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Diff for /imach/src/imach.c between versions 1.250 and 1.259

-version 1.250, 2016/09/08 16:07:27
+version 1.259, 2017/04/04 13:01:16
  Line 1
  /* $Id$
    $State$
    $Log$
+   Revision 1.259  2017/04/04 13:01:16  brouard
+   Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
+   Revision 1.258  2017/04/03 10:17:47  brouard
+   Summary: Version 0.99r12
+   Some cleanings, conformed with updated documentation.
+   Revision 1.257  2017/03/29 16:53:30  brouard
+   Summary: Temp
+   Revision 1.256  2017/03/27 05:50:23  brouard
+   Summary: Temporary
+   Revision 1.255  2017/03/08 16:02:28  brouard
+   Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
+   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
- Line 125
+ Line 154
    Author: Nicolas 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
    Author: N Brouard
- Line 915  typedef struct {
+ Line 942  typedef struct {
  /* #include <libintl.h> */
  /* #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 "..\\gp37mgw\\wgnuplot"*/
- Line 1158  int *TvarsQind;
+ Line 1185  int *TvarsQind;
  #define MAXRESULTLINES 10
  int nresult=0;
+ int parameterline=0; /* # of the parameter (type) line */
  int TKresult[MAXRESULTLINES];
  int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
  int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
- Line 2390  void powell(double p[], double **xi, int
+ Line 2418  void powell(double p[], double **xi, int
              flatd++;
          }
          if(flatd >0){
-           printf("%d flat directions\n",flatd);
+           printf("%d flat directions: ",flatd);
-           fprintf(ficlog,"%d flat directions\n",flatd);
+           fprintf(ficlog,"%d flat directions :",flatd);
            for (j=1;j<=n;j++) {
              if(flatdir[j]>0){
                printf("%d ",j);
- Line 4119  void ludcmp(double **a, int n, int *indx
+ Line 4147  void ludcmp(double **a, int n, int *indx
      big=0.0;
      for (j=1;j<=n;j++)
        if ((temp=fabs(a[i][j])) > big) big=temp;
-     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+     if (big == 0.0){
+       printf(" Singular Hessian matrix at row %d:\n",i);
+       for (j=1;j<=n;j++) {
+         printf(" a[%d][%d]=%f,",i,j,a[i][j]);
+         fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
+       }
+       fflush(ficlog);
+       fclose(ficlog);
+       nrerror("Singular matrix in routine ludcmp");
+     }
      vv[i]=1.0/big;
    }
    for (j=1;j<=n;j++) {
- Line 4185  void pstamp(FILE *fichier)
+ Line 4222  void pstamp(FILE *fichier)
    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 ********************/
- void  freqsummary(char fileres[], double p[], 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 firstpass,  int lastpass, int stepm, int weightopt, char model[])
  {  /* Some frequencies as well as proposing some starting values */
-   int i, m, jk, j1, bool, z1,j, k, iv, jj=0;
+   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0;
    int iind=0, iage=0;
    int mi; /* Effective wave */
    int first;
    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 **meanqt;
    double *pp, **prop, *posprop, *pospropt;
- Line 4204  void  freqsummary(char fileres[], double
+ Line 4308  void  freqsummary(char fileres[], double
    double agebegin, ageend;
    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 */
    pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
- Line 4248  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4352  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);
-   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;
    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
- Line 4265  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4371  Title=%s <br>Datafile=%s Firstpass=%d La
    dateintsum=0;
    k2cpt=0;
-   for (j = 0; j <= cptcoveff; j+=cptcoveff){
+   if(cptcoveff == 0 )
-   first=1;
+     nl=1;  /* Constant model only */
-   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 */
+   else
-     posproptt=0.;
+     nl=2;
-     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+   for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
-       scanf("%d", i);*/
+     if(nj==1)
-     for (i=-5; i<=nlstate+ndeath; i++)
+       j=0;  /* First pass for the constant */
-       for (jk=-5; jk<=nlstate+ndeath; jk++)
+     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++)
-           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;
+         if(j !=0){
-     /* For that combination of covariate j1, we count and print the frequencies in one pass */
+           if(anyvaryingduminmodel==0){ /* If All fixed covariates */
-     for (iind=1; iind<=imx; iind++) { /* For each individual iind */
+             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
-       bool=1;
+               /* for (z1=1; z1<= nqfveff; z1++) {   */
-       if(j !=0){
+               /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
-       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
+               /* } */
-         if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
+               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
-           /* for (z1=1; z1<= nqfveff; z1++) {   */
+                 /* if(Tvaraff[z1] ==-20){ */
-           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
+                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
-           /* } */
+                 /* }else  if(Tvaraff[z1] ==-10){ */
-           for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
+                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
-             /* if(Tvaraff[z1] ==-20){ */
+                 /* }else  */
-             /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
+                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
-             /* }else  if(Tvaraff[z1] ==-10){ */
