep Line 2705  double ***hpxij(double ***po, int nhstep
       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
                                 cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)        for (k=1; k<=cptcovn;k++)
                                 cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];          cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
                         /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */        /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
                                 /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                                 cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */        /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */        /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
                                                   
                                                   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       /* Careful transposed matrix */        /* Careful transposed matrix */
                         /* age is in cov[2] */        /* age is in cov[2] */
       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
                         /*                                               1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
                                                                          1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                     1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       /* if((int)age == 70){ */        /* if((int)age == 70){ */
       /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */        /*        printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
       /*        for(i=1; i<=nlstate+ndeath; i++) { */        /*        for(i=1; i<=nlstate+ndeath; i++) { */
Line 2735  double ***hpxij(double ***po, int nhstep Line 2745  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;
 }  }
   
Line 2769  double ***hpxij(double ***po, int nhstep Line 2779  double ***hpxij(double ***po, int nhstep
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
           int ioffset;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   int s1, s2;    int s1, s2;
     int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
   double bbh, survp;    double bbh, survp;
   long ipmx;    long ipmx;
   double agexact;    double agexact;
Line 2793  double func( double *x) Line 2805  double func( double *x)
   if(mle==1){    if(mle==1){
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /* Computes the values of the ncovmodel covariates of the model        /* Computes the values of the ncovmodel covariates of the model
          depending if the covariates are fixed or variying (age dependent) and stores them in cov[]           depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
          to be observed in j being in i according to the model.           to be observed in j being in i according to the model.
        */         */
         ioffset=2+nagesqr;
       for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+nagesqr+k]=covar[Tvar[k]][i];           cov[++ioffset]=covar[Tvar[k]][i];
       }        }
         for(iqv=1; iqv <= nqv; iqv++){ /* Varying quantitatives covariates */
           /* cov[2+nagesqr+cptcovn+iqv]=varq[mw[mi+1][i]][iqv][i]; */
         }
   
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
          has been calculated etc */           has been calculated etc */
         /* For an individual i, wav[i] gives the number of effective waves */
         /* We compute the contribution to Likelihood of each effective transition
            mw[mi][i] is real wave of the mi th effectve wave */
         /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
           s2=s[mw[mi+1][i]][i];
           And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
           But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
         */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(itv=1; itv <= ntv; itv++){ /* Varying dummy covariates */
             cov[++ioffset]=cotvar[mw[mi+1][i]][itv][i];
           }
           for(iqtv=1; iqtv <= nqtv; iqtv++){ /* Varying quantitatives covariates */
             /* cov[2+nagesqr+cptcovn+nqv+ntv+iqtv]=varq[mw[mi+1][i]][iqtv][i]; */
           }
           ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv;
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 2814  double func( double *x) Line 2847  double func( double *x)
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;            cov[2]=agexact;
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;              cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
           }            }
Line 3995  Title=%s <br>Datafile=%s Firstpass=%d La Line 4028  Title=%s <br>Datafile=%s Firstpass=%d La
  }   }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
 void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 {     {  
   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      in each health status at the date of interview (if between dateprev1 and dateprev2).        in each health status at the date of interview (if between dateprev1 and dateprev2).
      We still use firstpass and lastpass as another selection.        We still use firstpass and lastpass as another selection.
   */     */
     
   int i, m, jk, j1, bool, z1,j;     int i, m, jk, j1, bool, z1,j;
   int mi; /* Effective wave */     int mi; /* Effective wave */
   int iage;     int iage;
   double agebegin, ageend;     double agebegin, ageend;
   
   double **prop;     double **prop;
   double posprop;      double posprop; 
   double  y2; /* in fractional years */     double  y2; /* in fractional years */
   int iagemin, iagemax;     int iagemin, iagemax;
   int first; /** to stop verbosity which is redirected to log file */     int first; /** to stop verbosity which is redirected to log file */
   
   iagemin= (int) agemin;     iagemin= (int) agemin;
   iagemax= (int) agemax;     iagemax= (int) agemax;
   /*pp=vector(1,nlstate);*/     /*pp=vector(1,nlstate);*/
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);      prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); 
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;     j1=0;
       
   /*j=cptcoveff;*/     /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}     if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;     first=1;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */     for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
     for (i=1; i<=nlstate; i++)         for (i=1; i<=nlstate; i++)  
       for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)         for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
                                 prop[i][iage]=0.0;           prop[i][iage]=0.0;
           
     for (i=1; i<=imx; i++) { /* Each individual */       for (i=1; i<=imx; i++) { /* Each individual */
       bool=1;         bool=1;
       if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */         if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                                 for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/           for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
                                         if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
                                                 bool=0;               bool=0;
       }          } 
       if (bool==1) { /* For this combination of covariates values, this individual fits */         if (bool==1) { /* For this combination of covariates values, this individual fits */
                                 /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */           /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
                                 for(mi=1; mi<wav[i];mi++){           for(mi=1; mi<wav[i];mi++){
                                         m=mw[mi][i];             m=mw[mi][i];
                                         agebegin=agev[m][i]; /* Age at beginning of wave before transition*/             agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
                                         /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                                         if(m >=firstpass && m <=lastpass){             if(m >=firstpass && m <=lastpass){
                                                 y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                                                 if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                                                         if(agev[m][i]==0) agev[m][i]=iagemax+1;                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                                                         if(agev[m][i]==1) agev[m][i]=iagemax+2;                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                                                         if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){                 if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
                                                                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);                    printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                                                                 exit(1);                   exit(1);
                                                         }                 }
                                                         if (s[m][i]>0 && s[m][i]<=nlstate) {                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
                                                                 /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                                                                 prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */                   prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
                                                                 prop[s[m][i]][iagemax+3] += weight[i];                    prop[s[m][i]][iagemax+3] += weight[i]; 
                                                         } /* end valid statuses */                  } /* end valid statuses */ 
                                                 } /* end selection of dates */               } /* end selection of dates */
                                         } /* end selection of waves */             } /* end selection of waves */
                                 } /* end effective waves */           } /* end effective waves */
       } /* end bool */         } /* end bool */
     }       }
     for(i=iagemin; i <= iagemax+3; i++){         for(i=iagemin; i <= iagemax+3; i++){  
       for(jk=1,posprop=0; jk <=nlstate ; jk++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                                 posprop += prop[jk][i];            posprop += prop[jk][i]; 
       }          } 
               
       for(jk=1; jk <=nlstate ; jk++){                for(jk=1; jk <=nlstate ; jk++){      
                                 if( i <=  iagemax){            if( i <=  iagemax){ 
                                         if(posprop>=1.e-5){              if(posprop>=1.e-5){ 
                                                 probs[i][jk][j1]= prop[jk][i]/posprop;               probs[i][jk][j1]= prop[jk][i]/posprop;
                                         } else{             } else{
                                                 if(first==1){               if(first==1){
                                                         first=0;                 first=0;
                                                         printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                                                 }               }
                                         }             }
                                 }            } 
       }/* end jk */          }/* end jk */ 
     }/* end i */        }/* end i */ 
     /*} *//* end i1 */       /*} *//* end i1 */
   } /* end j1 */     } /* end j1 */
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/     /*free_vector(pp,1,nlstate);*/
   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);     free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
 }  /* End of prevalence */   }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
Line 4116  void  concatwav(int wav[], int **dh, int Line 4149  void  concatwav(int wav[], int **dh, int
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state */
       if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */        if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
         mw[++mi][i]=m;                                  mw[++mi][i]=m;
       }        }
       if(m >=lastpass){        if(m >=lastpass){
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){                                  if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
           if(firsthree == 0){                                          if(firsthree == 0){
             printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);                                                  printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
             firsthree=1;                                                  firsthree=1;
           }                                          }
           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);                                          fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);
           mw[++mi][i]=m;                                          mw[++mi][i]=m;
         }                                  }
         if(s[m][i]==-2){ /* Vital status is really unknown */                                  if(s[m][i]==-2){ /* Vital status is really unknown */
           nbwarn++;                                          nbwarn++;
           if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */                                          if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
             printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);                                                  printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
             fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);                                                  fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
           }                                          }
           break;                                          break;
         }                                  }
         break;                                  break;
       }        }
       else        else
         m++;                                  m++;
     }/* end while */      }/* end while */
           
     /* After last pass */      /* After last pass */
     if (s[m][i] > nlstate){  /* In a death state */      if (s[m][i] > nlstate){  /* In a death state */
       mi++;     /* Death is another wave */        mi++;     /* Death is another wave */
       /* if(mi==0)  never been interviewed correctly before death */        /* if(mi==0)  never been interviewed correctly before death */
          /* Only death is a correct wave */                          /* Only death is a correct wave */
       mw[mi][i]=m;        mw[mi][i]=m;
     }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */      }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
       /* m++; */        /* m++; */
Line 4154  void  concatwav(int wav[], int **dh, int Line 4187  void  concatwav(int wav[], int **dh, int
       /* mw[mi][i]=m; */        /* mw[mi][i]=m; */
       nberr++;        nberr++;
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if(firstwo==0){                                  if(firstwo==0){
           printf("Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                          printf("Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
           firstwo=1;                                          firstwo=1;
         }                                  }
         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                  fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
       }else{ /* end date of interview is known */        }else{ /* end date of interview is known */
         /* death is known but not confirmed by death status at any wave */                                  /* death is known but not confirmed by death status at any wave */
         if(firstfour==0){                                  if(firstfour==0){
           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                          printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
           firstfour=1;                                          firstfour=1;
         }                                  }
         fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );                                  fprintf(ficlog,"Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
       }        }
     }      }
     wav[i]=mi;      wav[i]=mi;
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
         printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);                                  printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         first=1;                                  first=1;
       }        }
       if(first==1){        if(first==1){
         fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);                                  fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
   /* wav and mw are no more changed */    /* wav and mw are no more changed */
           
