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Diff for /imach/src/imach.c between versions 1.28 and 1.35

version 1.28, 2002/03/01 17:56:23 version 1.35, 2002/03/26 17:08:39
Line 56 Line 56
 #include <unistd.h>  #include <unistd.h>
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  #define GNUPLOTPROGRAM "wgnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
Line 82  int cptcovn, cptcovage=0, cptcoveff=0,cp Line 83  int cptcovn, cptcovage=0, cptcoveff=0,cp
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
Line 686  double **prevalim(double **prlim, int nl Line 687  double **prevalim(double **prlim, int nl
     
       for (k=1; k<=cptcovn;k++) {        for (k=1; k<=cptcovn;k++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       }        }
       for (k=1; k<=cptcovage;k++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)        for (k=1; k<=cptcovprod;k++)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
     savm=oldm;      savm=oldm;
Line 1178  void lubksb(double **a, int n, int *indx Line 1178  void lubksb(double **a, int n, int *indx
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
 {  /* Some frequencies */  {  /* Some frequencies */
     
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp;    double *pp;
   double pos, k2, dateintsum=0,k2cpt=0;    double pos, k2, dateintsum=0,k2cpt=0;
   FILE *ficresp;    FILE *ficresp;
   char fileresp[FILENAMELENGTH];    char fileresp[FILENAMELENGTH];
     
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresp,"p");    strcpy(fileresp,"p");
Line 1196  void  freqsummary(char fileres[], int ag Line 1196  void  freqsummary(char fileres[], int ag
   }    }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   j1=0;    j1=0;
    
   j=cptcoveff;    j=cptcoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
   for(k1=1; k1<=j;k1++){    for(k1=1; k1<=j;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){      for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;        j1++;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          scanf("%d", i);*/          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)          for (i=-1; i<=nlstate+ndeath; i++)  
          for (jk=-1; jk<=nlstate+ndeath; jk++)            for (jk=-1; jk<=nlstate+ndeath; jk++)  
            for(m=agemin; m <= agemax+3; m++)            for(m=agemin; m <= agemax+3; m++)
              freq[i][jk][m]=0;              freq[i][jk][m]=0;
        
         dateintsum=0;        dateintsum=0;
         k2cpt=0;        k2cpt=0;
        for (i=1; i<=imx; i++) {        for (i=1; i<=imx; i++) {
          bool=1;          bool=1;
          if  (cptcovn>0) {          if  (cptcovn>0) {
            for (z1=1; z1<=cptcoveff; z1++)            for (z1=1; z1<=cptcoveff; z1++)
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                bool=0;                bool=0;
          }          }
          if (bool==1) {          if (bool==1) {
            for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){
              k2=anint[m][i]+(mint[m][i]/12.);              k2=anint[m][i]+(mint[m][i]/12.);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
                if(agev[m][i]==0) agev[m][i]=agemax+1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
                if(agev[m][i]==1) agev[m][i]=agemax+2;                if(agev[m][i]==1) agev[m][i]=agemax+2;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                if (m<lastpass) {
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
                  dateintsum=dateintsum+k2;                }
                  k2cpt++;               
                }                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
                   dateintsum=dateintsum+k2;
              }                  k2cpt++;
            }                }
          }              }
        }            }
           }
         }
                 
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
         if  (cptcovn>0) {        if  (cptcovn>0) {
          fprintf(ficresp, "\n#********** Variable ");          fprintf(ficresp, "\n#********** Variable ");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        fprintf(ficresp, "**********\n#");          fprintf(ficresp, "**********\n#");
         }        }
        for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        fprintf(ficresp, "\n");        fprintf(ficresp, "\n");
               