+                   /* Tests if this individual iind responded to combination j1 (V4=1 V3=0) */
-             /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
+                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
-             /* }else  */
+                   /* 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",
-             if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
+                      bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
-               /* Tests if this individual iind responded to combination j1 (V4=1 V3=0) */
+                      j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
-               bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
+                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
-               /* 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",
+                 } /* Onlyf fixed */
-                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
+               } /* end z1 */
-                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+             } /* cptcovn > 0 */
-               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
+           } /* end any */
-             } /* Onlyf fixed */
+         }/* end j==0 */
-           } /* end z1 */
+         if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
-         } /* cptcovn > 0 */
+           /* for(m=firstpass; m<=lastpass; m++){ */
-       } /* end any */
+           for(mi=1; mi<wav[iind];mi++){ /* For that wave */
-       }/* end j==0 */
+             m=mw[mi][iind];
-       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
+             if(j!=0){
-         /* for(m=firstpass; m<=lastpass; m++){ */
+               if(anyvaryingduminmodel==1){ /* Some are varying covariates */
-         for(mi=1; mi<wav[iind];mi++){ /* For that wave */
+                 for (z1=1; z1<=cptcoveff; z1++) {
-           m=mw[mi][iind];
+                   if( Fixed[Tmodelind[z1]]==1){
-           if(j!=0){
+                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
-           if(anyvaryingduminmodel==1){ /* Some are varying covariates */
+                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
-             for (z1=1; z1<=cptcoveff; z1++) {
+                                                                                       value is -1, we don't select. It differs from the
-               if( Fixed[Tmodelind[z1]]==1){
+                                                                                       constant and age model which counts them. */
-                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
+                       bool=0; /* not selected */
-                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
+                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
-                                                                                   value is -1, we don't select. It differs from the
+                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
-                                                                                   constant and age model which counts them. */
+                       bool=0;
-                   bool=0; /* not selected */
+                     }
-               }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;
-           } /* end j==0 */
+             }/* end bool 2 */
-           /* bool =0 we keep that guy which corresponds to the combination of dummy values */
+           } /* end m */
-           if(bool==1){
+         } /* end bool */
-             /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
+       } /* end iind = 1 to imx */
-                and mw[mi+1][iind]. dh depends on stepm. */
+       /* prop[s][age] is feeded for any initial and valid live state as well as
-             agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
+          freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
-             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.);
+       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
+       pstamp(ficresp);
-               if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
+       if  (cptcoveff>0 && j!=0){
-               if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
+         printf( "\n#********** Variable ");
-               if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
+         fprintf(ficresp, "\n#********** Variable ");
-                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
+         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
-               if (m<lastpass) {
+         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
-                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */
+         fprintf(ficlog, "\n#********** 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]); */
+         for (z1=1; z1<=cptcoveff; z1++){
-                 if(s[m][iind]==-1)
+           if(!FixedV[Tvaraff[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.));
+             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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 */
+             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                 /* if((int)agev[m][iind] == 55) */
+             fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-                 /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
+             fprintf(ficresphtmfr, "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(ficlog, "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 */
-               }
-             } /* 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{
-             bool=1;
+             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           }/* end bool 2 */
+             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-         } /* end m */
+             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-       } /* end bool */
