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Diff for /imach/src/imach.c between versions 1.245 and 1.254

version 1.245, 2016/09/02 07:25:01 version 1.254, 2017/03/08 07:13:00
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.254  2017/03/08 07:13:00  brouard
     Summary: Fixing data parameter line
   
     Revision 1.253  2016/12/15 11:59:41  brouard
     Summary: 0.99 in progress
   
     Revision 1.252  2016/09/15 21:15:37  brouard
     *** empty log message ***
   
     Revision 1.251  2016/09/15 15:01:13  brouard
     Summary: not working
   
     Revision 1.250  2016/09/08 16:07:27  brouard
     Summary: continue
   
     Revision 1.249  2016/09/07 17:14:18  brouard
     Summary: Starting values from frequencies
   
     Revision 1.248  2016/09/07 14:10:18  brouard
     *** empty log message ***
   
     Revision 1.247  2016/09/02 11:11:21  brouard
     *** empty log message ***
   
     Revision 1.246  2016/09/02 08:49:22  brouard
     *** empty log message ***
   
   Revision 1.245  2016/09/02 07:25:01  brouard    Revision 1.245  2016/09/02 07:25:01  brouard
   *** empty log message ***    *** empty log message ***
   
Line 110 Line 137
   Author: Nicolas Brouard    Author: Nicolas Brouard
   
   Revision 1.210  2015/11/18 17:41:20  brouard    Revision 1.210  2015/11/18 17:41:20  brouard
   Summary: Start working on projected prevalences    Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
   
   Revision 1.209  2015/11/17 22:12:03  brouard  
   Summary: Adding ftolpl parameter    Summary: Adding ftolpl parameter
   Author: N Brouard    Author: N Brouard
   
Line 900  typedef struct { Line 925  typedef struct {
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
 #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */  #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
Line 2581  Earliest age to start was %d-%d=%d, ncvl Line 2606  Earliest age to start was %d-%d=%d, ncvl
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j,k;
     int first=0;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
Line 2706  Earliest age to start was %d-%d=%d, ncvl Line 2732  Earliest age to start was %d-%d=%d, ncvl
     }      }
   } /* age loop */    } /* age loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\    if(first){
       first=1;
       printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
   Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
     }
     fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
 Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   free_vector(min,1,nlstate);    free_vector(min,1,nlstate);
Line 3593  double funcone( double *x) Line 3624  double funcone( double *x)
       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
         /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
         /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]          /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           and mw[mi+1][i]. dh depends on stepm.*/            and mw[mi+1][i]. dh depends on stepm.*/
         newm=savm;          newm=savm;
         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
         cov[2]=agexact;          cov[2]=agexact;
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= agexact*agexact;            cov[3]= agexact*agexact;
Line 3649  double funcone( double *x) Line 3681  double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\          fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
Line 4007  double hessij( double x[], double **hess Line 4039  double hessij( double x[], double **hess
       kmax=kmax+10;        kmax=kmax+10;
     }      }
     if(kmax >=10 || firstime ==1){      if(kmax >=10 || firstime ==1){
       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);        printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);        fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }      }
Line 4163  void pstamp(FILE *fichier) Line 4195  void pstamp(FILE *fichier)
   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
   int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
   
     /* y=a+bx regression */
     double   sumx = 0.0;                        /* sum of x                      */
     double   sumx2 = 0.0;                       /* sum of x**2                   */
     double   sumxy = 0.0;                       /* sum of x * y                  */
     double   sumy = 0.0;                        /* sum of y                      */
     double   sumy2 = 0.0;                       /* sum of y**2                   */
     double   sume2; /* sum of square or residuals */
     double yhat;
     
     double denom=0;
     int i;
     int ne=*no;
     
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       sumx  += x[i];       
       sumx2 += x[i]*x[i];  
       sumxy += x[i] * y[i];
       sumy  += y[i];      
       sumy2 += y[i]*y[i]; 
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     
     denom = (ne * sumx2 - sumx*sumx);
     if (denom == 0) {
       // vertical, slope m is infinity
       *b = INFINITY;
       *a = 0;
       if (r) *r = 0;
       return 1;
     }
     
     *b = (ne * sumxy  -  sumx * sumy) / denom;
     *a = (sumy * sumx2  -  sumx * sumxy) / denom;
     if (r!=NULL) {
       *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
         sqrt((sumx2 - sumx*sumx/ne) *
              (sumy2 - sumy*sumy/ne));
     }
     *no=ne;
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       yhat = y[i] - *a -*b* x[i];
       sume2  += yhat * yhat ;       
       