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for(i=(int)agemin; i <= (int)agemax+3; i++){
     if(i==(int)agemax+3)          if(i==(int)agemax+3)
       printf("Total");            printf("Total");
     else          else
       printf("Age %d", i);            printf("Age %d", i);
     for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         pp[jk] += freq[jk][m][i];              pp[jk] += freq[jk][m][i];
     }          }
     for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
       for(m=-1, pos=0; m <=0 ; m++)            for(m=-1, pos=0; m <=0 ; m++)
         pos += freq[jk][m][i];              pos += freq[jk][m][i];
       if(pp[jk]>=1.e-10)            if(pp[jk]>=1.e-10)
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       else            else
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);              printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     }          }
   
      for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         pp[jk] += freq[jk][m][i];              pp[jk] += freq[jk][m][i];
      }          }
   
     for(jk=1,pos=0; jk <=nlstate ; jk++)          for(jk=1,pos=0; jk <=nlstate ; jk++)
       pos += pp[jk];            pos += pp[jk];
     for(jk=1; jk <=nlstate ; jk++){          for(jk=1; jk <=nlstate ; jk++){
       if(pos>=1.e-5)            if(pos>=1.e-5)
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       else            else
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       if( i <= (int) agemax){            if( i <= (int) agemax){
         if(pos>=1.e-5){              if(pos>=1.e-5){
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
           probs[i][jk][j1]= pp[jk]/pos;                probs[i][jk][j1]= pp[jk]/pos;
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
               else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
             }
         }          }
       else         
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           if(i <= (int) agemax)
             fprintf(ficresp,"\n");
           printf("\n");
       }        }
     }      }
     for(jk=-1; jk <=nlstate+ndeath; jk++)    }
       for(m=-1; m <=nlstate+ndeath; m++)  
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  
     printf("\n");  
     }  
     }  
  }  
   dateintmean=dateintsum/k2cpt;    dateintmean=dateintsum/k2cpt;
     
   fclose(ficresp);    fclose(ficresp);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
    
   /* End of Freq */    /* End of Freq */
 }  }
   
Line 1346  void prevalence(int agemin, float agemax Line 1349  void prevalence(int agemin, float agemax
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              if ((k2>=dateprev1) && (k2<=dateprev2)) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;                if(agev[m][i]==0) agev[m][i]=agemax+1;
               if(agev[m][i]==1) agev[m][i]=agemax+2;                if(agev[m][i]==1) agev[m][i]=agemax+2;
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */                /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */
             }              }
           }            }
Line 1443  void  concatwav(int wav[], int **dh, int Line 1446  void  concatwav(int wav[], int **dh, int
           if (j >= jmax) jmax=j;            if (j >= jmax) jmax=j;
           if (j <= jmin) jmin=j;            if (j <= jmin) jmin=j;
           sum=sum+j;            sum=sum+j;
           /* if (j<10) printf("j=%d num=%d ",j,i); */            /*if (j<0) printf("j=%d num=%d \n",j,i); */
           }            }
         }          }
         else{          else{
Line 1451  void  concatwav(int wav[], int **dh, int Line 1454  void  concatwav(int wav[], int **dh, int
           k=k+1;            k=k+1;
           if (j >= jmax) jmax=j;            if (j >= jmax) jmax=j;
           else if (j <= jmin)jmin=j;            else if (j <= jmin)jmin=j;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           sum=sum+j;            sum=sum+j;
         }          }
         jk= j/stepm;          jk= j/stepm;
Line 1497  void tricode(int *Tvar, int **nbcode, in Line 1500  void tricode(int *Tvar, int **nbcode, in
       for (k=0; k<=19; k++) {        for (k=0; k<=19; k++) {
         if (Ndum[k] != 0) {          if (Ndum[k] != 0) {
           nbcode[Tvar[j]][ij]=k;            nbcode[Tvar[j]][ij]=k;
             /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/
           ij++;            ij++;
         }          }
         if (ij > ncodemax[j]) break;          if (ij > ncodemax[j]) break;
Line 1513  void tricode(int *Tvar, int **nbcode, in Line 1517  void tricode(int *Tvar, int **nbcode, in
   