+             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     } /* end iind = 1 to imx */
+             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-     /* prop[s][age] is feeded for any initial and valid live state as well as
+           }
-        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
+         }
+         printf( "**********\n#");
+         fprintf(ficresp, "**********\n#");
-     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
+         fprintf(ficresphtm, "**********</h3>\n");
-     pstamp(ficresp);
+         fprintf(ficresphtmfr, "**********</h3>\n");
-     if  (cptcoveff>0 && j!=0){
+         fprintf(ficlog, "**********\n");
-       fprintf(ficresp, "\n#********** Variable ");
+       }
-       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
+       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
-       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
+       for(i=1; i<=nlstate;i++) {
-       fprintf(ficlog, "\n#********** Variable ");
+         fprintf(ficresp, " Age Prev(%d)  N(%d)  N  ",i,i);
-       for (z1=1; z1<=cptcoveff; z1++){
+         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
-         if(DummyV[z1]){
+       }
-           fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       fprintf(ficresp, "\n");
-           fprintf(ficresphtm, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       fprintf(ficresphtm, "\n");
-           fprintf(ficresphtmfr, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
-           fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       /* Header of frequency table by age */
-         }else{
+       fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
-           fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       fprintf(ficresphtmfr,"<th>Age</th> ");
-           fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
-           fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+         for(m=-1; m <=nlstate+ndeath; m++){
-           fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
+           if(jk!=0 && m!=0)
-         }
+             fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
-       }
-       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++){
-         for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
-           pp[jk] += freq[jk][m][iage];
        }
-       for(jk=1; jk <=nlstate ; jk++){
+       fprintf(ficresphtmfr, "\n");
-         for(m=-1, pos=0; m <=0 ; m++)
-           pos += freq[jk][m][iage];
+       /* For each age */
-         if(pp[jk]>=1.e-10){
+       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){
-             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] */
-         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){
-             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)
-           else{
+               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
+             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
-             fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
+           }
+           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);
+             }
            }
-         }
+           pospropt[jk] +=posprop[jk];
-         pospropt[jk] +=posprop[jk];
+         } /* end loop jk */
-       } /* end loop jk */
+         /* pospropt=0.; */
-       /* pospropt=0.; */
+         for(jk=-1; jk <=nlstate+ndeath; jk++){
-       for(jk=-1; jk <=nlstate+ndeath; jk++){
+           for(m=-1; m <=nlstate+ndeath; m++){
-         for(m=-1; m <=nlstate+ndeath; m++){
+             if(freq[jk][m][iage] !=0 ) { /* minimizing output */
-           if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+               if(first==1){
-             if(first==1){
+                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
-               printf(" %d%d=%.0f",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]);
              }
-             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]);
            }
-           if(jk!=0 && m!=0)
+         } /* end loop jk */
-             fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
+         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("Others in log...\n");
+         fprintf(ficlog,"\n");
+       } /* end loop age iage */
+       fprintf(ficresphtm,"<tr><th>Tot</th>");
+       for(jk=1; jk <=nlstate ; jk++){
+         if(posproptt < 1.e-5){
+           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);
          }
-       } /* 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)
+       fprintf(ficresphtm,"</tr>\n");
-         printf("Others in log...\n");
+       fprintf(ficresphtm,"</table>\n");
-       fprintf(ficlog,"\n");
+       fprintf(ficresphtmfr,"</table>\n");
-     } /* end loop age iage */
-     fprintf(ficresphtm,"<tr><th>Tot</th>");
-     for(jk=1; jk <=nlstate ; jk++){
        if(posproptt < 1.e-5){
-         fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
+         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,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
+         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+         invalidvarcomb[j1]=0;
        }
-     }
+       fprintf(ficresphtmfr,"</table>\n");
-     fprintf(ficresphtm,"</tr>\n");
+       fprintf(ficlog,"\n");
-     fprintf(ficresphtm,"</table>\n");
+       if(j!=0){
-     fprintf(ficresphtmfr,"</table>\n");
+         printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
-     if(posproptt < 1.e-5){
+         for(i=1,jk=1; i <=nlstate; i++){
-       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+           for(k=1; k <=(nlstate+ndeath); k++){
-       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
+             if (k != i) {
-       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
+               for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */
-       invalidvarcomb[j1]=1;