       
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       if (stepm <=0)        if (stepm <=0)
         dh[mi][i]=1;                                  dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */                                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           if (agedc[i] < 2*AGESUP) {                                          if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                                                   j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */                                                  if(j==0) j=1;  /* Survives at least one month after exam */
             else if(j<0){                                                  else if(j<0){
               nberr++;                                                          nberr++;
               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                          printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               j=1; /* Temporary Dangerous patch */                                                          j=1; /* Temporary Dangerous patch */
               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                                                          printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                          fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                                                          fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }                                                  }
             k=k+1;                                                  k=k+1;
             if (j >= jmax){                                                  if (j >= jmax){
               jmax=j;                                                          jmax=j;
               ijmax=i;                                                          ijmax=i;
             }                                                  }
             if (j <= jmin){                                                  if (j <= jmin){
               jmin=j;                                                          jmin=j;
               ijmin=i;                                                          ijmin=i;
             }                                                  }
             sum=sum+j;                                                  sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i);*/                                                  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/                                                  /*        printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           }                                          }
         }                                  }
         else{                                  else{
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                                          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                                           
           k=k+1;                                          k=k+1;
           if (j >= jmax) {                                          if (j >= jmax) {
             jmax=j;                                                  jmax=j;
             ijmax=i;                                                  ijmax=i;
           }                                          }
           else if (j <= jmin){                                          else if (j <= jmin){
             jmin=j;                                                  jmin=j;
             ijmin=i;                                                  ijmin=i;
           }                                          }
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */                                          /*          if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/                                          /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           if(j<0){                                          if(j<0){
             nberr++;                                                  nberr++;
             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                  printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                                                  fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }                                          }
           sum=sum+j;                                          sum=sum+j;
         }                                  }
         jk= j/stepm;                                  jk= j/stepm;
         jl= j -jk*stepm;                                  jl= j -jk*stepm;
         ju= j -(jk+1)*stepm;                                  ju= j -(jk+1)*stepm;
         if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */                                  if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           if(jl==0){                                          if(jl==0){
             dh[mi][i]=jk;                                                  dh[mi][i]=jk;
             bh[mi][i]=0;                                                  bh[mi][i]=0;
           }else{ /* We want a negative bias in order to only have interpolation ie                                          }else{ /* We want a negative bias in order to only have interpolation ie
                   * to avoid the price of an extra matrix product in likelihood */                                                                          * to avoid the price of an extra matrix product in likelihood */
             dh[mi][i]=jk+1;                                                  dh[mi][i]=jk+1;
             bh[mi][i]=ju;                                                  bh[mi][i]=ju;
           }                                          }
         }else{                                  }else{
           if(jl <= -ju){                                          if(jl <= -ju){
             dh[mi][i]=jk;                                                  dh[mi][i]=jk;
             bh[mi][i]=jl;       /* bias is positive if real duration                                                  bh[mi][i]=jl;   /* bias is positive if real duration
                                  * is higher than the multiple of stepm and negative otherwise.                                                                                                           * is higher than the multiple of stepm and negative otherwise.
                                  */                                                                                                           */
           }                                          }
           else{                                          else{
             dh[mi][i]=jk+1;                                                  dh[mi][i]=jk+1;
             bh[mi][i]=ju;                                                  bh[mi][i]=ju;
           }                                          }
           if(dh[mi][i]==0){                                          if(dh[mi][i]==0){
             dh[mi][i]=1; /* At least one step */                                                  dh[mi][i]=1; /* At least one step */
             bh[mi][i]=ju; /* At least one step */                                                  bh[mi][i]=ju; /* At least one step */
             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/                                                  /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           }                                          }
         } /* end if mle */                                  } /* end if mle */
       }        }
     } /* end wave */      } /* end wave */
   }    }
Line 4520  void cvevsij(double ***eij, double x[], Line 4553  void cvevsij(double ***eij, double x[],
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
    to initial status i, ei. .       to initial status i, ei. .
   */    */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
Line 4626  void cvevsij(double ***eij, double x[], Line 4659  void cvevsij(double ***eij, double x[],
        decrease memory allocation */         decrease memory allocation */
     for(theta=1; theta <=npar; theta++){      for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){         for(i=1; i<=npar; i++){ 
                                 xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                                 xm[i] = x[i] - (i==theta ?delti[theta]:0);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
                                                   
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
                                 for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
                                         for(h=0; h<=nhstepm-1; h++){            for(h=0; h<=nhstepm-1; h++){
                                                 gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                                                 gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
                                         }            }
                                 }          }
       }        }
                                                   
       for(ij=1; ij<= nlstate*nlstate; ij++)        for(ij=1; ij<= nlstate*nlstate; ij++)
                                 for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
                                         gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
                                 }          }
     }/* End theta */      }/* End theta */
           
           
     for(h=0; h<=nhstepm-1; h++)      for(h=0; h<=nhstepm-1; h++)
       for(j=1; j<=nlstate*nlstate;j++)        for(j=1; j<=nlstate*nlstate;j++)
                                 for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
                                         trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
           
                                   
                 for(ij=1;ij<=nlstate*nlstate;ij++)      for(ij=1;ij<=nlstate*nlstate;ij++)
       for(ji=1;ji<=nlstate*nlstate;ji++)        for(ji=1;ji<=nlstate*nlstate;ji++)
                                 varhe[ij][ji][(int)age] =0.;          varhe[ij][ji][(int)age] =0.;
                                   
                 printf("%d|",(int)age);fflush(stdout);      printf("%d|",(int)age);fflush(stdout);
                 fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                 for(h=0;h<=nhstepm-1;h++){      for(h=0;h<=nhstepm-1;h++){
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
                                 matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                                 matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                                 for(ij=1;ij<=nlstate*nlstate;ij++)          for(ij=1;ij<=nlstate*nlstate;ij++)
                                         for(ji=1;ji<=nlstate*nlstate;ji++)            for(ji=1;ji<=nlstate*nlstate;ji++)
                                                 varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
                                   
Line 4674  void cvevsij(double ***eij, double x[], Line 4707  void cvevsij(double ***eij, double x[],
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
                                 for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                                         eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                                                                                   
                                         /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                                                                                   
                                 }          }
                                   
     fprintf(ficresstdeij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     for(i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++){
       eip=0.;        eip=0.;
       vip=0.;        vip=0.;
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
                                 eip += eij[i][j][(int)age];          eip += eij[i][j][(int)age];
                                 for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                                         vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
                                 fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       }        }
       fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     }      }
Line 4698  void cvevsij(double ***eij, double x[], Line 4731  void cvevsij(double ***eij, double x[],
     fprintf(ficrescveij,"%3.0f",age );      fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
                                 cptj= (j-1)*nlstate+i;          cptj= (j-1)*nlstate+i;
                                 for(i2=1; i2<=nlstate;i2++)          for(i2=1; i2<=nlstate;i2++)
                                         for(j2=1; j2<=nlstate;j2++){            for(j2=1; j2<=nlstate;j2++){
                                                 cptj2= (j2-1)*nlstate+i2;              cptj2= (j2-1)*nlstate+i2;
                                                 if(cptj2 <= cptj)              if(cptj2 <= cptj)
                                                         fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                                         }            }
       }        }
     fprintf(ficrescveij,"\n");      fprintf(ficrescveij,"\n");
                                   
Line 5161  void cvevsij(double ***eij, double x[], Line 5194  void cvevsij(double ***eij, double x[],
   