  ij=1;   ij=1;
  for (i=1; i<=10; i++) {   for (i=1; i<=10; i++) {
    if((Ndum[i]!=0) && (i<=ncov)){     if((Ndum[i]!=0) && (i<=ncovcol)){
      Tvaraff[ij]=i;       Tvaraff[ij]=i;
      ij++;       ij++;
    }     }
Line 1527  void tricode(int *Tvar, int **nbcode, in Line 1531  void tricode(int *Tvar, int **nbcode, in
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
 {  {
   /* Health expectancies */    /* Health expectancies */
   int i, j, nhstepm, hstepm, h;    int i, j, nhstepm, hstepm, h, nstepm, k;
   double age, agelim,hf;    double age, agelim, hf;
   double ***p3mat;    double ***p3mat;
     
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficreseij,"# Health expectancies\n");
Line 1538  void evsij(char fileres[], double ***eij Line 1542  void evsij(char fileres[], double ***eij
       fprintf(ficreseij," %1d-%1d",i,j);        fprintf(ficreseij," %1d-%1d",i,j);
   fprintf(ficreseij,"\n");    fprintf(ficreseij,"\n");
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */    k=1;             /* For example stepm=6 months */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */
     hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
        nhstepm is the number of hstepm from age to agelim
        nstepm is the number of stepm from age to agelin.
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */
   
   agelim=AGESUP;    agelim=AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */      /* nhstepm age range expressed in number of stepm */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      nstepm=(int) rint((agelim-age)*YEARM/stepm);
     /* Typically if 20 years = 20*12/6=40 stepm */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */
     if (stepm >= YEARM) hstepm=1;      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           eij[i][j][(int)age] +=p3mat[i][j][h];            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
         }          }
          fprintf(ficreseij,"%3.0f",age );
     hf=1;  
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);
       }        }
     fprintf(ficreseij,"\n");      fprintf(ficreseij,"\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 1579  void varevsij(char fileres[], double *** Line 1593  void varevsij(char fileres[], double ***
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   double **newm;    double **newm;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm, h;    int i, j, nhstepm, hstepm, h, nstepm, kk;
   int k, cptcode;    int k, cptcode;
   double *xp;    double *xp;
   double **gp, **gm;    double **gp, **gm;
   double ***gradg, ***trgradg;    double ***gradg, ***trgradg;
   double ***p3mat;    double ***p3mat;
   double age,agelim;    double age,agelim, hf;
   int theta;    int theta;
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");     fprintf(ficresvij,"# Covariances of life expectancies\n");
Line 1599  void varevsij(char fileres[], double *** Line 1613  void varevsij(char fileres[], double ***
   dnewm=matrix(1,nlstate,1,npar);    dnewm=matrix(1,nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    doldm=matrix(1,nlstate,1,nlstate);
     
   hstepm=1*YEARM; /* Every year of age */    kk=1;             /* For example stepm=6 months */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */
     hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
        nhstepm is the number of hstepm from age to agelim
        nstepm is the number of stepm from age to agelin.
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */
   agelim = AGESUP;    agelim = AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
     if (stepm >= YEARM) hstepm=1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     gp=matrix(0,nhstepm,1,nlstate);      gp=matrix(0,nhstepm,1,nlstate);
Line 1660  void varevsij(char fileres[], double *** Line 1686  void varevsij(char fileres[], double ***
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate;j++)        for(j=1;j<=nlstate;j++)
         vareij[i][j][(int)age] =0.;          vareij[i][j][(int)age] =0.;
   
     for(h=0;h<=nhstepm;h++){      for(h=0;h<=nhstepm;h++){
       for(k=0;k<=nhstepm;k++){        for(k=0;k<=nhstepm;k++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         for(i=1;i<=nlstate;i++)          for(i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate;j++)            for(j=1;j<=nlstate;j++)
             vareij[i][j][(int)age] += doldm[i][j];              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;  
     fprintf(ficresvij,"%.0f ",age );      fprintf(ficresvij,"%.0f ",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       }        }
     fprintf(ficresvij,"\n");      fprintf(ficresvij,"\n");
     free_matrix(gp,0,nhstepm,1,nlstate);      free_matrix(gp,0,nhstepm,1,nlstate);
Line 1882  fclose(ficresprob); Line 1909  fclose(ficresprob);
 }  }
   