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     *sb = sqrt(sume2/(ne-2)/(sumx2 - sumx * sumx /ne));
     *sa= *sb * sqrt(sumx2/ne);
     
     return 0; 
   }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \  void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies */  {  /* Some frequencies as well as proposing some starting values */
       
   int i, m, jk, j1, bool, z1,j, k, iv;    int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0;
   int iind=0, iage=0;    int iind=0, iage=0;
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
     double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */
     int no;
   double *meanq;    double *meanq;
   double **meanqt;    double **meanqt;
   double *pp, **prop, *posprop, *pospropt;    double *pp, **prop, *posprop, *pospropt;
Line 4182  void  freqsummary(char fileres[], int ia Line 4281  void  freqsummary(char fileres[], int ia
   double agebegin, ageend;    double agebegin, ageend;
           
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */     posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */     pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
Line 4226  Title=%s <br>Datafile=%s Firstpass=%d La Line 4325  Title=%s <br>Datafile=%s Firstpass=%d La
   }    }
   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
       
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);    y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   j1=0;    j1=0;
       
   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
   j=cptcoveff;  /* Only dummy covariates of the model */    j=cptcoveff;  /* Only dummy covariates of the model */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;  
       
   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:    /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
      reference=low_education V1=0,V2=0       reference=low_education V1=0,V2=0
Line 4241  Title=%s <br>Datafile=%s Firstpass=%d La Line 4341  Title=%s <br>Datafile=%s Firstpass=%d La
      high_educ               V1=0 V2=1       high_educ               V1=0 V2=1
      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff        Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
   */    */
       dateintsum=0;
   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */    k2cpt=0;
     posproptt=0.;  
     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    if(cptcoveff == 0 )
       scanf("%d", i);*/      nl=1;  /* Constant model only */
     for (i=-5; i<=nlstate+ndeath; i++)      else
       for (jk=-5; jk<=nlstate+ndeath; jk++)        nl=2;
     for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
       if(nj==1)
         j=0;  /* First pass for the constant */
       else
         j=cptcoveff; /* Other passes for the covariate values */
       first=1;
       for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
         posproptt=0.;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
         