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {   {
   int i, j=0,  k1, l1, tj;     int i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;     int k2, l2, j1,  z1;
   int k=0, l;     int k=0, l;
   int first=1, first1, first2;     int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;     double **dnewm,**doldm;
   double *xp;     double *xp;
   double *gp, *gm;     double *gp, *gm;
   double **gradg, **trgradg;     double **gradg, **trgradg;
   double **mu;     double **mu;
   double age, cov[NCOVMAX+1];     double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;     int theta;
   char fileresprob[FILENAMELENGTH];     char fileresprob[FILENAMELENGTH];
   char fileresprobcov[FILENAMELENGTH];     char fileresprobcov[FILENAMELENGTH];
   char fileresprobcor[FILENAMELENGTH];     char fileresprobcor[FILENAMELENGTH];
   double ***varpij;     double ***varpij;
   
   strcpy(fileresprob,"PROB_");      strcpy(fileresprob,"PROB_"); 
   strcat(fileresprob,fileres);     strcat(fileresprob,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);       printf("Problem with resultfile: %s\n", fileresprob);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }     }
   strcpy(fileresprobcov,"PROBCOV_");      strcpy(fileresprobcov,"PROBCOV_"); 
   strcat(fileresprobcov,fileresu);     strcat(fileresprobcov,fileresu);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcov);       printf("Problem with resultfile: %s\n", fileresprobcov);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }     }
   strcpy(fileresprobcor,"PROBCOR_");      strcpy(fileresprobcor,"PROBCOR_"); 
   strcat(fileresprobcor,fileresu);     strcat(fileresprobcor,fileresu);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprobcor);       printf("Problem with resultfile: %s\n", fileresprobcor);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }     }
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   pstamp(ficresprob);     pstamp(ficresprob);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");     fprintf(ficresprob,"# Age");
   pstamp(ficresprobcov);     pstamp(ficresprobcov);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");     fprintf(ficresprobcov,"# Age");
   pstamp(ficresprobcor);     pstamp(ficresprobcor);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcor,"# Age");     fprintf(ficresprobcor,"# Age");
   
   
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }    
  /* fprintf(ficresprob,"\n");  
   fprintf(ficresprobcov,"\n");  
   fprintf(ficresprobcor,"\n");  
  */  
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  
   first=1;  
   fprintf(ficgp,"\n# Routine varprob");  
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");  
   fprintf(fichtm,"\n");  
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);     for(i=1; i<=nlstate;i++)
   fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);       for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
        }  
      /* fprintf(ficresprob,"\n");
         fprintf(ficresprobcov,"\n");
         fprintf(ficresprobcor,"\n");
      */
      xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
      fprintf(ficgp,"\n# Routine varprob");
      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
   
      fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
      fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
 It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
 would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
 standard deviations wide on each axis. <br>\  standard deviations wide on each axis. <br>\
Line 5248  standard deviations wide on each axis. < Line 5281  standard deviations wide on each axis. <
  and made the appropriate rotation to look at the uncorrelated principal directions.<br>\   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
 To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   cov[1]=1;     cov[1]=1;
   /* tj=cptcoveff; */     /* tj=cptcoveff; */
   tj = (int) pow(2,cptcoveff);     tj = (int) pow(2,cptcoveff);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   j1=0;     j1=0;
   for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates */     for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates */
                 if  (cptcovn>0) {       if  (cptcovn>0) {
                         fprintf(ficresprob, "\n#********** Variable ");          fprintf(ficresprob, "\n#********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficresprob, "**********\n#\n");         fprintf(ficresprob, "**********\n#\n");
                         fprintf(ficresprobcov, "\n#********** Variable ");          fprintf(ficresprobcov, "\n#********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficresprobcov, "**********\n#\n");
                                                   
                         fprintf(ficgp, "\n#********** Variable ");          fprintf(ficgp, "\n#********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficgp, "**********\n#\n");         fprintf(ficgp, "**********\n#\n");
                                                   
                                                   
                         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                                                   
                         fprintf(ficresprobcor, "\n#********** Variable ");             fprintf(ficresprobcor, "\n#********** Variable ");    
                         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                         fprintf(ficresprobcor, "**********\n#");             fprintf(ficresprobcor, "**********\n#");    
                         if(invalidvarcomb[j1]){         if(invalidvarcomb[j1]){
                           fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);            fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
                           fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);            fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1); 
                           continue;           continue;
                         }         }
                 }       }
                 gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));       gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                 trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
                 gp=vector(1,(nlstate)*(nlstate+ndeath));       gp=vector(1,(nlstate)*(nlstate+ndeath));
                 gm=vector(1,(nlstate)*(nlstate+ndeath));       gm=vector(1,(nlstate)*(nlstate+ndeath));
                 for (age=bage; age<=fage; age ++){        for (age=bage; age<=fage; age ++){ 
                         cov[2]=age;         cov[2]=age;
                         if(nagesqr==1)         if(nagesqr==1)
                                 cov[3]= age*age;           cov[3]= age*age;
                         for (k=1; k<=cptcovn;k++) {         for (k=1; k<=cptcovn;k++) {
                                 cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
                                 /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4           /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
                                                                                                                                                                                                                                                                          * 1  1 1 1 1                                                                      * 1  1 1 1 1
                                                                                                                                                                                                                                                                          * 2  2 1 1 1                                                                      * 2  2 1 1 1
                                                                                                                                                                                                                                                                          * 3  1 2 1 1                                                                      * 3  1 2 1 1
                                                                                                                                                                                                                                                                          */                                                                      */
                                 /* nbcode[1][1]=0 nbcode[1][2]=1;*/           /* nbcode[1][1]=0 nbcode[1][2]=1;*/
                         }         }
                         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
                         for (k=1; k<=cptcovprod;k++)         for (k=1; k<=cptcovprod;k++)
                                 cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
                                                   
                                                   
                         for(theta=1; theta <=npar; theta++){         for(theta=1; theta <=npar; theta++){
                                 for(i=1; i<=npar; i++)           for(i=1; i<=npar; i++)
                                         xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);             xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                                                                   
                                 pmij(pmmij,cov,ncovmodel,xp,nlstate);           pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                                                   
                                 k=0;           k=0;
                                 for(i=1; i<= (nlstate); i++){           for(i=1; i<= (nlstate); i++){
                                         for(j=1; j<=(nlstate+ndeath);j++){             for(j=1; j<=(nlstate+ndeath);j++){
                                                 k=k+1;               k=k+1;
                                                 gp[k]=pmmij[i][j];               gp[k]=pmmij[i][j];
                                         }             }
                                 }           }
                                                                   
                                 for(i=1; i<=npar; i++)           for(i=1; i<=npar; i++)
                                         xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);             xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
                                                                   
                                 pmij(pmmij,cov,ncovmodel,xp,nlstate);           pmij(pmmij,cov,ncovmodel,xp,nlstate);
                                 k=0;           k=0;
                                 for(i=1; i<=(nlstate); i++){           for(i=1; i<=(nlstate); i++){
                                         for(j=1; j<=(nlstate+ndeath);j++){             for(j=1; j<=(nlstate+ndeath);j++){
                                                 k=k+1;               k=k+1;
                                                 gm[k]=pmmij[i][j];               gm[k]=pmmij[i][j];
                                         }             }
                                 }           }
                                                                   
                                 for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                                         gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
                         }         }
   
                         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                                 for(theta=1; theta <=npar; theta++)           for(theta=1; theta <=npar; theta++)
                                         trgradg[j][theta]=gradg[theta][j];             trgradg[j][theta]=gradg[theta][j];
                                                   
                         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                                                   
                         pmij(pmmij,cov,ncovmodel,x,nlstate);         pmij(pmmij,cov,ncovmodel,x,nlstate);
                                                   
                         k=0;         k=0;
                         for(i=1; i<=(nlstate); i++){         for(i=1; i<=(nlstate); i++){
                                 for(j=1; j<=(nlstate+ndeath);j++){           for(j=1; j<=(nlstate+ndeath);j++){
                                         k=k+1;             k=k+1;
                                         mu[k][(int) age]=pmmij[i][j];             mu[k][(int) age]=pmmij[i][j];
                                 }           }
                         }         }
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                                 for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                                         varpij[i][j][(int)age] = doldm[i][j];             varpij[i][j][(int)age] = doldm[i][j];
                                                   
                         /*printf("\n%d ",(int)age);         /*printf("\n%d ",(int)age);
                                 for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                                 printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));           printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                                 fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));           fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                                 }*/           }*/
                                                   
                         fprintf(ficresprob,"\n%d ",(int)age);         fprintf(ficresprob,"\n%d ",(int)age);
                         fprintf(ficresprobcov,"\n%d ",(int)age);         fprintf(ficresprobcov,"\n%d ",(int)age);
                         fprintf(ficresprobcor,"\n%d ",(int)age);         fprintf(ficresprobcor,"\n%d ",(int)age);
                                                   
                         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                                 fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                                 fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                                 fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
                         }         }
                         i=0;         i=0;
                         for (k=1; k<=(nlstate);k++){         for (k=1; k<=(nlstate);k++){
                                 for (l=1; l<=(nlstate+ndeath);l++){            for (l=1; l<=(nlstate+ndeath);l++){ 
                                         i++;             i++;
                                         fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                                         fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                                         for (j=1; j<=i;j++){             for (j=1; j<=i;j++){
                                                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */               /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                                                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                                                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                                         }             }
                                 }           }
                         }/* end of loop for state */         }/* end of loop for state */
                 } /* end of loop for age */       } /* end of loop for age */
                 free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
                 free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));       free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
                 free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                 free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           
                 /* Confidence intervalle of pij  */       /* Confidence intervalle of pij  */
                 /*       /*
                         fprintf(ficgp,"\nunset parametric;unset label");         fprintf(ficgp,"\nunset parametric;unset label");
                         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
                         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
                         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);         fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
                         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
                         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);         fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                 */       */
                                   