 /******************* Printing html file ***********/  /******************* Printing html file ***********/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
    int lastpass, int stepm, int weightopt, char model[],\
    int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
    char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
    char version[], int popforecast ){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   FILE *fichtm;    FILE *fichtm;
   /*char optionfilehtm[FILENAMELENGTH];*/    /*char optionfilehtm[FILENAMELENGTH];*/
Line 1893  void printinghtml(char fileres[], char t Line 1924  void printinghtml(char fileres[], char t
     printf("Problem with %s \n",optionfilehtm), exit(0);      printf("Problem with %s \n",optionfilehtm), exit(0);
   }    }
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">   fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
   \n
 Total number of observations=%d <br>  Total number of observations=%d <br>\n
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
 <hr  size=\"2\" color=\"#EC5E5E\">  <hr  size=\"2\" color=\"#EC5E5E\">
 <li>Outputs files<br><br>\n   <ul><li>Outputs files<br>\n
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n   - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>   - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>   - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>   - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>   - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>   fprintf(fichtm,"\n
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>   - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>   - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>   - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);   - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);
    
    if(popforecast==1) fprintf(fichtm,"\n
    - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
    - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
           <br>",fileres,fileres,fileres,fileres);
    else
      fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
 fprintf(fichtm," <li>Graphs</li><p>");  fprintf(fichtm," <li>Graphs</li><p>");
   
  m=cptcoveff;   m=cptcoveff;
Line 1953  fclose(fichtm); Line 1990  fclose(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   strcat(optionfilegnuplot,".plt");    strcat(optionfilegnuplot,".gp.txt");
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
     printf("Problem with file %s",optionfilegnuplot);      printf("Problem with file %s",optionfilegnuplot);
   }    }
Line 1973  m=pow(2,cptcoveff); Line 2010  m=pow(2,cptcoveff);
    for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) {
   
 #ifdef windows  #ifdef windows
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
 #endif  #endif
 #ifdef unix  #ifdef unix
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);  fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
 #endif  #endif
   
 for (i=1; i<= nlstate ; i ++) {  for (i=1; i<= nlstate ; i ++) {
Line 2003  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2040  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
   /*2 eme*/    /*2 eme*/
   
   for (k1=1; k1<= m ; k1 ++) {    for (k1=1; k1<= m ; k1 ++) {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);
         
     for (i=1; i<= nlstate+1 ; i ++) {      for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;        k=2*i;
Line 2036  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2073  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
   for (k1=1; k1<= m ; k1 ++) {    for (k1=1; k1<= m ; k1 ++) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(cpt-1);        k=2+nlstate*(cpt-1);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);
       }        }
Line 2048  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2085  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
     for (k1=1; k1<= m ; k1 ++) {      for (k1=1; k1<= m ; k1 ++) {
     for (cpt=1; cpt<nlstate ; cpt ++) {      for (cpt=1; cpt<nlstate ; cpt ++) {
       k=3;        k=3;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
   
       for (i=1; i< nlstate ; i ++)        for (i=1; i< nlstate ; i ++)
         fprintf(ficgp,"+$%d",k+i+1);          fprintf(ficgp,"+$%d",k+i+1);
Line 2080  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2117  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
     }      }
   
     for(jk=1; jk <=m; jk++) {      for(jk=1; jk <=m; jk++) {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
    i=1;     i=1;
    for(k2=1; k2<=nlstate; k2++) {     for(k2=1; k2<=nlstate; k2++) {
      k3=i;       k3=i;
Line 2125  ij=1; Line 2162  ij=1;
   