         for (i=1; i<=nlstate; i++)  {
         for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
           freq[i][jk][m]=0;            prop[i][m]=0;
               posprop[i]=0;
     for (i=1; i<=nlstate; i++)  {          pospropt[i]=0;
       for(m=iagemin; m <= iagemax+3; m++)        }
         prop[i][m]=0;        /* for (z1=1; z1<= nqfveff; z1++) {   */
       posprop[i]=0;        /*   meanq[z1]+=0.; */
       pospropt[i]=0;        /*   for(m=1;m<=lastpass;m++){ */
     }        /*        meanqt[m][z1]=0.; */
     /* for (z1=1; z1<= nqfveff; z1++) {   */        /*   } */
     /*   meanq[z1]+=0.; */        /* } */
     /*   for(m=1;m<=lastpass;m++){ */        
     /*  meanqt[m][z1]=0.; */        /* dateintsum=0; */
     /*   } */        /* k2cpt=0; */
     /* } */        
             /* For that combination of covariate j1, we count and print the frequencies in one pass */
     dateintsum=0;        for (iind=1; iind<=imx; iind++) { /* For each individual iind */
     k2cpt=0;          bool=1;
     /* For that combination of covariate j1, we count and print the frequencies in one pass */          if(j !=0){
     for (iind=1; iind<=imx; iind++) { /* For each individual iind */            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
       bool=1;              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       if(anyvaryingduminmodel==0){ /* If All fixed covariates */                /* for (z1=1; z1<= nqfveff; z1++) {   */
         if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */                /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
           /* for (z1=1; z1<= nqfveff; z1++) {   */                /* } */
           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
           /* } */                  /* if(Tvaraff[z1] ==-20){ */
           for (z1=1; z1<=cptcoveff; z1++) {                    /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
             /* if(Tvaraff[z1] ==-20){ */                  /* }else  if(Tvaraff[z1] ==-10){ */
             /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
             /* }else  if(Tvaraff[z1] ==-10){ */                  /* }else  */
             /*   /\* sumnew+=coqvar[z1][iind]; *\/ */                  if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
             /* }else  */                    /* Tests if this individual iind responded to combination j1 (V4=1 V3=0) */
             if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){                    bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
               /* Tests if this individual iind responded to j1 (V4=1 V3=0) */                    /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
               bool=0;                       bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",                        j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                    /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/                  } /* Onlyf fixed */
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/                } /* end z1 */
             } /* Onlyf fixed */              } /* cptcovn > 0 */
           } /* end z1 */            } /* end any */
         } /* cptcovn > 0 */          }/* end j==0 */
       } /* end any */          if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */            /* for(m=firstpass; m<=lastpass; m++){ */
         /* for(m=firstpass; m<=lastpass; m++){ */            for(mi=1; mi<wav[iind];mi++){ /* For that wave */
         for(mi=1; mi<wav[iind];mi++){ /* For that wave */              m=mw[mi][iind];
           m=mw[mi][iind];              if(j!=0){
           if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
             for (z1=1; z1<=cptcoveff; z1++) {                  for (z1=1; z1<=cptcoveff; z1++) {
               if( Fixed[Tmodelind[z1]]==1){                    if( Fixed[Tmodelind[z1]]==1){
                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;                      iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */                      if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's 
                   bool=0;                                                                                        value is -1, we don't select. It differs from the 
               }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */                                                                                        constant and age model which counts them. */
                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {                        bool=0; /* not selected */
                   bool=0;                    }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                       if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                         bool=0;
                       }
                     }
                 }                  }
                 }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
               } /* end j==0 */
               /* bool =0 we keep that guy which corresponds to the combination of dummy values */
               if(bool==1){
                 /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                    and mw[mi+1][iind]. dh depends on stepm. */
                 agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
                 ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
                 if(m >=firstpass && m <=lastpass){
                   k2=anint[m][iind]+(mint[m][iind]/12.);
                   /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                   if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                   if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                   if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                     prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                   if (m<lastpass) {
                     /* if(s[m][iind]==4 && s[m+1][iind]==4) */
                     /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
                     if(s[m][iind]==-1)
                       printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                     freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                     /* if((int)agev[m][iind] == 55) */
                     /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
                     /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                     freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
                   }
                 } /* end if between passes */  
                 if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
                   dateintsum=dateintsum+k2; /* on all covariates ?*/
                   k2cpt++;
                   /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
               }                }
             }              }else{
           }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */                bool=1;
           /* bool =0 we keep that guy which corresponds to the combination of dummy values */              }/* end bool 2 */
           if(bool==1){            } /* end m */
             /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]          } /* end bool */
                and mw[mi+1][iind]. dh depends on stepm. */        } /* end iind = 1 to imx */
             agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/        /* prop[s][age] is feeded for any initial and valid live state as well as
             ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */           freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
             if(m >=firstpass && m <=lastpass){        
               k2=anint[m][iind]+(mint[m][iind]/12.);        
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
               if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */        pstamp(ficresp);
               if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */        if  (cptcoveff>0 && j!=0){
               if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */          printf( "\n#********** Variable "); 
                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */          fprintf(ficresp, "\n#********** Variable "); 
               if (m<lastpass) {          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */          fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
                 /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */          fprintf(ficlog, "\n#********** Variable "); 
                 if(s[m][iind]==-1)          for (z1=1; z1<=cptcoveff; z1++){
                   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));            if(!FixedV[Tvaraff[z1]]){
                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */              printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                 /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */              fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                 freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */              fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               }              fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             } /* end if between passes */                fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {            }else{
               dateintsum=dateintsum+k2;              printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               k2cpt++;              fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
               /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */              fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }              fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
           } /* end bool 2 */              fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         } /* end m */            }
       } /* end bool */          }
     } /* end iind = 1 to imx */          printf( "**********\n#");
     /* prop[s][age] is feeded for any initial and valid live state as well as          fprintf(ficresp, "**********\n#");
        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */          fprintf(ficresphtm, "**********</h3>\n");
               fprintf(ficresphtmfr, "**********</h3>\n");
               fprintf(ficlog, "**********\n");
     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        }
     pstamp(ficresp);        fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
     if  (cptcoveff>0){        for(i=1; i<=nlstate;i++) {
       fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, " Age Prev(%d)  N(%d)  N  ",i,i);
       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");         }
       fprintf(ficlog, "\n#********** Variable ");         fprintf(ficresp, "\n");
       for (z1=1; z1<=cptcoveff; z1++){        fprintf(ficresphtm, "\n");
         if(DummyV[z1]){        
           fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);        /* Header of frequency table by age */
           fprintf(ficresphtm, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);        fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
           fprintf(ficresphtmfr, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);        fprintf(ficresphtmfr,"<th>Age</th> ");
           fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);        for(jk=-1; jk <=nlstate+ndeath; jk++){
         }else{          for(m=-1; m <=nlstate+ndeath; m++){
           fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);            if(jk!=0 && m!=0)
           fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
           fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
           fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
         }  
       }  
       fprintf(ficresp, "**********\n#");  
       fprintf(ficresphtm, "**********</h3>\n");  
       fprintf(ficresphtmfr, "**********</h3>\n");  
       fprintf(ficlog, "**********\n");  
     }  
     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");  
     for(i=1; i<=nlstate;i++) {  
       fprintf(ficresp, " Age Prev(%d)  N(%d)  N  ",i,i);  
       fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);  
     }  
     fprintf(ficresp, "\n");  
     fprintf(ficresphtm, "\n");  
       
     /* Header of frequency table by age */  
     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");  
     fprintf(ficresphtmfr,"<th>Age</th> ");  
     for(jk=-1; jk <=nlstate+ndeath; jk++){  
       for(m=-1; m <=nlstate+ndeath; m++){  
         if(jk!=0 && m!=0)  
           fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);  
       }  
     }  
     fprintf(ficresphtmfr, "\n");  
       