                 /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                 first1=1;first2=2;       first1=1;first2=2;
                 for (k2=1; k2<=(nlstate);k2++){       for (k2=1; k2<=(nlstate);k2++){
                         for (l2=1; l2<=(nlstate+ndeath);l2++){          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                                 if(l2==k2) continue;           if(l2==k2) continue;
                                 j=(k2-1)*(nlstate+ndeath)+l2;           j=(k2-1)*(nlstate+ndeath)+l2;
                                 for (k1=1; k1<=(nlstate);k1++){           for (k1=1; k1<=(nlstate);k1++){
                                         for (l1=1; l1<=(nlstate+ndeath);l1++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                                                 if(l1==k1) continue;               if(l1==k1) continue;
                                                 i=(k1-1)*(nlstate+ndeath)+l1;               i=(k1-1)*(nlstate+ndeath)+l1;
                                                 if(i<=j) continue;               if(i<=j) continue;
                                                 for (age=bage; age<=fage; age ++){                for (age=bage; age<=fage; age ++){ 
                                                         if ((int)age %5==0){                 if ((int)age %5==0){
                                                                 v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                                                                 v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                                                                 cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                                                                 mu1=mu[i][(int) age]/stepm*YEARM ;                   mu1=mu[i][(int) age]/stepm*YEARM ;
                                                                 mu2=mu[j][(int) age]/stepm*YEARM;                   mu2=mu[j][(int) age]/stepm*YEARM;
                                                                 c12=cv12/sqrt(v1*v2);                   c12=cv12/sqrt(v1*v2);
                                                                 /* Computing eigen value of matrix of covariance */                   /* Computing eigen value of matrix of covariance */
                                                                 lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                                                                 lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                                                                 if ((lc2 <0) || (lc1 <0) ){                   if ((lc2 <0) || (lc1 <0) ){
                                                                         if(first2==1){                     if(first2==1){
                                                                                 first1=0;                       first1=0;
                                                                                 printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                                                                         }                     }
                                                                         fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);                     fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                                                                         /* lc1=fabs(lc1); */ /* If we want to have them positive */                     /* lc1=fabs(lc1); */ /* If we want to have them positive */
                                                                         /* lc2=fabs(lc2); */                     /* lc2=fabs(lc2); */
                                                                 }                   }
                                                                                                                                   
                                                                 /* Eigen vectors */                   /* Eigen vectors */
                                                                 v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                                                                 /*v21=sqrt(1.-v11*v11); *//* error */                   /*v21=sqrt(1.-v11*v11); *//* error */
                                                                 v21=(lc1-v1)/cv12*v11;                   v21=(lc1-v1)/cv12*v11;
                                                                 v12=-v21;                   v12=-v21;
                                                                 v22=v11;                   v22=v11;
                                                                 tnalp=v21/v11;                   tnalp=v21/v11;
                                                                 if(first1==1){                   if(first1==1){
                                                                         first1=0;                     first1=0;
                                                                         printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);                     printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                                                                 }                   }
                                                                 fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                                                                 /*printf(fignu*/                   /*printf(fignu*/
                                                                 /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                                                                 /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                                                                 if(first==1){                   if(first==1){
                                                                         first=0;                     first=0;
                                                                         fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");                     fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
                                                                         fprintf(ficgp,"\nset parametric;unset label");                     fprintf(ficgp,"\nset parametric;unset label");
                                                                         fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                                                                         fprintf(ficgp,"\nset ter svg size 640, 480");                     fprintf(ficgp,"\nset ter svg size 640, 480");
                                                                         fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\                     fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
 %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                                                                                                         subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
                                                                                                         subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                                                                         fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                     fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                                                                         fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                                                                         fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);                     fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",     \                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
                                                                 mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                            \                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                                                         \
                                                                 mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                                                                 }else{                   }else{
                                                                         first=0;                     first=0;
                                                                         fprintf(fichtmcov," %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                                                                         fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                                                                         fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                                                                         fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
                                                                                                         mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                    \                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),                                 \
                                                                                                         mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                                                                 }/* if first */                   }/* if first */
                                                         } /* age mod 5 */                 } /* age mod 5 */
                                                 } /* end loop age */               } /* end loop age */
                                                 fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);               fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
                                                 first=1;               first=1;
                                         } /*l12 */             } /*l12 */
                                 } /* k12 */           } /* k12 */
                         } /*l1 */         } /*l1 */
                 }/* k1 */       }/* k1 */
         }  /* loop on combination of covariates j1 */     }  /* loop on combination of covariates j1 */
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   free_vector(xp,1,npar);     free_vector(xp,1,npar);
   fclose(ficresprob);     fclose(ficresprob);
   fclose(ficresprobcov);     fclose(ficresprobcov);
   fclose(ficresprobcor);     fclose(ficresprobcor);
   fflush(ficgp);     fflush(ficgp);
   fflush(fichtmcov);     fflush(fichtmcov);
 }   }
   
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
Line 5536  void printinghtml(char fileresu[], char Line 5569  void printinghtml(char fileresu[], char
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
    }     }
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
  m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
   
    /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
          jj1++;       jj1++;
          if (cptcovn > 0) {       if (cptcovn > 0) {
                  fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                  for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcoveff;cpt++){ 
                          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
                          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);           printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
                  }         }
                  fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
                  if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
                          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
                          printf("\nCombination (%d) ignored because no cases \n",k1);            printf("\nCombination (%d) ignored because no cases \n",k1); 
                          continue;           continue;
                  }         }
          }       }
          /* aij, bij */       /* aij, bij */
          fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \       fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
 <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);  <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
          /* Pij */       /* Pij */
          fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \       fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
 <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);       <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);     
          /* Quasi-incidences */       /* Quasi-incidences */
          fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
 divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
 <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);   <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); 
          /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
          for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
                  fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
 <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);  <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
          }       }
          /* State specific survival functions (period) */       /* State specific survival functions (period) */
          for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
                  fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\         fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \   Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);   <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
          }       }
          /* Period (stable) prevalence in each health state */       /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){  
                  fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \  
 <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);  
          }  
          if(backcast==1){  
      /* Period (stable) back prevalence in each health state */  
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
        }
        if(backcast==1){
          /* Period (stable) back prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);  <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
          }
      }       }
          }       if(prevfcast==1){
          if(prevfcast==1){         /* Projection of prevalence up to period (stable) prevalence in each health state */
                  /* Projection of prevalence up to period (stable) prevalence in each health state */         for(cpt=1; cpt<=nlstate;cpt++){
                  for(cpt=1; cpt<=nlstate;cpt++){           fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
                          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \  
 <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);  <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
                  }         }
          }       }
                     
          for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
                  fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
 <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);  <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
          }       }
    /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
   
  fprintf(fichtm,"\     fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
  - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
Line 5622  variances but at the covariance matrix. Line 5655  variances but at the covariance matrix.
 covariance matrix of the one-step probabilities. \  covariance matrix of the one-step probabilities. \
 See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);  See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",     fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));             subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));             subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
   
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));             subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));             estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
          estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
          estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
  fprintf(fichtm,"\     fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 5655  See page 'Matrix of variance-covariance Line 5688  See page 'Matrix of variance-covariance
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
  fflush(fichtm);     fflush(fichtm);
  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");     fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
  m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  jj1=0;     jj1=0;
  for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
   /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
                  jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++) 
                                                          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
                          if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
                                  fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
                                  continue;           continue;
                          }         }
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
Line 5687  true period expectancies (those weighted Line 5720  true period expectancies (those weighted
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\   observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
 <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);  <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
    /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
  }/* End k1 */     }/* End k1 */
  fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
  fflush(fichtm);     fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
         char gplotcondition[132];    char gplotcondition[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
         int ioffset; /* variable offset for columns */    int ioffset; /* variable offset for columns */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 5711  true period expectancies (those weighted Line 5744  true period expectancies (those weighted
   
   /*#ifdef windows */    /*#ifdef windows */
   fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */    /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
   
   /* Contribution to likelihood */    /* Contribution to likelihood */
   /* Plot the probability implied in the likelihood */    /* Plot the probability implied in the likelihood */
     fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");    fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
     /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */    /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");    fprintf(ficgp,"\nset ter pngcairo size 640, 480");
 /* nice for mle=4 plot by number of matrix products.  /* nice for mle=4 plot by number of matrix products.
    replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */     replot  "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
 /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */  /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)"  */
     /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */    /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
     fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));    fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));    fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
     fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));    fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
     fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));    fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
     for (i=1; i<= nlstate ; i ++) {    for (i=1; i<= nlstate ; i ++) {
       fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);      fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
       fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));      fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot  \"%s\"",subdirf(fileresilk));
       fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);      fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
       for (j=2; j<= nlstate+ndeath ; j ++) {      for (j=2; j<= nlstate+ndeath ; j ++) {
                                 fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);        fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
       }      }
       fprintf(ficgp,";\nset out; unset ylabel;\n");       fprintf(ficgp,";\nset out; unset ylabel;\n"); 
     }    }
     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                  /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                
     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */    /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */    /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
     fprintf(ficgp,"\nset out;unset log\n");    fprintf(ficgp,"\nset out;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */    /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
  /* 1eme*/    /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
     for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */      for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */          lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
                         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;          continue;
                         }        }
   