   
 /*************** Moving average **************/  /*************** Moving average **************/
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){  void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){
   
   int i, cpt, cptcod;    int i, cpt, cptcod;
     for (agedeb=agemin; agedeb<=fage; agedeb++)      for (agedeb=ageminpar; agedeb<=fage; agedeb++)
       for (i=1; i<=nlstate;i++)        for (i=1; i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
           mobaverage[(int)agedeb][i][cptcod]=0.;            mobaverage[(int)agedeb][i][cptcod]=0.;
         
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){      for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
       for (i=1; i<=nlstate;i++){        for (i=1; i<=nlstate;i++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           for (cpt=0;cpt<=4;cpt++){            for (cpt=0;cpt<=4;cpt++){
Line 2148  void movingaverage(double agedeb, double Line 2185  void movingaverage(double agedeb, double
   
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
     
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
Line 2160  prevforecast(char fileres[], double anpr Line 2197  prevforecast(char fileres[], double anpr
  agelim=AGESUP;   agelim=AGESUP;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     
     
   strcpy(fileresf,"f");    strcpy(fileresf,"f");
Line 2174  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 2211  calagedate=(anproj1+mproj1/12.+jproj1/36
   
   if (mobilav==1) {    if (mobilav==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     movingaverage(agedeb, fage, agemin, mobaverage);      movingaverage(agedeb, fage, ageminpar, mobaverage);
   }    }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 2211  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 2248  calagedate=(anproj1+mproj1/12.+jproj1/36
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);  
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
           nhstepm = nhstepm/hstepm;            nhstepm = nhstepm/hstepm;
                     
Line 2221  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 2258  calagedate=(anproj1+mproj1/12.+jproj1/36
                 
           for (h=0; h<=nhstepm; h++){            for (h=0; h<=nhstepm; h++){
             if (h==(int) (calagedate+YEARM*cpt)) {              if (h==(int) (calagedate+YEARM*cpt)) {
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
             }              }
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
               kk1=0.;kk2=0;                kk1=0.;kk2=0;
Line 2250  calagedate=(anproj1+mproj1/12.+jproj1/36 Line 2287  calagedate=(anproj1+mproj1/12.+jproj1/36
   fclose(ficresf);    fclose(ficresf);
 }  }
 /************** Forecasting ******************/  /************** Forecasting ******************/
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
Line 2264  populforecast(char fileres[], double anp Line 2301  populforecast(char fileres[], double anp
   agelim=AGESUP;    agelim=AGESUP;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     
     
   strcpy(filerespop,"pop");    strcpy(filerespop,"pop");
Line 2278  populforecast(char fileres[], double anp Line 2315  populforecast(char fileres[], double anp
   
   if (mobilav==1) {    if (mobilav==1) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     movingaverage(agedeb, fage, agemin, mobaverage);      movingaverage(agedeb, fage, ageminpar, mobaverage);
   }    }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 2319  populforecast(char fileres[], double anp Line 2356  populforecast(char fileres[], double anp
       for (cpt=0; cpt<=0;cpt++) {        for (cpt=0; cpt<=0;cpt++) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);  
                 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
           nhstepm = nhstepm/hstepm;            nhstepm = nhstepm/hstepm;
                     
Line 2365  populforecast(char fileres[], double anp Line 2402  populforecast(char fileres[], double anp
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);  
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){          for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
           nhstepm = nhstepm/hstepm;            nhstepm = nhstepm/hstepm;
                     
Line 2411  int main(int argc, char *argv[]) Line 2448  int main(int argc, char *argv[])
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   double agedeb, agefin,hf;    double agedeb, agefin,hf;
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
   double fret;    double fret;
   double **xi,tmp,delta;    double **xi,tmp,delta;
Line 2424  int main(int argc, char *argv[]) Line 2461  int main(int argc, char *argv[])
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
     
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
   char filerest[FILENAMELENGTH];    char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];    char fileregp[FILENAMELENGTH];
Line 2456  int main(int argc, char *argv[]) Line 2493  int main(int argc, char *argv[])
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
     