     /* For each age */  
     for(iage=iagemin; iage <= iagemax+3; iage++){  
       fprintf(ficresphtm,"<tr>");  
       if(iage==iagemax+1){  
         fprintf(ficlog,"1");  
         fprintf(ficresphtmfr,"<tr><th>0</th> ");  
       }else if(iage==iagemax+2){  
         fprintf(ficlog,"0");  
         fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");  
       }else if(iage==iagemax+3){  
         fprintf(ficlog,"Total");  
         fprintf(ficresphtmfr,"<tr><th>Total</th> ");  
       }else{  
         if(first==1){  
           first=0;  
           printf("See log file for details...\n");  
         }          }
         fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);  
         fprintf(ficlog,"Age %d", iage);  
       }        }
       for(jk=1; jk <=nlstate ; jk++){        fprintf(ficresphtmfr, "\n");
         for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      
           pp[jk] += freq[jk][m][iage];         /* For each age */
       }        for(iage=iagemin; iage <= iagemax+3; iage++){
       for(jk=1; jk <=nlstate ; jk++){          fprintf(ficresphtm,"<tr>");
         for(m=-1, pos=0; m <=0 ; m++)          if(iage==iagemax+1){
           pos += freq[jk][m][iage];            fprintf(ficlog,"1");
         if(pp[jk]>=1.e-10){            fprintf(ficresphtmfr,"<tr><th>0</th> ");
           }else if(iage==iagemax+2){
             fprintf(ficlog,"0");
             fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
           }else if(iage==iagemax+3){
             fprintf(ficlog,"Total");
             fprintf(ficresphtmfr,"<tr><th>Total</th> ");
           }else{
           if(first==1){            if(first==1){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              first=0;
               printf("See log file for details...\n");
             }
             fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
             fprintf(ficlog,"Age %d", iage);
           }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][iage]; 
           }
           for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][iage];
             if(pp[jk]>=1.e-10){
               if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
               if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           }            }
           fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
         }else{  
           if(first==1)  
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
           fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
         }          }
       }  
         
       for(jk=1; jk <=nlstate ; jk++){   
         /* posprop[jk]=0; */  
         for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */  
           pp[jk] += freq[jk][m][iage];  
       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */  
               
       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){ 
         pos += pp[jk]; /* pos is the total number of transitions until this age */            /* posprop[jk]=0; */
         posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
               pp[jk] += freq[jk][m][iage];
           }       /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
         