                         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
                         fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);        fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
                         fprintf(ficgp,"set xlabel \"Age\" \n\        fprintf(ficgp,"set xlabel \"Age\" \n\
 set ylabel \"Probability\" \n   \  set ylabel \"Probability\" \n   \
 set ter svg size 640, 480\n     \  set ter svg size 640, 480\n     \
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
                                                   
                         for (i=1; i<= nlstate ; i ++) {        for (i=1; i<= nlstate ; i ++) {
                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                                 else        fprintf(ficgp," %%*lf (%%*lf)");          else        fprintf(ficgp," %%*lf (%%*lf)");
                         }        }
                         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
                         for (i=1; i<= nlstate ; i ++) {        for (i=1; i<= nlstate ; i ++) {
                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                                 else fprintf(ficgp," %%*lf (%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
                         }         } 
                         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);         fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); 
                         for (i=1; i<= nlstate ; i ++) {        for (i=1; i<= nlstate ; i ++) {
                                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                                 else fprintf(ficgp," %%*lf (%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
                         }          }  
                         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
                         if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */        if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
                                 /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */          /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
                                 fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */          fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
                                 kl=0;          if(cptcoveff ==0){
                                 for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */            fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );
                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */          }else{
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            kl=0;
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */              lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                                         vlv= nbcode[Tvaraff[k]][lv];              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         kl++;              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         /* 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 *\/ */              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */               vlv= nbcode[Tvaraff[k]][lv];
                                         /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */               kl++;
                                         /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/              /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                                         if(k==cptcoveff){              /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                                                         fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \              /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
                                                                                         6+(cpt-1),  cpt );              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
                                         }else{              if(k==cptcoveff){
                                                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);                fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                                                 kl++;                        6+(cpt-1),  cpt );
                                         }              }else{
                                 } /* end covariate */                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                         }                kl++;
                         fprintf(ficgp,"\nset out \n");              }
             } /* end covariate */
           } /* end if no covariate */
         } /* end if backcast */
         fprintf(ficgp,"\nset out \n");
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
   /*2 eme*/    /*2 eme*/
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
   
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");      fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */      for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */        lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */        /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];        vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }      }
       fprintf(ficgp,"\n#\n");      fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){      if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;        continue;
                         }      }
                                                   
                         fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);      fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
                         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/      for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
                                 if(vpopbased==0)        if(vpopbased==0)
                                         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);          fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
                                 else        else
                                         fprintf(ficgp,"\nreplot ");          fprintf(ficgp,"\nreplot ");
                                 for (i=1; i<= nlstate+1 ; i ++) {        for (i=1; i<= nlstate+1 ; i ++) {
                                         k=2*i;          k=2*i;
                                         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
                                         for (j=1; j<= nlstate+1 ; j ++) {          for (j=1; j<= nlstate+1 ; j ++) {
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                                                 else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
                                         }             }   
                                         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
                                         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);          else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
                                         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
                                         for (j=1; j<= nlstate+1 ; j ++) {          for (j=1; j<= nlstate+1 ; j ++) {
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                                                 else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
                                         }             }   
                                         fprintf(ficgp,"\" t\"\" w l lt 0,");          fprintf(ficgp,"\" t\"\" w l lt 0,");
                                         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
                                         for (j=1; j<= nlstate+1 ; j ++) {          for (j=1; j<= nlstate+1 ; j ++) {
                                                 if (j==i) fprintf(ficgp," %%lf (%%lf)");            if (j==i) fprintf(ficgp," %%lf (%%lf)");
                                                 else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
                                         }             }   
                                         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
                                         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");          else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
                                 } /* state */        } /* state */
                         } /* vpopbased */      } /* vpopbased */
                         fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */      fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
   } /* k1 */    } /* k1 */
                   
                   
Line 5872  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 5909  plot [%.f:%.f] \"%s\" every :::%d::%d u
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);        fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;          continue;
                         }        }
                                                   
       /*       k=2+nlstate*(2*cpt-2); */        /*       k=2+nlstate*(2*cpt-2); */
       k=2+(nlstate+1)*(cpt-1);        k=2+(nlstate+1)*(cpt-1);
Line 5891  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 5928  plot [%.f:%.f] \"%s\" every :::%d::%d u
       fprintf(ficgp,"set ter svg size 640, 480\n\        fprintf(ficgp,"set ter svg size 640, 480\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
                                 for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                                 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                                                   
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
                                 fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
                                 /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/          /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                                                                   
       }         } 
       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);        fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
     }      }
   }    }
       
         /* 4eme */    /* 4eme */
   /* Survival functions (period) from state i in state j by initial state i */    /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */    for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
   
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                         continue;          continue;
                         }        }
                                                   
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
Line 5934  unset log y\n Line 5971  unset log y\n
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
       k=3;        k=3;
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
                                 if(i==1){          if(i==1){
                                         fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
                                 }else{          }else{
                                         fprintf(ficgp,", '' ");            fprintf(ficgp,", '' ");
                                 }          }
                                 l=(nlstate+ndeath)*(i-1)+1;          l=(nlstate+ndeath)*(i-1)+1;
                                 fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
                                 for (j=2; j<= nlstate+ndeath ; j ++)          for (j=2; j<= nlstate+ndeath ; j ++)
                                         fprintf(ficgp,"+$%d",k+l+j-1);            fprintf(ficgp,"+$%d",k+l+j-1);
                                 fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
Line 5953  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 5990  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   /* Survival functions (period) from state i in state j by final state j */    /* Survival functions (period) from state i in state j by final state j */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */    for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
                           
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */                                  lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 5964  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6001  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);                                  fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                   fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;                                  continue;
                         }        }
                                                   
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
Line 6003  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6040  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */    for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                           
       fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
                                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */                                  lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6014  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6051  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);                                  fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
                         if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                   fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                 continue;                                  continue;
                         }        }
                           
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n\  set ter svg size 640, 480\n                                                                                                                                                                              \
 unset log y\n\  unset log y\n                                                                                                                                                                                                                                    \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
       k=3; /* Offset */        k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
Line 6039  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6076  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
           
           
 /* 7eme */  /* 7eme */
   if(backcast == 1){    if(backcast == 1){
     /* CV back preval stable (period) for each covariate */      /* CV back preval stable (period) for each covariate */
Line 6051  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6088  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */                                          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                                          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                                          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         vlv= nbcode[Tvaraff[k]][lv];                                          vlv= nbcode[Tvaraff[k]][lv];
                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);                                          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                 }                                  }
                                 fprintf(ficgp,"\n#\n");                                  fprintf(ficgp,"\n#\n");
                                 if(invalidvarcomb[k1]){                                  if(invalidvarcomb[k1]){
                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                                 continue;                                          continue;
                                 }                                  }
                                                                   
                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);                                  fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
Line 6087  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6124  plot [%.f:%.f]  ", ageminpar, agemaxpar)
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if backcast */
       
         /* 8eme */    /* 8eme */
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to stable (period) for each covariate */
           
Line 6104  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6141  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                 }                                  }
                                 fprintf(ficgp,"\n#\n");                                  fprintf(ficgp,"\n#\n");
                                 if(invalidvarcomb[k1]){                                  if(invalidvarcomb[k1]){
                                                                 fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);                                           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
                                                                 continue;                                          continue;
                                 }                                  }
                                                                   
                                 fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");                                  fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
                                 fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);                                  fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
                                 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\                                  fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
 set ter svg size 640, 480\n     \  set ter svg size 640, 480\n                                                                                                                                                                                     \
 unset log y\n   \  unset log y\n                                                                                                                                                                                                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
                                 for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */                                  for (i=1; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
                                         /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/                                          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
Line 6142  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6179  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                                         ioffset=4; /* Age is in 4 */                                                          ioffset=4; /* Age is in 4 */
                                                 }else{                                                  }else{
                                                         ioffset=6; /* Age is in 6 */                                                          ioffset=6; /* Age is in 6 */
                                                 /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/                                                          /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
                                                 /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */                                                          /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
                                                 }                                                     }   
                                                 fprintf(ficgp," u %d:(",ioffset);                                                   fprintf(ficgp," u %d:(",ioffset); 
                                                 kl=0;                                                  kl=0;
Line 6169  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6206  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                                         fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \                                                          fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
                                                                                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                                                 }else{                                                  }else{
                                                                 fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \                                                          fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
                                                                                                 ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );                                                                                          ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
                                                 }                                                  }
                                         } /* end if covariate */                                          } /* end if covariate */
                                 } /* nlstate */                                  } /* nlstate */
                                 fprintf(ficgp,"\nset out\n");                                  fprintf(ficgp,"\nset out\n");
                         } /* end cpt state*/        } /* end cpt state*/
                 } /* end covariate */      } /* end covariate */
         } /* End if prevfcast */    } /* End if prevfcast */
                   