   
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
Line 2469  int main(int argc, char *argv[]) Line 2506  int main(int argc, char *argv[])
   struct timeval start_time, end_time;    struct timeval start_time, end_time;
     
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
   printf("\n%s",version);    printf("\n%s",version);
   if(argc <=1){    if(argc <=1){
Line 2517  int main(int argc, char *argv[]) Line 2554  int main(int argc, char *argv[])
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
 while((c=getc(ficpar))=='#' && c!= EOF){  while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
Line 2624  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2661  while((c=getc(ficpar))=='#' && c!= EOF){
   printf("\n");    printf("\n");
   
   
     /*-------- data file ----------*/      /*-------- Rewriting paramater file ----------*/
     if((ficres =fopen(fileres,"w"))==NULL) {       strcpy(rfileres,"r");    /* "Rparameterfile */
       printf("Problem with resultfile: %s\n", fileres);goto end;       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
        strcat(rfileres,".");    /* */
        strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
     }      }
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
         
       /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {      if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;        printf("Problem with datafile: %s\n", datafile);goto end;
     }      }
Line 2671  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2713  while((c=getc(ficpar))=='#' && c!= EOF){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncov;j>=1;j--){          for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }          }
         num[i]=atol(stra);          num[i]=atol(stra);
Line 2690  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2732  while((c=getc(ficpar))=='#' && c!= EOF){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
     }      }*/
    
     for (i=1; i<=imx; i++)    /* for (i=1; i<=imx; i++){
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/       if (s[4][i]==9)  s[4][i]=-1;
        printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}
     */
    
   /* Calculation of the number of parameter from char model*/    /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15);    Tvar=ivector(1,15);
   Tprod=ivector(1,15);    Tprod=ivector(1,15);
Line 2709  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2753  while((c=getc(ficpar))=='#' && c!= EOF){
     cptcovn=j+1;      cptcovn=j+1;
     cptcovprod=j1;      cptcovprod=j1;
         
      
     strcpy(modelsav,model);      strcpy(modelsav,model);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
       printf("Error. Non available option model=%s ",model);        printf("Error. Non available option model=%s ",model);
Line 2740  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2783  while((c=getc(ficpar))=='#' && c!= EOF){
         }          }
         else {          else {
           cutv(strb,stre,strc,'V');            cutv(strb,stre,strc,'V');
           Tvar[i]=ncov+k1;            Tvar[i]=ncovcol+k1;
           cutv(strb,strc,strd,'V');            cutv(strb,strc,strd,'V');
           Tprod[k1]=i;            Tprod[k1]=i;
           Tvard[k1][1]=atoi(strc);            Tvard[k1][1]=atoi(strc);
Line 2748  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2791  while((c=getc(ficpar))=='#' && c!= EOF){
           Tvar[cptcovn+k2]=Tvard[k1][1];            Tvar[cptcovn+k2]=Tvard[k1][1];
           Tvar[cptcovn+k2+1]=Tvard[k1][2];            Tvar[cptcovn+k2+1]=Tvard[k1][2];
           for (k=1; k<=lastobs;k++)            for (k=1; k<=lastobs;k++)
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];              covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
           k1++;            k1++;
           k2=k2+2;            k2=k2+2;
         }          }
Line 2765  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2808  while((c=getc(ficpar))=='#' && c!= EOF){
     }      }
 }  }
     
