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Diff for /imach/src/imach.c between versions 1.191 and 1.192

version 1.191, 2015/07/14 10:00:33 version 1.192, 2015/07/16 16:49:02
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.192  2015/07/16 16:49:02  brouard
     Summary: Fixing some outputs
   
   Revision 1.191  2015/07/14 10:00:33  brouard    Revision 1.191  2015/07/14 10:00:33  brouard
   Summary: Some fixes    Summary: Some fixes
   
Line 605 Line 608
 /* #define DEBUG */  /* #define DEBUG */
 /* #define DEBUGBRENT */  /* #define DEBUGBRENT */
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
   #define POWELLF1F3 /* Skip test */
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   
Line 692  typedef struct { Line 696  typedef struct {
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";  char version[]="Imach version 0.98q3, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 827  int estepm; Line 831  int estepm;
   
 int m,nb;  int m,nb;
 long *num;  long *num;
 int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;  int firstpass=0, lastpass=4,*cod, *Tage,*cens;
   int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                      covariate for which somebody answered excluding 
                      undefined. Usually 2: 0 and 1. */
   int *ncodemaxwundef;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs;
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
Line 1559  void linmin(double p[], double xi[], int Line 1569  void linmin(double p[], double xi[], int
     xicom[j]=xi[j];       xicom[j]=xi[j]; 
   }     } 
   
   axs=0.0;    /* axs=0.0; */
   xxss=1; /* 1 and using scale */    /* xxss=1; /\* 1 and using scale *\/ */
   xxs=1;    xxs=1;
   do{    /* do{ */
     ax=0.;      ax=0.;
     xx= xxs;      xx= xxs;
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
Line 1572  void linmin(double p[], double xi[], int Line 1582  void linmin(double p[], double xi[], int
     /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */      /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
     /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */      /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
     /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/      /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus  [0:xi[j]]*/
     if (fx != fx){    /*   if (fx != fx){ */
         xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */    /*    xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
         printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx);    /*    printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n",  axs, xxs, fx,fb, fa, xx, ax, bx); */
     }    /*   } */
   }while(fx != fx);    /* }while(fx != fx); */
   
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
   printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);    printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n",  ax,xx,bx,fa,fx,fb);
Line 1653  void powell(double p[], double **xi, int Line 1663  void powell(double p[], double **xi, int
     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 1761  void powell(double p[], double **xi, int Line 1771  void powell(double p[], double **xi, int
       free_vector(ptt,1,n);         free_vector(ptt,1,n); 
       free_vector(pt,1,n);         free_vector(pt,1,n); 
       return;         return; 
     }       } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
Line 1769  void powell(double p[], double **xi, int Line 1779  void powell(double p[], double **xi, int
       pt[j]=p[j];         pt[j]=p[j]; 
     }       } 
     fptt=(*func)(ptt); /* f_3 */      fptt=(*func)(ptt); /* f_3 */
   #ifdef POWELLF1F3
   #else
     if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   #endif
       /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       /* From x1 (P0) distance of x2 is at h and x3 is 2h */        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
       /* Let f"(x2) be the 2nd derivative equal everywhere.  */        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
Line 1798  void powell(double p[], double **xi, int Line 1811  void powell(double p[], double **xi, int
       if (t < 0.0) { /* Then we use it for new direction */        if (t < 0.0) { /* Then we use it for new direction */
 #else  #else
       if (directest*t < 0.0) { /* Contradiction between both tests */        if (directest*t < 0.0) { /* Contradiction between both tests */
       printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);          printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
       printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);          fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
       fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
     }         } 
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use it for new direction */
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
Line 1838  void powell(double p[], double **xi, int Line 1851  void powell(double p[], double **xi, int
         printf("\n");          printf("\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t negative */        } /* end of t or directest negative */
   #ifdef POWELLF1F3
   #else
     } /* end if (fptt < fp)  */      } /* end if (fptt < fp)  */
   }   #endif
     } /* loop iteration */ 
 }   } 
   
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
Line 3298  void tricode(int *Tvar, int **nbcode, in Line 3314  void tricode(int *Tvar, int **nbcode, in
   
   cptcoveff=0;     cptcoveff=0; 
     