                   
         /* proba elementaires */    /* proba elementaires */
         fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
     fprintf(ficgp,"# initial state %d\n",i);      fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {        if (k != i) {
         fprintf(ficgp,"#   current state %d\n",k);                                  fprintf(ficgp,"#   current state %d\n",k);
         for(j=1; j <=ncovmodel; j++){                                  for(j=1; j <=ncovmodel; j++){
           fprintf(ficgp,"p%d=%f; ",jk,p[jk]);                                          fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
           jk++;                                           jk++; 
         }                                  }
         fprintf(ficgp,"\n");                                  fprintf(ficgp,"\n");
       }        }
     }      }
    }    }
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
           
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");    fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
Line 6212  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6249  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");    fprintf(ficgp,"#       +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
      fprintf(ficgp,"# ng=%d\n",ng);      fprintf(ficgp,"# ng=%d\n",ng);
      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);
      for(jk=1; jk <=m; jk++) {      for(jk=1; jk <=m; jk++) {
        fprintf(ficgp,"#    jk=%d\n",jk);        fprintf(ficgp,"#    jk=%d\n",jk);
        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
        fprintf(ficgp,"\nset ter svg size 640, 480 ");        fprintf(ficgp,"\nset ter svg size 640, 480 ");
        if (ng==1){        if (ng==1){
          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
          fprintf(ficgp,"\nunset log y");          fprintf(ficgp,"\nunset log y");
        }else if (ng==2){        }else if (ng==2){
          fprintf(ficgp,"\nset ylabel \"Probability\"\n");          fprintf(ficgp,"\nset ylabel \"Probability\"\n");
          fprintf(ficgp,"\nset log y");          fprintf(ficgp,"\nset log y");
        }else if (ng==3){        }else if (ng==3){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          fprintf(ficgp,"\nset log y");          fprintf(ficgp,"\nset log y");
        }else        }else
          fprintf(ficgp,"\nunset title ");          fprintf(ficgp,"\nunset title ");
        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        fprintf(ficgp,"\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
        i=1;        i=1;
        for(k2=1; k2<=nlstate; k2++) {        for(k2=1; k2<=nlstate; k2++) {
          k3=i;          k3=i;
          for(k=1; k<=(nlstate+ndeath); k++) {          for(k=1; k<=(nlstate+ndeath); k++) {
            if (k != k2){            if (k != k2){
              switch( ng) {              switch( ng) {
              case 1:              case 1:
                if(nagesqr==0)                if(nagesqr==0)
                  fprintf(ficgp," p%d+p%d*x",i,i+1);                  fprintf(ficgp," p%d+p%d*x",i,i+1);
                else /* nagesqr =1 */                else /* nagesqr =1 */
                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);                  fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                break;                break;
              case 2: /* ng=2 */              case 2: /* ng=2 */
                if(nagesqr==0)                if(nagesqr==0)
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                else /* nagesqr =1 */                else /* nagesqr =1 */
                    fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);                  fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
                break;                break;
              case 3:              case 3:
                if(nagesqr==0)                if(nagesqr==0)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else /* nagesqr =1 */                else /* nagesqr =1 */
                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);                  fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
                break;                break;
              }              }
              ij=1;/* To be checked else nbcode[0][0] wrong */              ij=1;/* To be checked else nbcode[0][0] wrong */
              for(j=3; j <=ncovmodel-nagesqr; j++) {              for(j=3; j <=ncovmodel-nagesqr; j++) {
                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                if(ij <=cptcovage) { /* Bug valgrind */                if(ij <=cptcovage) { /* Bug valgrind */
                  if((j-2)==Tage[ij]) { /* Bug valgrind */                  if((j-2)==Tage[ij]) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                    fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                    ij++;                    ij++;
                  }                  }
                }                }
                else                else
                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
              }              }
            }else{            }else{
              i=i-ncovmodel;              i=i-ncovmodel;
              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
                fprintf(ficgp," (1.");                fprintf(ficgp," (1.");
            }            }
                         
            if(ng != 1){            if(ng != 1){
              fprintf(ficgp,")/(1");              fprintf(ficgp,")/(1");
                             
              for(k1=1; k1 <=nlstate; k1++){               for(k1=1; k1 <=nlstate; k1++){ 
                if(nagesqr==0)                if(nagesqr==0)
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                else /* nagesqr =1 */                else /* nagesqr =1 */
                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
                                 
                ij=1;                ij=1;
                for(j=3; j <=ncovmodel-nagesqr; j++){                for(j=3; j <=ncovmodel-nagesqr; j++){
                  if(ij <=cptcovage) { /* Bug valgrind */                  if(ij <=cptcovage) { /* Bug valgrind */
                    if((j-2)==Tage[ij]) { /* Bug valgrind */                    if((j-2)==Tage[ij]) { /* Bug valgrind */
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                      /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                      /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
                      ij++;                      ij++;
                    }                    }
                  }                  }
                  else                  else
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                }                }
                fprintf(ficgp,")");                fprintf(ficgp,")");
              }              }
              fprintf(ficgp,")");              fprintf(ficgp,")");
              if(ng ==2)              if(ng ==2)
                fprintf(ficgp," t \"p%d%d\" ", k2,k);                fprintf(ficgp," t \"p%d%d\" ", k2,k);
              else /* ng= 3 */              else /* ng= 3 */
                fprintf(ficgp," t \"i%d%d\" ", k2,k);                fprintf(ficgp," t \"i%d%d\" ", k2,k);
            }else{ /* end ng <> 1 */            }else{ /* end ng <> 1 */
              if( k !=k2) /* logit p11 is hard to draw */              if( k !=k2) /* logit p11 is hard to draw */
                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);                fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
            }            }
            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
              fprintf(ficgp,",");              fprintf(ficgp,",");
            if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))            if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
              fprintf(ficgp,",");              fprintf(ficgp,",");
            i=i+ncovmodel;            i=i+ncovmodel;
          } /* end k */          } /* end k */
        } /* end k2 */        } /* end k2 */
        fprintf(ficgp,"\n set out\n");        fprintf(ficgp,"\n set out\n");
      } /* end jk */      } /* end jk */
    } /* end ng */    } /* end ng */
  /* avoid: */    /* avoid: */
    fflush(ficgp);     fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
 /*************** Moving average **************/  /*************** Moving average **************/
 /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */  /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
 int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){   int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
         
   int i, cpt, cptcod;     int i, cpt, cptcod;
   int modcovmax =1;     int modcovmax =1;
   int mobilavrange, mob;     int mobilavrange, mob;
   int iage=0;     int iage=0;
   
   double sum=0.;     double sum=0.;
   double age;     double age;
   double *sumnewp, *sumnewm;     double *sumnewp, *sumnewm;
   double *agemingood, *agemaxgood; /* Currently identical for all covariates */     double *agemingood, *agemaxgood; /* Currently identical for all covariates */
       
       
   /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */     /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */
         /*                 a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */     /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */
   
   sumnewp = vector(1,ncovcombmax);     sumnewp = vector(1,ncovcombmax);
   sumnewm = vector(1,ncovcombmax);     sumnewm = vector(1,ncovcombmax);
   agemingood = vector(1,ncovcombmax);        agemingood = vector(1,ncovcombmax);  
   agemaxgood = vector(1,ncovcombmax);     agemaxgood = vector(1,ncovcombmax);
   
   for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                 sumnewm[cptcod]=0.;       sumnewm[cptcod]=0.;
                 sumnewp[cptcod]=0.;       sumnewp[cptcod]=0.;
                 agemingood[cptcod]=0;       agemingood[cptcod]=0;
                 agemaxgood[cptcod]=0;       agemaxgood[cptcod]=0;
         }     }
   if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
       