           for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
             pos += pp[jk]; /* pos is the total number of transitions until this age */
             posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
                                               from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
             pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
                                           from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */                                            from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
         pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state  
                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */  
       }  
       for(jk=1; jk <=nlstate ; jk++){  
         if(pos>=1.e-5){  
           if(first==1)  
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
         }else{  
           if(first==1)  
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
           fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
         }          }
         if( iage <= iagemax){          for(jk=1; jk <=nlstate ; jk++){
           if(pos>=1.e-5){            if(pos>=1.e-5){
             fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);              if(first==1)
             fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             /*probs[iage][jk][j1]= pp[jk]/pos;*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/            }else{
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
             if( iage <= iagemax){
               if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
                 /*probs[iage][jk][j1]= pp[jk]/pos;*/
                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
               }
               else{
                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
               }
           }            }
           else{            pospropt[jk] +=posprop[jk];
             fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);          } /* end loop jk */
             fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);          /* pospropt=0.; */
           for(jk=-1; jk <=nlstate+ndeath; jk++){
             for(m=-1; m <=nlstate+ndeath; m++){
               if(freq[jk][m][iage] !=0 ) { /* minimizing output */
                 if(first==1){
                   printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
                 }
                 /* printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); */
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
               }
               if(jk!=0 && m!=0)
                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
           }            }
           } /* end loop jk */
           posproptt=0.; 
           for(jk=1; jk <=nlstate; jk++){
             posproptt += pospropt[jk];
           }
           fprintf(ficresphtmfr,"</tr>\n ");
           if(iage <= iagemax){
             fprintf(ficresp,"\n");
             fprintf(ficresphtm,"</tr>\n");
         }          }
         pospropt[jk] +=posprop[jk];          if(first==1)
       } /* end loop jk */            printf("Others in log...\n");
       /* pospropt=0.; */          fprintf(ficlog,"\n");
       for(jk=-1; jk <=nlstate+ndeath; jk++){        } /* end loop age iage */
         for(m=-1; m <=nlstate+ndeath; m++){        fprintf(ficresphtm,"<tr><th>Tot</th>");
           if(freq[jk][m][iage] !=0 ) { /* minimizing output */        for(jk=1; jk <=nlstate ; jk++){
             if(first==1){          if(posproptt < 1.e-5){
               printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);            fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt); 
           }else{
             fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);  
           }
         }
         fprintf(ficresphtm,"</tr>\n");
         fprintf(ficresphtm,"</table>\n");
         fprintf(ficresphtmfr,"</table>\n");
         if(posproptt < 1.e-5){
           fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
           fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
           fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
           invalidvarcomb[j1]=1;
         }else{
           fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
           invalidvarcomb[j1]=0;
         }
         fprintf(ficresphtmfr,"</table>\n");
         fprintf(ficlog,"\n");
         if(j!=0){
           printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
           for(i=1,jk=1; i <=nlstate; i++){
             for(k=1; k <=(nlstate+ndeath); k++){
               if (k != i) {
                 for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */
                   if(jj==1){  /* Constant case (in fact cste + age) */
                     if(j1==1){ /* All dummy covariates to zero */
                       freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
                       freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
                       printf("%d%d ",i,k);
                       fprintf(ficlog,"%d%d ",i,k);
                       printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
                       fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                       pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                     }
                   }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
                     for(iage=iagemin; iage <= iagemax+3; iage++){
                       x[iage]= (double)iage;
                       y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
                       /* printf("i=%d, k=%d, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */
                     }
                     linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
                     pstart[jk]=b;
                     pstart[jk-1]=a;
                   }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ 
                     printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     pstart[jk]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
                     printf("%d%d ",i,k);
                     fprintf(ficlog,"%d%d ",i,k);
                     printf("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
                   }else{ /* Other cases, like quantitative fixed or varying covariates */
                     ;
                   }
                   /* printf("%12.7f )", param[i][jj][k]); */
                   /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                   jk++; 
                 } /* end jj */
               } /* end k!= i */
             } /* end k */
           } /* end i, jk */
         } /* end j !=0 */
       } /* end selected combination of covariate j1 */
       if(j==0){ /* We can estimate starting values from the occurences in each case */
         printf("#Freqsummary: Starting values for the constants:\n");
         fprintf(ficlog,"\n");
         for(i=1,jk=1; i <=nlstate; i++){
           for(k=1; k <=(nlstate+ndeath); k++){
             if (k != i) {
               printf("%d%d ",i,k);
               fprintf(ficlog,"%d%d ",i,k);
               for(jj=1; jj <=ncovmodel; jj++){
                 pstart[jk]=p[jk]; /* Setting pstart to p values by default */
                 if(jj==1){ /* Age has to be done */
                   pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                   printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                 }
                 /* printf("%12.7f )", param[i][jj][k]); */
                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                 jk++; 
             }              }
             fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);              printf("\n");
               fprintf(ficlog,"\n");
           }            }
           if(jk!=0 && m!=0)  
             fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);  
         }          }
       } /* end loop jk */  
       posproptt=0.;   
       for(jk=1; jk <=nlstate; jk++){  
         posproptt += pospropt[jk];  
       }  
       fprintf(ficresphtmfr,"</tr>\n ");  
       if(iage <= iagemax){  
         fprintf(ficresp,"\n");  
         fprintf(ficresphtm,"</tr>\n");  
       }        }
       if(first==1)        printf("#Freqsummary\n");
         printf("Others in log...\n");  
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
     } /* end loop age iage */        for(jk=-1; jk <=nlstate+ndeath; jk++){
     fprintf(ficresphtm,"<tr><th>Tot</th>");          for(m=-1; m <=nlstate+ndeath; m++){
     for(jk=1; jk <=nlstate ; jk++){            /* param[i]|j][k]= freq[jk][m][iagemax+3] */
       if(posproptt < 1.e-5){            printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
         fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
       }else{            /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */
         fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);                /*   printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
             /*   fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
             /* } */
           }
         } /* end loop jk */
         
         printf("\n");
         fprintf(ficlog,"\n");
       } /* end j=0 */
     } /* end j */
   
     if(mle == -2){  /* We want to use these values as starting values */
       for(i=1, jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j!=i){
             /*ca[0]= k+'a'-1;ca[1]='\0';*/
             printf("%1d%1d",i,j);
             fprintf(ficparo,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               /*    printf(" %lf",param[i][j][k]); */
               /*    fprintf(ficparo," %lf",param[i][j][k]); */
               p[jk]=pstart[jk];
               printf(" %f ",pstart[jk]);
               fprintf(ficparo," %f ",pstart[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficparo,"\n");
           }
       }        }
     }      }
     fprintf(ficresphtm,"</tr>\n");    } /* end mle=-2 */
     fprintf(ficresphtm,"</table>\n");  
     fprintf(ficresphtmfr,"</table>\n");  
     if(posproptt < 1.e-5){  
       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);  
       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);  
       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);  
       invalidvarcomb[j1]=1;  
     }else{  
       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);  
       invalidvarcomb[j1]=0;  
     }  
     fprintf(ficresphtmfr,"</table>\n");  
   } /* end selected combination of covariate j1 */  
   dateintmean=dateintsum/k2cpt;     dateintmean=dateintsum/k2cpt; 
       