   for (k=-1; k < maxncov; k++) Ndum[k]=0;  
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   /* Loop on covariates without age and products */    /* Loop on covariates without age and products */
   for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
       for (k=-1; k < maxncov; k++) Ndum[k]=0;
     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the       for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                modality of this covariate Vj*/                                  modality of this covariate Vj*/ 
       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
Line 3325  void tricode(int *Tvar, int **nbcode, in Line 3341  void tricode(int *Tvar, int **nbcode, in
       /* getting the maximum value of the modality of the covariate        /* getting the maximum value of the modality of the covariate
          (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
          female is 1, then modmaxcovj=1.*/           female is 1, then modmaxcovj=1.*/
     } /* end for loop on individuals */      } /* end for loop on individuals i */
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     cptcode=modmaxcovj;      cptcode=modmaxcovj;
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
    /*for (i=0; i<=cptcode; i++) {*/     /*for (i=0; i<=cptcode; i++) {*/
     for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */      for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], i, Ndum[i]);        printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
       if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */        fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
         ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */        if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
           if( k != -1){
             ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered excluding 
                                undefined. Usually 2: 0 and 1. */
           }
           ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
                                covariate for which somebody answered including 
                                undefined. Usually 3: -1, 0 and 1. */
       }        }
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
          historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
Line 3351  void tricode(int *Tvar, int **nbcode, in Line 3376  void tricode(int *Tvar, int **nbcode, in
        nbcode[Tvar[j]][2]=1;         nbcode[Tvar[j]][2]=1;
        nbcode[Tvar[j]][3]=2;         nbcode[Tvar[j]][3]=2;
     */      */
     ij=1; /* ij is similar to i but can jumps over null modalities */      ij=0; /* ij is similar to i but can jumps over null modalities */
     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */          if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
         /*recode from 0 */            break;
         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */          }
           nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode.           ij++;
                                      k is a modality. If we have model=V1+V1*sex           nbcode[Tvar[j]][ij]=i;  /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */          cptcode = ij; /* New max modality for covar j */
           ij++;      } /* end of loop on modality i=-1 to 1 or more */
         }        
         if (ij > ncodemax[j]) break;       /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
       }  /* end of loop on */      /*  /\*recode from 0 *\/ */
     } /* end of loop on modality */       /*                               k is a modality. If we have model=V1+V1*sex  */
       /*                               then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       /*                            But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
       /*  } */
       /*  /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
       /*  if (ij > ncodemax[j]) { */
       /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
       /*    fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
       /*    break; */
       /*  } */
       /*   }  /\* end of loop on modality k *\/ */
   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/      } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       
  for (k=-1; k< maxncov; k++) Ndum[k]=0;    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
Line 3374  void tricode(int *Tvar, int **nbcode, in Line 3409  void tricode(int *Tvar, int **nbcode, in
    Ndum[ij]++; /* Might be supersed V1 + V1*age */     Ndum[ij]++; /* Might be supersed V1 + V1*age */
  }    } 
   
  ij=1;   ij=0;
  for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
    /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){     if((Ndum[i]!=0) && (i<=ncovcol)){
        ij++;
      /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
      Tvaraff[ij]=i; /*For printing (unclear) */       Tvaraff[ij]=i; /*For printing (unclear) */
      ij++;     }else{
    }else         /* Tvaraff[ij]=0; */
        Tvaraff[ij]=0;     }
  }   }
  ij--;   /* ij--; */
  cptcoveff=ij; /*Number of total covariates*/   cptcoveff=ij; /*Number of total covariates*/
   
 }  }
Line 4470  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4506  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   
  jj1=0;   jj1=0;
  for(k1=1; k1<=m;k1++){   for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){     /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
            printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
          }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      /* Pij */       /* Pij */
Line 4494  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4532  fprintf(fichtm," \n<ul><li><b>Graphs</b>
         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
 <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);  <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }       }
    } /* end i1 */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
   
Line 4544  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4582  fprintf(fichtm," \n<ul><li><b>Graphs</b>
   
  jj1=0;   jj1=0;
  for(k1=1; k1<=m;k1++){   for(k1=1; k1<=m;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){     /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
Line 4563  true period expectancies (those weighted Line 4601  true period expectancies (those weighted
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences: %s%d.png<br>\   observed and cahotic prevalences: %s%d.png<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */     /* } /\* end i1 *\/ */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
  fflush(fichtm);   fflush(fichtm);
Line 5597  int decodemodel ( char model[], int last Line 5635  int decodemodel ( char model[], int last
   if (strlen(model) >1){ /* If there is at least 1 covariate */    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;      j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
     if (strstr(model,"AGE") !=0){      if (strstr(model,"AGE") !=0){
       printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model);        printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     if (strstr(model,"v") !=0){      if (strstr(model,"v") !=0){
Line 5611  int decodemodel ( char model[], int last Line 5649  int decodemodel ( char model[], int last
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
       printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \        printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
       fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \        fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
       return 1;        return 1;
     }      }
Line 6498  int main(int argc, char *argv[]) Line 6536  int main(int argc, char *argv[])
   }    }
   else if(mle==-3) { /* Main Wizard */    else if(mle==-3) { /* Main Wizard */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
   }    }
Line 6673  run imach with mle=-1 to get a correct t Line 6711  run imach with mle=-1 to get a correct t
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
     ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
   /* Reads data from file datafile */    /* Reads data from file datafile */
   if (readdata(datafile, firstobs, lastobs, &imx)==1)    if (readdata(datafile, firstobs, lastobs, &imx)==1)
Line 7142  Interval (in months) between two waves: Line 7181  Interval (in months) between two waves:
     }      }
           
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);      fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 7646  Interval (in months) between two waves: Line 7685  Interval (in months) between two waves:
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
     free_ivector(ncodemax,1,NCOVMAX);      free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(ncodemaxwundef,1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);      free_ivector(Tvar,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);      free_ivector(Tprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);      free_ivector(Tvaraff,1,NCOVMAX);
Removed from v.1.191  
changed lines
  Added in v.1.192

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