   if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     if(mobilav==1) mobilavrange=5; /* default */       if(mobilav==1) mobilavrange=5; /* default */
     else mobilavrange=mobilav;       else mobilavrange=mobilav;
     for (age=bage; age<=fage; age++)       for (age=bage; age<=fage; age++)
       for (i=1; i<=nlstate;i++)         for (i=1; i<=nlstate;i++)
                                 for (cptcod=1;cptcod<=ncovcombmax;cptcod++)           for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
                                         mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     /* We keep the original values on the extreme ages bage, fage and for        /* We keep the original values on the extreme ages bage, fage and for 
        fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
        we use a 5 terms etc. until the borders are no more concerned.           we use a 5 terms etc. until the borders are no more concerned. 
     */        */ 
     for (mob=3;mob <=mobilavrange;mob=mob+2){       for (mob=3;mob <=mobilavrange;mob=mob+2){
       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
                                 for (i=1; i<=nlstate;i++){           for (i=1; i<=nlstate;i++){
                                         for (cptcod=1;cptcod<=ncovcombmax;cptcod++){             for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
                                                 mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                                                 for (cpt=1;cpt<=(mob-1)/2;cpt++){               for (cpt=1;cpt<=(mob-1)/2;cpt++){
                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                                                         mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                                                 }               }
                                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
                                         }             }
                                 }           }
       }/* end age */         }/* end age */
     }/* end mob */       }/* end mob */
   }else     }else
     return -1;       return -1;
   for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
     /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
     agemingood[cptcod]=fage-(mob-1)/2;       if(invalidvarcomb[cptcod]){
     for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */         printf("\nCombination (%d) ignored because no cases \n",cptcod); 
       sumnewm[cptcod]=0.;         continue;
       for (i=1; i<=nlstate;i++){       }
         sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];  
       }       agemingood[cptcod]=fage-(mob-1)/2;
       if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */       for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
                                 agemingood[cptcod]=age;         sumnewm[cptcod]=0.;
       }else{ /* bad */         for (i=1; i<=nlstate;i++){
                                 for (i=1; i<=nlstate;i++){           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                                         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];         }
                                 } /* i */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
       } /* end bad */           agemingood[cptcod]=age;
     }/* age */         }else{ /* bad */
     sum=0.;           for (i=1; i<=nlstate;i++){
     for (i=1; i<=nlstate;i++){             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
       sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];           } /* i */
     }         } /* end bad */
     if(fabs(sum - 1.) > 1.e-3) { /* bad */       }/* age */
       printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);       sum=0.;
       /* for (i=1; i<=nlstate;i++){ */       for (i=1; i<=nlstate;i++){
       /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */         sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
       /* } /\* i *\/ */       }
     } /* end bad */       if(fabs(sum - 1.) > 1.e-3) { /* bad */
     /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
                 /* From youngest, finding the oldest wrong */         /* for (i=1; i<=nlstate;i++){ */
                 agemaxgood[cptcod]=bage+(mob-1)/2;         /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
                 for (age=bage+(mob-1)/2; age<=fage; age++){         /* } /\* i *\/ */
                         sumnewm[cptcod]=0.;       } /* end bad */
                         for (i=1; i<=nlstate;i++){       /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
                                 sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];       /* From youngest, finding the oldest wrong */
                         }       agemaxgood[cptcod]=bage+(mob-1)/2;
                         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */       for (age=bage+(mob-1)/2; age<=fage; age++){
                                 agemaxgood[cptcod]=age;         sumnewm[cptcod]=0.;
                         }else{ /* bad */         for (i=1; i<=nlstate;i++){
                                 for (i=1; i<=nlstate;i++){           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
                                         mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];         }
                                 } /* i */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
                         } /* end bad */           agemaxgood[cptcod]=age;
                 }/* age */         }else{ /* bad */
                 sum=0.;           for (i=1; i<=nlstate;i++){
                 for (i=1; i<=nlstate;i++){             mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                         sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];           } /* i */
                 }         } /* end bad */
                 if(fabs(sum - 1.) > 1.e-3) { /* bad */       }/* age */
                         printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);       sum=0.;
                         /* for (i=1; i<=nlstate;i++){ */       for (i=1; i<=nlstate;i++){
                         /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */         sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                         /* } /\* i *\/ */       }
                 } /* end bad */       if(fabs(sum - 1.) > 1.e-3) { /* bad */
                          printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
                 for (age=bage; age<=fage; age++){         /* for (i=1; i<=nlstate;i++){ */
                         printf("%d %d ", cptcod, (int)age);         /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
                         sumnewp[cptcod]=0.;         /* } /\* i *\/ */
                         sumnewm[cptcod]=0.;       } /* end bad */
                         for (i=1; i<=nlstate;i++){                  
                                 sumnewp[cptcod]+=probs[(int)age][i][cptcod];       for (age=bage; age<=fage; age++){
                                 sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];         printf("%d %d ", cptcod, (int)age);
                                 /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */         sumnewp[cptcod]=0.;
                         }         sumnewm[cptcod]=0.;
                         /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */         for (i=1; i<=nlstate;i++){
                 }           sumnewp[cptcod]+=probs[(int)age][i][cptcod];
                 /* printf("\n"); */           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
     /* } */           /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
     /* brutal averaging */         }
     for (i=1; i<=nlstate;i++){         /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
       for (age=1; age<=bage; age++){       }
                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];       /* printf("\n"); */
                                 /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /* } */
       }        /* brutal averaging */
       for (age=fage; age<=AGESUP; age++){       for (i=1; i<=nlstate;i++){
                                 mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];         for (age=1; age<=bage; age++){
                                 /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */           mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
       }           /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
     } /* end i status */         }        
     for (i=nlstate+1; i<=nlstate+ndeath;i++){         for (age=fage; age<=AGESUP; age++){
       for (age=1; age<=AGESUP; age++){           mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
                                 /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/           /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
                                 mobaverage[(int)age][i][cptcod]=0.;         }
       }       } /* end i status */
     }       for (i=nlstate+1; i<=nlstate+ndeath;i++){
   }/* end cptcod */         for (age=1; age<=AGESUP; age++){
   free_vector(sumnewm,1, ncovcombmax);           /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
   free_vector(sumnewp,1, ncovcombmax);           mobaverage[(int)age][i][cptcod]=0.;
   free_vector(agemaxgood,1, ncovcombmax);         }
   free_vector(agemingood,1, ncovcombmax);       }
   return 0;     }/* end cptcod */
 }/* End movingaverage */     free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
      free_vector(agemaxgood,1, ncovcombmax);
      free_vector(agemingood,1, ncovcombmax);
      return 0;
    }/* End movingaverage */
     
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
Line 7148  int readdata(char datafile[], int firsto Line 7190  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i=0, j=0, n=0;    int i=0, j=0, n=0, iv=0;
     int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   int lstra;  
   
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
Line 7180  int readdata(char datafile[], int firsto Line 7223  int readdata(char datafile[], int firsto
     }      }
     trimbb(linetmp,line); /* Trims multiple blanks in line */      trimbb(linetmp,line); /* Trims multiple blanks in line */
     strcpy(line, linetmp);      strcpy(line, linetmp);
         
       /* Loops on waves */
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
         for (iv=nqtv;iv>=1;iv--){  /* Loop  on time varying quantitative variables */
                                   cutv(stra, strb, line, ' '); 
                                   if(strb[0]=='.') { /* Missing value */
                                           lval=-1;
                                   }else{
                                           errno=0;
                                           /* what_kind_of_number(strb); */
                                           dval=strtod(strb,&endptr); 
                                           /* if( strb[0]=='\0' || (*endptr != '\0')){ */
                                           /* if(strb != endptr && *endptr == '\0') */
                                           /*    dval=dlval; */
                                           /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                                           if( strb[0]=='\0' || (*endptr != '\0')){
                                                   printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
                                                   fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
                                                   return 1;
                                           }
                                           cotqvar[j][iv][i]=dval; 
                                   }
                                   strcpy(line,stra);
         }/* end loop ntqv */
                           
         for (iv=ntv;iv>=1;iv--){  /* Loop  on time varying dummies */
                                   cutv(stra, strb, line, ' '); 
                                   if(strb[0]=='.') { /* Missing value */
                                           lval=-1;
                                   }else{
                                           errno=0;
                                           lval=strtol(strb,&endptr,10); 
                                           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
                                           if( strb[0]=='\0' || (*endptr != '\0')){
                                                   printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
                                                   fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
                                                   return 1;
                                           }
                                   }
                                   if(lval <-1 || lval >1){
                                           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                                                                 \
    build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
           V1=1 V2=0 for (2) \n                                                                                                                                                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                                                                                                                \
    Exiting.\n",lval,linei, i,line,j);
                                           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n                                                                 \
    build V1=0 V2=0 for the reference value (1),\n                                                                                                 \
           V1=1 V2=0 for (2) \n                                                                                                                                                                            \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n                                \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
                                           return 1;
                                   }
                                   cotvar[j][iv][i]=(double)(lval);
                                   strcpy(line,stra);
         }/* end loop ntv */
   
         /* Statuses  at wave */
       cutv(stra, strb, line, ' ');         cutv(stra, strb, line, ' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing value */
         lval=-1;                                  lval=-1;
       }else{        }else{
         errno=0;                                  errno=0;
         lval=strtol(strb,&endptr,10);                                   lval=strtol(strb,&endptr,10); 
       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/                                  /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){                                  if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);                                          printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);                                          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
           return 1;                                          return 1;
         }                                  }
       }        }
        
       s[j][i]=lval;        s[j][i]=lval;
         
         /* Date of Interview */
       strcpy(line,stra);        strcpy(line,stra);
       cutv(stra, strb,line,' ');        cutv(stra, strb,line,' ');
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){        if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }        }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){        else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;                                  month=99;
         year=9999;                                  year=9999;
       }else{        }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);                                  printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);                                  fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
         return 1;                                  return 1;
       }        }
       anint[j][i]= (double) year;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month; 
       strcpy(line,stra);        strcpy(line,stra);
     } /* ENd Waves */      } /* End loop on waves */
       
       /* Date of death */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
Line 7223  int readdata(char datafile[], int firsto Line 7331  int readdata(char datafile[], int firsto
       year=9999;        year=9999;
     }else{      }else{
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);                          fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;                          return 1;
     }      }
     andc[i]=(double) year;       andc[i]=(double) year; 
     moisdc[i]=(double) month;       moisdc[i]=(double) month; 
     strcpy(line,stra);      strcpy(line,stra);
           