+                 if(jj==1){  /* Constant case (in fact cste + age) */
-     }else{
+                   if(j1==1){ /* All dummy covariates to zero */
-       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
+                     freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
-       invalidvarcomb[j1]=0;
+                     freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
-     }
+                     printf("%d%d ",i,k);
-     fprintf(ficresphtmfr,"</table>\n");
+                     fprintf(ficlog,"%d%d ",i,k);
-   } /* end selected combination of covariate j1 */
+                     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]));
-   if(j==0){ /* We can estimate starting values from the occurences in each case */
+                     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]));
-     printf("#Freqsummary\n");
+                     pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
-     fprintf(ficlog,"\n");
+                   }
-     for(i=1,jk=1; i <=nlstate; i++){
+                 }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
-       for(k=1; k <=(nlstate+ndeath); k++){
+                   for(iage=iagemin; iage <= iagemax+3; iage++){
-         if (k != i) {
+                     x[iage]= (double)iage;
-           printf("%d%d ",i,k);
+                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
-           fprintf(ficlog,"%d%d ",i,k);
+                     /* printf("i=%d, k=%d, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */
-           for(jj=1; jj <=ncovmodel; jj++){
+                   }
-             if(jj==1){
+                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
-               printf("%12.7f ln(%12.1f/%12.1f)= %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]));
+                   pstart[jk]=b;
-               fprintf(ficlog,"%12.7f ln(%12.1f/%12.1f)= %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]));
+                   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++;
              }
-             /* printf("%12.7f )", param[i][jj][k]); */
+             printf("\n");
-             /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
+             fprintf(ficlog,"\n");
-             jk++;
            }
-           printf("\n");
-           fprintf(ficlog,"\n");
          }
        }
-     }
+       printf("#Freqsummary\n");
-     printf("#Freqsummary\n");
+       fprintf(ficlog,"\n");
-     fprintf(ficlog,"\n");
+       for(jk=-1; jk <=nlstate+ndeath; jk++){
-     for(jk=-1; jk <=nlstate+ndeath; jk++){
+         for(m=-1; m <=nlstate+ndeath; m++){
-       for(m=-1; m <=nlstate+ndeath; m++){
+           /* param[i]|j][k]= freq[jk][m][iagemax+3] */
-         /* param[i]|j][k]= freq[jk][m][iagemax+3] */
            printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
            fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
-         /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */
+           /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */
-         /*   printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
+           /*   printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
-         /*   fprintf(ficlog," %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 */
+       } /* end loop jk */
-     printf("\n");
-     fprintf(ficlog,"\n");
+       printf("\n");
-   } /* if j=0 */
+       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");
+         }
+       }
+     }
+   } /* end mle=-2 */
    dateintmean=dateintsum/k2cpt;
    fclose(ficresp);
- Line 4594  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 4782  Title=%s <br>Datafile=%s Firstpass=%d La
    fclose(ficresphtmfr);
    free_vector(meanq,1,nqfveff);
    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(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);
    /* End of freqsummary */
  }
- Line 4624  void prevalence(double ***probs, double
+ Line 4814  void prevalence(double ***probs, double
    iagemin= (int) agemin;
    iagemax= (int) agemax;
    /*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);*/
    j1=0;
- Line 4634  void prevalence(double ***probs, double
+ Line 4824  void prevalence(double ***probs, double
    first=1;
    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
      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;
      printf("Prevalence combination of varying and fixed dummies %d\n",j1);
      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
- Line 4665  void prevalence(double ***probs, double
+ Line 4855  void prevalence(double ***probs, double
              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]==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);
                  exit(1);
                }
- Line 4702  void prevalence(double ***probs, double
+ Line 4892  void prevalence(double ***probs, double
    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    /*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 */
  /************* Waves Concatenation ***************/
- Line 4781  void  concatwav(int wav[], int **dh, int
+ Line 4971  void  concatwav(int wav[], int **dh, int
        /* if(mi==0)  never been interviewed correctly before death */
        /* Only death is a correct wave */
        mw[mi][i]=m;
-     }
+     } /* else not in a death state */
  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
-     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
+     else if ((int) andc[i] != 9999) {  /* Date of death is known */
-       /* m++; */
-       /* mi++; */
-       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
-       /* mw[mi][i]=m; */
        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
            nbwarn++;
- Line 4800  void  concatwav(int wav[], int **dh, int
+ Line 4986  void  concatwav(int wav[], int **dh, int
          }else{ /* Death occured afer last wave potential bias */
            nberr++;
            if(firstwo==0){