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
   printf("cptcovprod=%d ", cptcovprod);    printf("cptcovprod=%d ", cptcovprod);
   scanf("%d ",i);*/    scanf("%d ",i);*/
     fclose(fic);      fclose(fic);
Line 2777  while((c=getc(ficpar))=='#' && c!= EOF){ Line 2820  while((c=getc(ficpar))=='#' && c!= EOF){
     /*-calculation of age at interview from date of interview and age at death -*/      /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);      agev=matrix(1,maxwav,1,imx);
   
    for (i=1; i<=imx; i++)      for (i=1; i<=imx; i++) {
      for(m=2; (m<= maxwav); m++)        for(m=2; (m<= maxwav); m++) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
          anint[m][i]=9999;           anint[m][i]=9999;
          s[m][i]=-1;           s[m][i]=-1;
        }         }
           if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
         }
       }
   
     for (i=1; i<=imx; i++)  {      for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){        for(m=1; (m<= maxwav); m++){
         if(s[m][i] >0){          if(s[m][i] >0){
           if (s[m][i] == nlstate+1) {            if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)              if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)                if(moisdc[i]!=99 && andc[i]!=9999)
               agev[m][i]=agedc[i];                  agev[m][i]=agedc[i];
             else {              /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
              else {
               if (andc[i]!=9999){                if (andc[i]!=9999){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                printf("Warning negative age at death: %d line:%d\n",num[i],i);
               agev[m][i]=-1;                agev[m][i]=-1;
Line 2867  printf("Total number of individuals= %d, Line 2914  printf("Total number of individuals= %d,
        for(j=1; j <= ncodemax[k]; j++){         for(j=1; j <= ncodemax[k]; j++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
            h++;             h++;
            if (h>m) h=1;codtab[h][k]=j;             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
              /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
          }           }
        }         }
      }       }
    }     }
      /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
         codtab[1][2]=1;codtab[2][2]=2; */
    /*for(i=1; i <=m ;i++){     /* for(i=1; i <=m ;i++){
      for(k=1; k <=cptcovn; k++){        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
      }        }
      printf("\n");        printf("\n");
    }        }
    scanf("%d",i);*/        scanf("%d",i);*/
         
    /* Calculates basic frequencies. Computes observed prevalence at single age     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */         and prints on file fileres'p'. */
Line 2902  printf("Total number of individuals= %d, Line 2950  printf("Total number of individuals= %d,
     }      }
         
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
    jk=1;     jk=1;
    fprintf(ficres,"# Parameters\n");     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    printf("# Parameters\n");     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    for(i=1,jk=1; i <=nlstate; i++){     for(i=1,jk=1; i <=nlstate; i++){
      for(k=1; k <=(nlstate+ndeath); k++){       for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i)         if (k != i)
Line 2929  printf("Total number of individuals= %d, Line 2977  printf("Total number of individuals= %d,
     ftolhess=ftol; /* Usually correct */      ftolhess=ftol; /* Usually correct */
     hesscov(matcov, p, npar, delti, ftolhess, func);      hesscov(matcov, p, npar, delti, ftolhess, func);
  }   }
     fprintf(ficres,"# Scales\n");      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales\n");      printf("# Scales (for hessian or gradient estimation)\n");
      for(i=1,jk=1; i <=nlstate; i++){       for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){        for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {          if (j!=i) {
Line 2948  printf("Total number of individuals= %d, Line 2996  printf("Total number of individuals= %d,
      }       }
         
     k=1;      k=1;
     fprintf(ficres,"# Covariance\n");      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     printf("# Covariance\n");      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1;i<=npar;i++){      for(i=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;        /*  if (k>nlstate) k=1;
       i1=(i-1)/(ncovmodel*nlstate)+1;        i1=(i-1)/(ncovmodel*nlstate)+1;
Line 2974  printf("Total number of individuals= %d, Line 3022  printf("Total number of individuals= %d,
     }      }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);      fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);
         
     if (fage <= 2) {      if (fage <= 2) {
       bage = agemin;        bage = ageminpar;
       fage = agemaxpar;        fage = agemaxpar;
     }      }
         
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);
     
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
Line 3041  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3089  while((c=getc(ficpar))=='#' && c!= EOF){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
 /*------------ gnuplot -------------*/  /*------------ gnuplot -------------*/
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);   printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);
     