       /* Date of birth */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
Line 7239  int readdata(char datafile[], int firsto Line 7348  int readdata(char datafile[], int firsto
     }else{      }else{
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;                          return 1;
     }      }
     if (year==9999) {      if (year==9999) {
       printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);        printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
       fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);        fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
         return 1;                          return 1;
   
     }      }
     annais[i]=(double)(year);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month); 
     strcpy(line,stra);      strcpy(line,stra);
       
       /* Sample weight */
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     errno=0;      errno=0;
     dval=strtod(strb,&endptr);       dval=strtod(strb,&endptr); 
Line 7262  int readdata(char datafile[], int firsto Line 7372  int readdata(char datafile[], int firsto
     }      }
     weight[i]=dval;       weight[i]=dval; 
     strcpy(line,stra);      strcpy(line,stra);
   
       for (iv=nqv;iv>=1;iv--){  /* Loop  on fixed quantitative variables */
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing value */
                                   lval=-1;
         }else{
                                   errno=0;
                                   /* what_kind_of_number(strb); */
                                   dval=strtod(strb,&endptr);
                                   /* if(strb != endptr && *endptr == '\0') */
                                   /*   dval=dlval; */
                                   /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
                                   if( strb[0]=='\0' || (*endptr != '\0')){
                                           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
                                           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
                                           return 1;
                                   }
                                   coqvar[iv][i]=dval; 
         }
         strcpy(line,stra);
       }/* end loop nqv */
           
       /* Covariate values */
     for (j=ncovcol;j>=1;j--){      for (j=ncovcol;j>=1;j--){
       cutv(stra, strb,line,' ');         cutv(stra, strb,line,' '); 
       if(strb[0]=='.') { /* Missing status */        if(strb[0]=='.') { /* Missing covariate value */
         lval=-1;                                  lval=-1;
       }else{        }else{
         errno=0;                                  errno=0;
         lval=strtol(strb,&endptr,10);                                   lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){                                  if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);                                          printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);                                          fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
           return 1;                                          return 1;
         }                                  }
       }        }
       if(lval <-1 || lval >1){        if(lval <-1 || lval >1){
         printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \                                  printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n \   For example, for multinomial values like 1, 2 and 3,\n \
Line 7286  int readdata(char datafile[], int firsto Line 7418  int readdata(char datafile[], int firsto
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
  output of IMaCh is often meaningless.\n \   output of IMaCh is often meaningless.\n \
  Exiting.\n",lval,linei, i,line,j);   Exiting.\n",lval,linei, i,line,j);
         fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \                                  fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
  Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
  for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \   for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
  For example, for multinomial values like 1, 2 and 3,\n \   For example, for multinomial values like 1, 2 and 3,\n \
Line 7295  int readdata(char datafile[], int firsto Line 7427  int readdata(char datafile[], int firsto
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \   and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
  output of IMaCh is often meaningless.\n \   output of IMaCh is often meaningless.\n \
  Exiting.\n",lval,linei, i,line,j);fflush(ficlog);   Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
         return 1;                                  return 1;
       }        }
       covar[j][i]=(double)(lval);        covar[j][i]=(double)(lval);
       strcpy(line,stra);        strcpy(line,stra);
Line 7319  int readdata(char datafile[], int firsto Line 7451  int readdata(char datafile[], int firsto
     
   return (0);    return (0);
   /* endread: */    /* endread: */
     printf("Exiting readdata: ");          printf("Exiting readdata: ");
     fclose(fic);          fclose(fic);
     return (1);          return (1);
   
   
   
 }  }
   
 void removespace(char *str) {  void removespace(char *str) {
   char *p1 = str, *p2 = str;    char *p1 = str, *p2 = str;
   do    do
Line 7456  int decodemodel ( char model[], int last Line 7586  int decodemodel ( char model[], int last
         Tvar[k]=0;          Tvar[k]=0;
       cptcovage=0;        cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'                                   cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                          modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */                                                                                                                                                                    modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */                                  if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                                  /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/                                  /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */                                  if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */                                          cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */                                          if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */                                                  /* covar is not filled and then is empty */
             cptcovprod--;                                                  cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */                                                  cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */                                                  Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
             cptcovage++; /* Sums the number of covariates which include age as a product */                                                  cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */                                                  Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/                                                  /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */                                          } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;                                                  cptcovprod--;
             cutl(stre,strb,strc,'V');                                                  cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);                                                  Tvar[k]=atoi(stre);
             cptcovage++;                                                  cptcovage++;
             Tage[cptcovage]=k;                                                  Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/                                          } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */                                                  /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;                                                  cptcovn++;
             cptcovprodnoage++;k1++;                                                  cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/                                                  cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but                                                  Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                    because this model-covariate is a construction we invent a new column                                                                                                                                           because this model-covariate is a construction we invent a new column
                                    ncovcol + k1                                                                                                                                           ncovcol + k1
                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                                                                                                                           If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                                                                                                                           Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */                                                  cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */                                                  Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/                                                  Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/                                                  Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;                                                  k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */                                                  Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */                                                  Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){                                                  for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of                                                          /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */                                                                   covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];                                                          covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }                                                  }
           } /* End age is not in the model */                                          } /* End age is not in the model */
         } /* End if model includes a product */                                  } /* End if model includes a product */
         else { /* no more sum */                                  else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                                          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/                                          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');                                          cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */                                          ks++; /**< Number of simple covariates */
           cptcovn++;                                          cptcovn++;
           Tvar[k]=atoi(strd);                                          Tvar[k]=atoi(strd);
         }                                  }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */                                   strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/                                          scanf("%d",i);*/
       } /* end of loop + on total covariates */        } /* end of loop + on total covariates */
     } /* end if strlen(modelsave == 0) age*age might exist */      } /* end if strlen(modelsave == 0) age*age might exist */
   } /* end if strlen(model == 0) */    } /* end if strlen(model == 0) */
Line 8131  int hPijx(double *p, int bage, int fage) Line 8261  int hPijx(double *p, int bage, int fage)
     for(j=1;j<=cptcoveff;j++)      for(j=1;j<=cptcoveff;j++)
       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     fprintf(ficrespijb,"******\n");      fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;
       }
           
     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */      /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */      for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
Line 8445  int main(int argc, char *argv[]) Line 8579  int main(int argc, char *argv[])
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \    if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                         &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){                          &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
     if (num_filled != 8) {      if (num_filled != 11) {
       printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");        printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
       printf("but line=%s\n",line);        printf("but line=%s\n",line);
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);      printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
   }    }
   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
Line 8489  int main(int argc, char *argv[]) Line 8623  int main(int argc, char *argv[])
   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */    /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
   /* numlinepar=numlinepar+3; /\* In general *\/ */    /* numlinepar=numlinepar+3; /\* In general *\/ */
   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */    /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
   fflush(ficlog);    fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */    /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
Line 8519  int main(int argc, char *argv[]) Line 8653  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);  /**< used in readdata */
     cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< used in readdata */
     cotqvar=ma3x(1,maxwav,1,ntqv,1,n);  /**< used in readdata */
   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 8786  Please run with mle=-1 to get a correct Line 8923  Please run with mle=-1 to get a correct
 /* Main decodemodel */  /* Main decodemodel */
   
   
   if(decodemodel(model, lastobs) == 1)    if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3  = {4, 3, 5}*/
     goto end;      goto end;
   
   if((double)(lastobs-imx)/(double)imx > 1.10){    if((double)(lastobs-imx)/(double)imx > 1.10){
Line 9014  Title=%s <br>Datafile=%s Firstpass=%d La Line 9151  Title=%s <br>Datafile=%s Firstpass=%d La
                  and for any valid combination of covariates                   and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart,    \
               firstpass, lastpass,  stepm,  weightopt, model);                                                          firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
Line 9043  Interval (in months) between two waves: Line 9180  Interval (in months) between two waves:
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
     dcwave=ivector(1,n);      dcwave=ivector(1,n);
                    
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
       for (m=firstpass; m<=lastpass; m++)        for (m=firstpass; m<=lastpass; m++)
Line 9543  Please run with mle=-1 to get a correct Line 9680  Please run with mle=-1 to get a correct
     ungetc(c,ficpar);      ungetc(c,ficpar);
           
     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);      fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
     fprintf(ficparo,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     fprintf(ficlog,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     fprintf(ficres,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           
           
Line 9648  Please run with mle=-1 to get a correct Line 9785  Please run with mle=-1 to get a correct
       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);        back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
       fclose(ficresplb);        fclose(ficresplb);
   
       /* hBijx(p, bage, fage, mobaverage); */        hBijx(p, bage, fage, mobaverage);
       /* fclose(ficrespijb); */        fclose(ficrespijb);
       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */        free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
   
       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,        /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
Line 9893  Please run with mle=-1 to get a correct Line 10030  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,ntqv,1,n);
       free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
       free_matrix(coqvar,1,maxwav,1,n);
     free_matrix(covar,0,NCOVMAX,1,n);      free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);      free_matrix(matcov,1,npar,1,npar);
     free_matrix(hess,1,npar,1,npar);      free_matrix(hess,1,npar,1,npar);

Removed from v.1.221  
changed lines
  Added in v.1.223


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