-             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
              firstwo=1;
            }
-           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
+           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
          }
-       }else{ /* end date of interview is known */
+       }else{ /* if date of interview is unknown */
          /* death is known but not confirmed by death status at any wave */
          if(firstfour==0){
            printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
- Line 6198  To be simple, these graphs help to under
+ Line 6384  To be simple, these graphs help to under
  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                    int lastpass, int stepm, int weightopt, char model[],\
                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
-                   int popforecast, int prevfcast, int backcast, int estepm , \
+                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
                    double jprev1, double mprev1,double anprev1, double dateprev1, \
                    double jprev2, double mprev2,double anprev2, double dateprev2){
    int jj1, k1, i1, cpt, k4, nres;
- Line 6245  void printinghtml(char fileresu[], char
+ Line 6431  void printinghtml(char fileresu[], char
     for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
-      if(TKresult[nres]!= k1)
+      if(m != 1 && TKresult[nres]!= k1)
         continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
- Line 6272  void printinghtml(char fileresu[], char
+ Line 6458  void printinghtml(char fileresu[], char
         }
       }
       /* aij, bij */
-      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
+      fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
  <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
       /* Pij */
       fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
- Line 6296  divided by h: <sub>h</sub>P<sub>ij</sub>
+ Line 6482  divided by h: <sub>h</sub>P<sub>ij</sub>
       }
       /* Period (stable) prevalence in each health state */
       for(cpt=1; cpt<=nlstate;cpt++){
-        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d some years earlier, knowing that we will be in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
       }
       if(backcast==1){
         /* Period (stable) back prevalence in each health state */
         for(cpt=1; cpt<=nlstate;cpt++){
-          fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability to be in state %d at a younger age, knowing that we will be in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
         }
       }
       if(prevfcast==1){
         /* Projection of prevalence up to period (stable) prevalence in each health state */
         for(cpt=1; cpt<=nlstate;cpt++){
-          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
- <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
         }
       }
- Line 6377  See page 'Matrix of variance-covariance
+ Line 6563  See page 'Matrix of variance-covariance
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k1=1; k1<=m;k1++){
-      if(TKresult[nres]!= k1)
+      if(m != 1 && TKresult[nres]!= k1)
         continue;
       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
       jj1++;
- Line 6398  See page 'Matrix of variance-covariance
+ Line 6584  See page 'Matrix of variance-covariance
         }
       }
       for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
+        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
- <img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
+ <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
       }
       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
- Line 6473  void printinggnuplot(char fileresu[], ch
+ Line 6659  void printinggnuplot(char fileresu[], ch
      for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
-         if(TKresult[nres]!= k1)
+         if(m != 1 && TKresult[nres]!= k1)
            continue;
          /* We are interested in selected combination by the resultline */
          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
- Line 6555  void printinggnuplot(char fileresu[], ch
+ Line 6741  void printinggnuplot(char fileresu[], ch
    /*2 eme*/
    for (k1=1; k1<= m ; k1 ++){
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
- Line 6615  void printinggnuplot(char fileresu[], ch
+ Line 6801  void printinggnuplot(char fileresu[], ch
    /*3eme*/
    for (k1=1; k1<= m ; k1 ++){
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        for (cpt=1; cpt<= nlstate ; cpt ++) {
- Line 6664  plot [%.f:%.f] \"%s\" every :::%d::%d u
+ Line 6850  plot [%.f:%.f] \"%s\" every :::%d::%d u
    /* 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(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        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);
- Line 6710  set ter svg size 640, 480\nunset log y\n
+ Line 6896  set ter svg size 640, 480\nunset log y\n
    /* 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(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        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);
- Line 6764  set ter svg size 640, 480\nunset log y\n
+ Line 6950  set ter svg size 640, 480\nunset log y\n
    /* CV preval stable (period) for each covariate */
    for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-     if(TKresult[nres]!= k1)
+     if(m != 1 && TKresult[nres]!= k1)
        continue;
-     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
        fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
        for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
- Line 6790  set ter svg size 640, 480\nunset log y\n
+ Line 6976  set ter svg size 640, 480\nunset log y\n
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
        k=3; /* Offset */
-       for (i=1; i<= nlstate ; i ++){
+       for (i=1; i<= nlstate ; i ++){ /* State of origin */
          if(i==1)