 /*------------ free_vector  -------------*/  /*------------ free_vector  -------------*/
  chdir(path);   chdir(path);
Line 3057  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3105  while((c=getc(ficpar))=='#' && c!= EOF){
   
 /*--------- index.htm --------*/  /*--------- index.htm --------*/
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);    printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);
   
     
   /*--------------- Prevalence limit --------------*/    /*--------------- Prevalence limit --------------*/
Line 3080  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3128  while((c=getc(ficpar))=='#' && c!= EOF){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   k=0;    k=0;
   agebase=agemin;    agebase=ageminpar;
   agelim=agemaxpar;    agelim=agemaxpar;
   ftolpl=1.e-10;    ftolpl=1.e-10;
   i1=cptcoveff;    i1=cptcoveff;
Line 3160  while((c=getc(ficpar))=='#' && c!= EOF){ Line 3208  while((c=getc(ficpar))=='#' && c!= EOF){
   
   
   /*---------- Forecasting ------------------*/    /*---------- Forecasting ------------------*/
   if(stepm == 1) {    if((stepm == 1) && (strcmp(model,".")==0)){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
     free_matrix(mint,1,maxwav,1,n);      free_matrix(mint,1,maxwav,1,n);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
     free_vector(weight,1,n);}      free_vector(weight,1,n);}
   else{    else{
     erreur=108;      erreur=108;
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);      printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
   }    }
     
   
Line 3207  if (popforecast==1) populforecast(filere Line 3255  if (popforecast==1) populforecast(filere
   
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
   
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
Line 3228  if (popforecast==1) populforecast(filere Line 3276  if (popforecast==1) populforecast(filere
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
       fprintf(ficrest,"\n");        fprintf(ficrest,"\n");
   
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);        epj=vector(1,nlstate+1);
       for(age=bage; age <=fage ;age++){        for(age=bage; age <=fage ;age++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
Line 3238  if (popforecast==1) populforecast(filere Line 3284  if (popforecast==1) populforecast(filere
             prlim[i][i]=probs[(int)age][i][k];              prlim[i][i]=probs[(int)age][i][k];
         }          }
                 
         fprintf(ficrest," %.0f",age);          fprintf(ficrest," %4.0f",age);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(i=1, epj[j]=0.;i <=nlstate;i++) {
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];              epj[j] += prlim[i][i]*eij[i][j][(int)age];
           }            }
           epj[nlstate+1] +=epj[j];            epj[nlstate+1] +=epj[j];
         }          }
         for(i=1, vepp=0.;i <=nlstate;i++)          for(i=1, vepp=0.;i <=nlstate;i++)
           for(j=1;j <=nlstate;j++)            for(j=1;j <=nlstate;j++)
             vepp += vareij[i][j][(int)age];              vepp += vareij[i][j][(int)age];
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));
         for(j=1;j <=nlstate;j++){          for(j=1;j <=nlstate;j++){
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));            fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));
         }          }
         fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
       }        }
Line 3308  if (popforecast==1) populforecast(filere Line 3354  if (popforecast==1) populforecast(filere
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
   if(erreur >0)    if(erreur >0)
     printf("End of Imach with error %d\n",erreur);      printf("End of Imach with error or warning %d\n",erreur);
   else   printf("End of Imach\n");    else   printf("End of Imach\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
Line 3332  if (popforecast==1) populforecast(filere Line 3378  if (popforecast==1) populforecast(filere
   
 #ifdef windows  #ifdef windows
   while (z[0] != 'q') {    while (z[0] != 'q') {
     chdir(path);      /* chdir(path); */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
     scanf("%s",z);      scanf("%s",z);
     if (z[0] == 'c') system("./imach");      if (z[0] == 'c') system("./imach");
     else if (z[0] == 'e') {      else if (z[0] == 'e') system(optionfilehtm);
       chdir(path);      else if (z[0] == 'g') system(plotcmd);
       system(optionfilehtm);  
     }  
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
 #endif  #endif
Removed from v.1.28  
changed lines
  Added in v.1.35

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