   fclose(ficresp);    fclose(ficresp);
Line 4519  Title=%s <br>Datafile=%s Firstpass=%d La Line 4755  Title=%s <br>Datafile=%s Firstpass=%d La
   fclose(ficresphtmfr);    fclose(ficresphtmfr);
   free_vector(meanq,1,nqfveff);    free_vector(meanq,1,nqfveff);
   free_matrix(meanqt,1,lastpass,1,nqtveff);    free_matrix(meanqt,1,lastpass,1,nqtveff);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);    free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
   free_vector(pospropt,1,nlstate);    free_vector(pospropt,1,nlstate);
   free_vector(posprop,1,nlstate);    free_vector(posprop,1,nlstate);
   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);    free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
   /* End of freqsummary */    /* End of freqsummary */
 }  }
Line 4549  void prevalence(double ***probs, double Line 4787  void prevalence(double ***probs, double
   iagemin= (int) agemin;    iagemin= (int) agemin;
   iagemax= (int) agemax;    iagemax= (int) agemax;
   /*pp=vector(1,nlstate);*/    /*pp=vector(1,nlstate);*/
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;    j1=0;
       
Line 4559  void prevalence(double ***probs, double Line 4797  void prevalence(double ***probs, double
   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+4+AGEMARGE; iage++)
         prop[i][iage]=0.0;          prop[i][iage]=0.0;
     printf("Prevalence combination of varying and fixed dummies %d\n",j1);      printf("Prevalence combination of varying and fixed dummies %d\n",j1);
     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
Line 4590  void prevalence(double ***probs, double Line 4828  void prevalence(double ***probs, double
             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+4+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);
               }                }
Line 4627  void prevalence(double ***probs, double Line 4865  void prevalence(double ***probs, double
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/    /*free_vector(pp,1,nlstate);*/
   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
 }  /* End of prevalence */  }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
Line 6170  void printinghtml(char fileresu[], char Line 6408  void printinghtml(char fileresu[], char
   
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++) /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */     for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
      if(TKresult[nres]!= k1)       if(m != 1 && TKresult[nres]!= k1)
        continue;         continue;
   
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
Line 6302  See page 'Matrix of variance-covariance Line 6540  See page 'Matrix of variance-covariance
   
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
      if(TKresult[nres]!= k1)       if(m != 1 && TKresult[nres]!= k1)
        continue;         continue;
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
Line 6398  void printinggnuplot(char fileresu[], ch Line 6636  void printinggnuplot(char fileresu[], ch
     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */      for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
         if(TKresult[nres]!= k1)          if(m != 1 && TKresult[nres]!= k1)
           continue;            continue;
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         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 */
Line 6410  void printinggnuplot(char fileresu[], ch Line 6648  void printinggnuplot(char fileresu[], ch
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv 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 */
           printf(" V%d=%d ",Tvaraff[k],vlv);            /* printf(" V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
         }          }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }                 }       
         printf("\n#\n");          /* printf("\n#\n"); */
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 6480  void printinggnuplot(char fileresu[], ch Line 6718  void printinggnuplot(char fileresu[], ch
   /*2 eme*/    /*2 eme*/
   for (k1=1; k1<= m ; k1 ++){      for (k1=1; k1<= m ; k1 ++){  
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
Line 6540  void printinggnuplot(char fileresu[], ch Line 6778  void printinggnuplot(char fileresu[], ch
   /*3eme*/    /*3eme*/
   for (k1=1; k1<= m ; k1 ++){    for (k1=1; k1<= m ; k1 ++){
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
   
       for (cpt=1; cpt<= nlstate ; cpt ++) {        for (cpt=1; cpt<= nlstate ; cpt ++) {
Line 6589  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6827  plot [%.f:%.f] \"%s\" every :::%d::%d u
   /* 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 covariate and each value */    for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
         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);
Line 6635  set ter svg size 640, 480\nunset log y\n Line 6873  set ter svg size 640, 480\nunset log y\n
   /* 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 combination if any */    for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         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);
Line 6689  set ter svg size 640, 480\nunset log y\n Line 6927  set ter svg size 640, 480\nunset log y\n
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */    for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     if(TKresult[nres]!= k1)      if(m != 1 && TKresult[nres]!= k1)
       continue;        continue;
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
               