            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
          else
            fprintf(ficgp,", '' ");
-         l=(nlstate+ndeath)*(i-1)+1;
+         l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
          for (j=2; j<= nlstate ; j ++)
            fprintf(ficgp,"+$%d",k+l+j-1);
- Line 6811  set ter svg size 640, 480\nunset log y\n
+ Line 6997  set ter svg size 640, 480\nunset log y\n
      /* CV back preval stable (period) for each covariate */
      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
-       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending 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): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
- Line 6836  set ter svg size 640, 480\nunset log y\n
+ Line 7022  set ter svg size 640, 480\nunset log y\n
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
          k=3; /* Offset */
-         for (i=1; i<= nlstate ; i ++){
+         for (i=1; i<= nlstate ; i ++){ /* State of origin */
            if(i==1)
              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
            else
              fprintf(ficgp,", '' ");
            /* l=(nlstate+ndeath)*(i-1)+1; */
-           l=(nlstate+ndeath)*(cpt-1)+1;
+           l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
-           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
+           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
            /* for (j=2; j<= nlstate ; j ++) */
            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
- Line 6862  set ter svg size 640, 480\nunset log y\n
+ Line 7048  set ter svg size 640, 480\nunset log y\n
      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= k1)
+       if(m != 1 && TKresult[nres]!= k1)
          continue;
        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);
- Line 6993  set ter svg size 640, 480\nunset log y\n
+ Line 7179  set ter svg size 640, 480\nunset log y\n
      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(nres=1; nres <= nresult; nres++){ /* For each resultline */
-       if(TKresult[nres]!= jk)
+       if(m != 1 && TKresult[nres]!= jk)
          continue;
        fprintf(ficgp,"# Combination of dummy  jk=%d and ",jk);
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
- Line 7355  set ter svg size 640, 480\nunset log y\n
+ Line 7541  set ter svg size 640, 480\nunset log y\n
  /*            if (h==(int)(YEARM*yearp)){ */
    for(nres=1; nres <= nresult; nres++) /* For each resultline */
    for(k=1; k<=i1;k++){
-     if(TKresult[nres]!= k)
+     if(i1 != 1 && TKresult[nres]!= k)
        continue;
      if(invalidvarcomb[k]){
        printf("\nCombination (%d) projection ignored because no cases \n",k);
- Line 8306  int decoderesult ( char resultline[], in
+ Line 8492  int decoderesult ( char resultline[], in
    if (strlen(resultsav) >1){
      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 */
      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);
- Line 8917  int calandcheckages(int imx, int maxwav,
+ Line 9108  int calandcheckages(int imx, int maxwav,
            s[m][i]=-1;
        }
        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
-         *nberr = *nberr + 1;
+         *nbwarn = *nbwarn + 1;
          if(firstone == 0){
            firstone=1;
-         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we believe in a death.\nOther similar cases in log file\n", *nbwarn,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
          }
-         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
+         fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we believe in a death.\nOther similar cases in log file\n", *nbwarn,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
-         s[m][i]=-1;
+         /* s[m][i]=-1; */ /* Keeping the death status */
        }
        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
          (*nberr)++;
-         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
+         printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
+         fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
-         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
+         s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
        }
      }
    }
- Line 9242  int prevalence_limit(double *p, double *
+ Line 9433  int prevalence_limit(double *p, double *
    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 */
-       if(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
- Line 9339  int back_prevalence_limit(double *p, dou
+ Line 9530  int back_prevalence_limit(double *p, dou
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
      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;
        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
        fprintf(ficresplb,"#******");
- Line 9398  int back_prevalence_limit(double *p, dou
+ Line 9589  int back_prevalence_limit(double *p, dou
          fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
        } /* Age */
        /* was end of cptcod */
+       /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
      } /* end of any combination */
    } /* end of nres */
    /* hBijx(p, bage, fage); */
- Line 9442  int hPijx(double *p, int bage, int fage)
+ Line 9634  int hPijx(double *p, int bage, int fage)
                  /*      k=k+1;  */
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k=1; k<=i1;k++){
-       if(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
        fprintf(ficrespij,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
- Line 9514  int hPijx(double *p, int bage, int fage)
+ Line 9706  int hPijx(double *p, int bage, int fage)
    /* hstepm=1;   aff par mois*/
    pstamp(ficrespijb);
-   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
+   fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
    i1= pow(2,cptcoveff);
    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
    /*    k=k+1;  */
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
      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;
        fprintf(ficrespijb,"\n#****** ");
        for(j=1;j<=cptcoveff;j++)
- Line 9548  int hPijx(double *p, int bage, int fage)
+ Line 9740  int hPijx(double *p, int bage, int fage)
          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
          hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
-         fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
+         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate+ndeath;j++)
              fprintf(ficrespijb," %1d-%1d",i,j);
- Line 9594  int main(int argc, char *argv[])
+ Line 9786  int main(int argc, char *argv[])
    int NDIM=2;
    int vpopbased=0;
    int nres=0;
+   int endishere=0;
    char ca[32], cb[32];
    /*  FILE *fichtm; *//* Html File */
- Line 9638  int main(int argc, char *argv[])
+ Line 9831  int main(int argc, char *argv[])
    double **prlim;
    double **bprlim;
    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 **hess; /* Hessian matrix */
    double ***delti3; /* Scale */
- Line 9963  int main(int argc, char *argv[])
+ Line 10157  int main(int argc, char *argv[])
      fclose (ficlog);
      goto end;
      exit(0);
-   } else if(mle==-2) { /* Guessing from means */
-     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
-     printf(" You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso);
-     fprintf(ficlog," You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso);
    }  else if(mle==-5) { /* Main Wizard */
      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
- Line 9989  int main(int argc, char *argv[])
+ Line 10178  int main(int argc, char *argv[])
      ungetc(c,ficpar);
      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++){
        j=0;
        for(jj=1; jj <=nlstate+ndeath; jj++){
- Line 10025  run imach with mle=-1 to get a correct t
+ Line 10215  run imach with mle=-1 to get a correct t
      }
      fflush(ficlog);
-     /* Reads scales values */
+     /* Reads parameters values */
      p=param[1][1];
+     pstart=paramstart[1][1];
      /* Reads comments: lines beginning with '#' */
      while((c=getc(ficpar))=='#' && c!= EOF){
- Line 10472  Title=%s <br>Datafile=%s Firstpass=%d La
+ Line 10663  Title=%s <br>Datafile=%s Firstpass=%d La
    /* Calculates basic frequencies. Computes observed prevalence at single age
                   and for any valid combination of covariates
       and prints on file fileres'p'. */
-   freqsummary(fileres, p, 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);
    fprintf(fichtm,"\n");
- Line 10951  Please run with mle=-1 to get a correct
+ Line 11142  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);
      /* 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);
-     ungetc(c,ficpar);
+         fputs(line,ficlog);
+         continue;
-     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);
+       }else
-     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);
+         break;
-     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
-       ungetc(c,ficpar);
-       fgets(line, MAXLINE, ficpar);
-       fputs(line,stdout);
-       fputs(line,ficparo);
-     }
-     ungetc(c,ficpar);
-     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-     fscanf(ficpar,"pop_based=%d\n",&popbased);
-     fprintf(ficlog,"pop_based=%d\n",popbased);
-     fprintf(ficparo,"pop_based=%d\n",popbased);
-     fprintf(ficres,"pop_based=%d\n",popbased);
-     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);
+     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,"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(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 (num_filled != 7) {
-     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);
+         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);
-     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(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(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);
+         goto end;
-     /* day and month of proj2 are not used but only year anproj2.*/
+       }
+       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     while((c=getc(ficpar))=='#' && c!= EOF){
+       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);
-       ungetc(c,ficpar);
+       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);
-       fgets(line, MAXLINE, ficpar);
+       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);
-       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);
-     fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
-     /* day and month of proj2 are not used but only year anproj2.*/
-     /* Results */
-     nresult=0;
      while(fgets(line, MAXLINE, ficpar)) {
        /* If line starts with a # it is a comment */
        if (line[0] == '#') {
- Line 11022  Please run with mle=-1 to get a correct
+ Line 11174  Please run with mle=-1 to get a correct
          fputs(line,stdout);
          fputs(line,ficparo);
          fputs(line,ficlog);
-         fputs(line,ficres);
          continue;
        }else
          break;
      }
-     if (!feof(ficpar))
-     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
-       if (num_filled == 0){
+     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
-         resultline[0]='\0';
+     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-       break;
-       } else if (num_filled != 1){
+     if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
-         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
+       if (num_filled != 1) {
-       }
+         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);
-       nresult++; /* Sum of resultlines */
+         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);
-       printf("Result %d: result=%s\n",nresult, resultline);
-       if(nresult > MAXRESULTLINES){
-         printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