Line 6736  set ter svg size 640, 480\nunset log y\n Line 6974  set ter svg size 640, 480\nunset log y\n
     /* CV back preval stable (period) for each covariate */      /* CV back preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
Line 6787  set ter svg size 640, 480\nunset log y\n Line 7025  set ter svg size 640, 480\nunset log y\n
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k1)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
Line 6918  set ter svg size 640, 480\nunset log y\n Line 7156  set ter svg size 640, 480\nunset log y\n
     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */      fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
     for(jk=1; jk <=m; jk++)  /* For each combination of covariate */      for(jk=1; jk <=m; jk++)  /* For each combination of covariate */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= jk)        if(m != 1 && TKresult[nres]!= jk)
         continue;          continue;
       fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);        fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
Line 7280  set ter svg size 640, 480\nunset log y\n Line 7518  set ter svg size 640, 480\nunset log y\n
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++) /* For each resultline */
   for(k=1; k<=i1;k++){    for(k=1; k<=i1;k++){
     if(TKresult[nres]!= k)      if(i1 != 1 && TKresult[nres]!= k)
       continue;        continue;
     if(invalidvarcomb[k]){      if(invalidvarcomb[k]){
       printf("\nCombination (%d) projection ignored because no cases \n",k);         printf("\nCombination (%d) projection ignored because no cases \n",k); 
Line 8231  int decoderesult ( char resultline[], in Line 8469  int decoderesult ( char resultline[], in
   if (strlen(resultsav) >1){    if (strlen(resultsav) >1){
     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
   }    }
     if(j == 0){ /* Resultline but no = */
       TKresult[nres]=0; /* Combination for the nresult and the model */
       return (0);
     }
       
   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
     printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
     fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);      fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
Line 8830  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 9073  Dummy[k] 0=dummy (0 1), 1 quantitative (
 }  }
   
 int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 {  {/* Check ages at death */
   int i, m;    int i, m;
   int firstone=0;    int firstone=0;
       
Line 9167  int prevalence_limit(double *p, double * Line 9410  int prevalence_limit(double *p, double *
   
   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */    for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
   
       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
Line 9264  int back_prevalence_limit(double *p, dou Line 9507  int back_prevalence_limit(double *p, dou
       
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)       if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
       fprintf(ficresplb,"#******");        fprintf(ficresplb,"#******");
Line 9367  int hPijx(double *p, int bage, int fage) Line 9610  int hPijx(double *p, int bage, int fage)
                 /*      k=k+1;  */                  /*      k=k+1;  */
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){      for(k=1; k<=i1;k++){
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
Line 9446  int hPijx(double *p, int bage, int fage) Line 9689  int hPijx(double *p, int bage, int fage)
   /*    k=k+1;  */    /*    k=k+1;  */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficrespijb,"\n#****** ");        fprintf(ficrespijb,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
Line 9563  int main(int argc, char *argv[]) Line 9806  int main(int argc, char *argv[])
   double **prlim;    double **prlim;
   double **bprlim;    double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
   double  *p;    double ***paramstart; /* Matrix of starting parameter values */
     double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
   double **hess; /* Hessian matrix */    double **hess; /* Hessian matrix */
   double ***delti3; /* Scale */    double ***delti3; /* Scale */
Line 9874  int main(int argc, char *argv[]) Line 10118  int main(int argc, char *argv[])
   delti=delti3[1][1];    delti=delti3[1][1];
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
   /* We could also provide initial parameters values giving by simple logistic regression 
    * only one way, that is without matrix product. We will have nlstate maximizations */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
Line 9903  int main(int argc, char *argv[]) Line 10153  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
           
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       j=0;        j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
Line 9939  run imach with mle=-1 to get a correct t Line 10190  run imach with mle=-1 to get a correct t
     }        }  
     fflush(ficlog);      fflush(ficlog);
           
     /* Reads scales values */      /* Reads parameters values */
     p=param[1][1];      p=param[1][1];
       pstart=paramstart[1][1];
           
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
Line 10205  Please run with mle=-1 to get a correct Line 10457  Please run with mle=-1 to get a correct
   */    */
   
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   /* */    /* Concatenates waves */
     
   free_vector(moisdc,1,n);    free_vector(moisdc,1,n);
   free_vector(andc,1,n);    free_vector(andc,1,n);
Line 10386  Title=%s <br>Datafile=%s Firstpass=%d La Line 10638  Title=%s <br>Datafile=%s Firstpass=%d La
   /* Calculates basic frequencies. Computes observed prevalence at single age     /* Calculates basic frequencies. Computes observed prevalence at single age 
                  and for any valid combination of covariates                   and 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, p, pstart, 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");
Line 10408  Interval (in months) between two waves: Line 10660  Interval (in months) between two waves:
   /* For mortality only */    /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(1,NDIM,1,NDIM); 
                 for(i=1;i<=NDIM;i++)      for(i=1;i<=NDIM;i++)
                         for(j=1;j<=NDIM;j++)        for(j=1;j<=NDIM;j++)
                                 ximort[i][j]=0.;          ximort[i][j]=0.;
     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
Line 10646  Please run with mle=-1 to get a correct Line 10898  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2, Real Maximization */      if(mle>=1){ /* Could be 1 or 2, Real Maximization */
       /* mlikeli uses func not funcone */        /* mlikeli uses func not funcone */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }      }
     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */      if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
Line 10861  Please run with mle=-1 to get a correct Line 11117  Please run with mle=-1 to get a correct
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                                   
     /* Other stuffs, more or less useful */          /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while(fgets(line, MAXLINE, ficpar)) {
       ungetc(c,ficpar);        /* If line starts with a # it is a comment */
       fgets(line, MAXLINE, ficpar);        if (line[0] == '#') {
       fputs(line,stdout);          numlinepar++;
       fputs(line,ficparo);          fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);  
           if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        if (num_filled != 7) {
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          goto end;
             }
     while((c=getc(ficpar))=='#' && c!= EOF){      /* fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); */
       ungetc(c,ficpar);        printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fgets(line, MAXLINE, ficpar);        fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fputs(line,stdout);        fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fputs(line,ficparo);        printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
         fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       }
   