-         fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
          goto end;
        }
-       decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+       printf("pop_based=%d\n",popbased);
-       fprintf(ficparo,"result: %s\n",resultline);
+       fprintf(ficlog,"pop_based=%d\n",popbased);
-       fprintf(ficres,"result: %s\n",resultline);
+       fprintf(ficparo,"pop_based=%d\n",popbased);
-       fprintf(ficlog,"result: %s\n",resultline);
+       fprintf(ficres,"pop_based=%d\n",popbased);
-       while(fgets(line, MAXLINE, ficpar)) {
+     }
+     /* Results */
+     nresult=0;
+     do{
+       if(!fgets(line, MAXLINE, ficpar)){
+         endishere=1;
+         parameterline=14;
+       }else if (line[0] == '#') {
          /* If line starts with a # it is a comment */
-         if (line[0] == '#') {
+         numlinepar++;
-           numlinepar++;
+         fputs(line,stdout);
-           fputs(line,stdout);
+         fputs(line,ficparo);
-           fputs(line,ficparo);
+         fputs(line,ficlog);
-           fputs(line,ficres);
+         continue;
-           fputs(line,ficlog);
+       }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
-           continue;
+         parameterline=11;
-         }else
+       else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
-           break;
+         parameterline=12;
+       else if(sscanf(line,"result:%[^\n]\n",modeltemp))
+         parameterline=13;
+       else{
+         parameterline=14;
        }
-       if (feof(ficpar))
+       switch (parameterline){
+       case 11:
+         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.*/
+         }
          break;
-       else{ /* Processess output results for this combination of covariate values */
+       case 12:
-       }
+         /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/
-     } /* end while */
+         if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
+           if (num_filled != 8) {
+             printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
+             goto end;
+           }
+           printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
+           /* day and month of proj2 are not used but only year anproj2.*/
+         }
+         break;
+       case 13:
+         if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
+           if (num_filled == 0){
+             resultline[0]='\0';
+             printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
+             break;
+           } else if (num_filled != 1){
+             printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+             fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
+           }
+           nresult++; /* Sum of resultlines */
+           printf("Result %d: result=%s\n",nresult, resultline);
+           if(nresult > MAXRESULTLINES){
+             printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
+             goto end;
+           }
+           decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
+           fprintf(ficparo,"result: %s\n",resultline);
+           fprintf(ficres,"result: %s\n",resultline);
+           fprintf(ficlog,"result: %s\n",resultline);
+           break;
+         case 14:
+           if(ncovmodel >2 && nresult==0 ){
+             printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
+             goto end;
+           }
+           break;
+         default:
+           nresult=1;
+           decoderesult(".",nresult ); /* No covariate */
+         }
+       } /* End switch parameterline */
+     }while(endishere==0); /* End do */
      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
- Line 11081  Please run with mle=-1 to get a correct
+ Line 11298  Please run with mle=-1 to get a correct
        printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
      }
      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
-                  model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
+                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
                   jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
      /*------------ free_vector  -------------*/
- Line 11134  Please run with mle=-1 to get a correct
+ Line 11351  Please run with mle=-1 to get a correct
        mobaverage=mobaverages;
        if (mobilav!=0) {
          printf("Movingaveraging observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging observed prevalence\n");
          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf(" Error in movingaverage mobilav=%d\n",mobilav);
- Line 11143  Please run with mle=-1 to get a correct
+ Line 11361  Please run with mle=-1 to get a correct
        /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
        else if (mobilavproj !=0) {
          printf("Movingaveraging projected observed prevalence\n");
+         fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
- Line 11205  Please run with mle=-1 to get a correct
+ Line 11424  Please run with mle=-1 to get a correct
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      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;
        fprintf(ficreseij,"\n#****** ");
        printf("\n#****** ");
- Line 11278  Please run with mle=-1 to get a correct
+ Line 11497  Please run with mle=-1 to get a correct
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      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;
        printf("\n#****** Result for:");
        fprintf(ficrest,"\n#****** Result for:");
- Line 11419  Please run with mle=-1 to get a correct
+ Line 11638  Please run with mle=-1 to get a correct
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k=1; k<=i1;k++){
-       if(TKresult[nres]!= k)
+       if(i1 != 1 && TKresult[nres]!= k)
          continue;
        fprintf(ficresvpl,"\n#****** ");
        printf("\n#****** ");

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	Added in v.1.259