       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
     }      }
     ungetc(c,ficpar);  
           
           
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
           
     fscanf(ficpar,"pop_based=%d\n",&popbased);      if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
     fprintf(ficlog,"pop_based=%d\n",popbased);        if (num_filled != 1) {
     fprintf(ficparo,"pop_based=%d\n",popbased);             printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     fprintf(ficres,"pop_based=%d\n",popbased);             fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
     while((c=getc(ficpar))=='#' && c!= EOF){        }
       ungetc(c,ficpar);        printf("pop_based=%d\n",popbased);
       fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"pop_based=%d\n",popbased);
       fputs(line,stdout);        fprintf(ficparo,"pop_based=%d\n",popbased);   
       fputs(line,ficres);        fprintf(ficres,"pop_based=%d\n",popbased);   
       fputs(line,ficparo);  
     }      }
     ungetc(c,ficpar);       
           while(fgets(line, MAXLINE, ficpar)) {
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);        /* If line starts with a # it is a comment */
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);        if (line[0] == '#') {
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);          numlinepar++;
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);          fputs(line,stdout);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);          fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
      /* while((c=getc(ficpar))=='#' && c!= EOF){ */
      /*    ungetc(c,ficpar); */
      /*    fgets(line, MAXLINE, ficpar); */
      /*    fputs(line,stdout); */
      /*    fputs(line,ficres); */
      /*    fputs(line,ficparo); */
      /*  } */
      /*  ungetc(c,ficpar); */
       
       /* fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj); */
       if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){
         if (num_filled != 8) {
           printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           goto end;
         }
        fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
        printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
        fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
        fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
       
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  
       fputs(line,stdout);  
       fputs(line,ficparo);  
       fputs(line,ficres);  
     }      }
     ungetc(c,ficpar);       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
       /* while((c=getc(ficpar))=='#' && c!= EOF){ */
       /*   ungetc(c,ficpar); */
       /*   fgets(line, MAXLINE, ficpar); */
       /*   fputs(line,stdout); */
       /*   fputs(line,ficparo); */
       /*   fputs(line,ficres); */
       /* } */
       /* ungetc(c,ficpar); */
           
     fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);      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);      if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
     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);        if (num_filled != 8) {
     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);          printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
           goto end;
         }
         printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
         fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
         fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
         fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           }
     /* Results */      /* Results */
     nresult=0;      nresult=0;
     while(fgets(line, MAXLINE, ficpar)) {      while(fgets(line, MAXLINE, ficpar)) {
Line 10941  Please run with mle=-1 to get a correct Line 11256  Please run with mle=-1 to get a correct
     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){      while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
       if (num_filled == 0){        if (num_filled == 0){
         resultline[0]='\0';          resultline[0]='\0';
           printf("Warning %d: no result line should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
       break;        break;
       } else if (num_filled != 1){        } else if (num_filled != 1){
         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);          printf("ERROR %d: result line should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
       }        }
       nresult++; /* Sum of resultlines */        nresult++; /* Sum of resultlines */
       printf("Result %d: result=%s\n",nresult, resultline);        printf("Result %d: result=%s\n",nresult, resultline);
Line 11115  Please run with mle=-1 to get a correct Line 11431  Please run with mle=-1 to get a correct
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
Line 11188  Please run with mle=-1 to get a correct Line 11504  Please run with mle=-1 to get a correct
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       printf("\n#****** Result for:");        printf("\n#****** Result for:");
       fprintf(ficrest,"\n#****** Result for:");        fprintf(ficrest,"\n#****** Result for:");
Line 11329  Please run with mle=-1 to get a correct Line 11645  Please run with mle=-1 to get a correct
   
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){      for(k=1; k<=i1;k++){
       if(TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficresvpl,"\n#****** ");        fprintf(ficresvpl,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
Removed from v.1.245  
changed lines
  Added in v.1.254

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