--- imach/src/imach.c	2002/02/22 18:08:30	1.23
+++ imach/src/imach.c	2002/03/08 16:17:18	1.30
@@ -1,5 +1,5 @@
-/* $Id: imach.c,v 1.23 2002/02/22 18:08:30 lievre Exp $
-   Interpolate Markov Chain
+/* $Id: imach.c,v 1.30 2002/03/08 16:17:18 lievre Exp $
+   Interpolated Markov Chain
 
   Short summary of the programme:
   
@@ -94,8 +94,8 @@ int **dh; /* dh[mi][i] is number of step
 double jmean; /* Mean space between 2 waves */
 double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;
-FILE *ficgp, *fichtm,*ficresprob,*ficpop;
+FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+FILE *ficgp,*ficresprob,*ficpop;
 FILE *ficreseij;
   char filerese[FILENAMELENGTH];
  FILE  *ficresvij;
@@ -123,7 +123,7 @@ FILE *ficreseij;
 static double maxarg1,maxarg2;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
- 
+  
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)
 
@@ -1176,7 +1176,7 @@ void lubksb(double **a, int n, int *indx
 } 
 
 /************ 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)
+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 */
  
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;
@@ -1185,7 +1185,7 @@ void  freqsummary(char fileres[], int ag
   double pos, k2, dateintsum=0,k2cpt=0;
   FILE *ficresp;
   char fileresp[FILENAMELENGTH];
-
+ 
   pp=vector(1,nlstate);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileresp,"p");
@@ -1236,6 +1236,9 @@ void  freqsummary(char fileres[], int ag
 	   }
 	 }
        }
+       
+       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+
         if  (cptcovn>0) {
 	 fprintf(ficresp, "\n#********** Variable "); 
 	 for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
@@ -1304,7 +1307,7 @@ void  freqsummary(char fileres[], int ag
 }
 
 /************ Prevalence ********************/
-void prevalence(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 calagedate)
+void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
 {  /* Some frequencies */
  
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;
@@ -1329,14 +1332,14 @@ void prevalence(int agemin, int agemax,
 	for (jk=-1; jk<=nlstate+ndeath; jk++)  
 	  for(m=agemin; m <= agemax+3; m++)
 	    freq[i][jk][m]=0;
-      
+     
       for (i=1; i<=imx; i++) {
 	bool=1;
 	if  (cptcovn>0) {
 	  for (z1=1; z1<=cptcoveff; z1++) 
 	    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 	      bool=0;
-	}
+	} 
 	if (bool==1) { 
 	  for(m=firstpass; m<=lastpass; m++){
 	    k2=anint[m][i]+(mint[m][i]/12.);
@@ -1344,12 +1347,11 @@ void prevalence(int agemin, int agemax,
 	      if(agev[m][i]==0) agev[m][i]=agemax+1;
 	      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];
-	      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];  */ 
 	    }
 	  }
 	}
       }
-      
 	for(i=(int)agemin; i <= (int)agemax+3; i++){ 
 	  for(jk=1; jk <=nlstate ; jk++){
 	    for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
@@ -1441,7 +1443,7 @@ void  concatwav(int wav[], int **dh, int
 	  if (j >= jmax) jmax=j;
 	  if (j <= jmin) jmin=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{
@@ -1449,7 +1451,7 @@ void  concatwav(int wav[], int **dh, int
 	  k=k+1;
 	  if (j >= jmax) jmax=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;
 	}
 	jk= j/stepm;
@@ -1544,26 +1546,29 @@ void evsij(char fileres[], double ***eij
     /* nhstepm age range expressed in number of stepm */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years = 20*12/6=40 stepm */ 
-    if (stepm >= YEARM) hstepm=1;
+    /*if (stepm >= YEARM) hstepm=1;*/
+hstepm=1;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
-
-
+hf=stepm/YEARM;
+/*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
-	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){
-	  eij[i][j][(int)age] +=p3mat[i][j][h];
+	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+	  eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;
 	}
     
-    hf=1;
-    if (stepm >= YEARM) hf=stepm/YEARM;
-    fprintf(ficreseij,"%.0f",age );
+    /* hf=1;
+       if (stepm >= YEARM) hf=stepm/YEARM;*/
+hf=stepm/YEARM;
+ 
+    fprintf(ficreseij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)
       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");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
@@ -1620,7 +1625,7 @@ void varevsij(char fileres[], double ***
 	for(i=1; i<=nlstate;i++)
 	  prlim[i][i]=probs[(int)age][i][ij];
       }
-      
+  
       for(j=1; j<= nlstate; j++){
 	for(h=0; h<=nhstepm; h++){
 	  for(i=1, gp[h][j]=0.;i<=nlstate;i++)
@@ -1632,7 +1637,7 @@ void varevsij(char fileres[], double ***
 	xp[i] = x[i] - (i==theta ?delti[theta]:0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-
+ 
       if (popbased==1) {
 	for(i=1; i<=nlstate;i++)
 	  prlim[i][i]=probs[(int)age][i][ij];
@@ -1684,7 +1689,7 @@ void varevsij(char fileres[], double ***
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   } /* End age */
- 
+  
   free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);
@@ -1876,146 +1881,665 @@ if (i== 4) fprintf(ficresprob,"%.3e %.3e
 }
  free_vector(xp,1,npar);
 fclose(ficresprob);
- exit(0);
-}
-
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
-
-int main(int argc, char *argv[])
-{
-
-  int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
-  double agedeb, agefin,hf;
-  double agemin=1.e20, agemax=-1.e20;
 
-  double fret;
-  double **xi,tmp,delta;
-
-  double dum; /* Dummy variable */
-  double ***p3mat;
-  int *indx;
-  char line[MAXLINE], linepar[MAXLINE];
-  char title[MAXLINE];
-  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
-  char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
-  
-  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];
-
-  char filerest[FILENAMELENGTH];
-  char fileregp[FILENAMELENGTH];
-  char popfile[FILENAMELENGTH];
-  char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
-  int firstobs=1, lastobs=10;
-  int sdeb, sfin; /* Status at beginning and end */
-  int c,  h , cpt,l;
-  int ju,jl, mi;
-  int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
-  int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
-  int mobilav=0,popforecast=0;
-  int hstepm, nhstepm;
-  int *popage;/*boolprev=0 if date and zero if wave*/
-  double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;
+}
 
-  double bage, fage, age, agelim, agebase;
-  double ftolpl=FTOL;
-  double **prlim;
-  double *severity;
-  double ***param; /* Matrix of parameters */
-  double  *p;
-  double **matcov; /* Matrix of covariance */
-  double ***delti3; /* Scale */
-  double *delti; /* Scale */
-  double ***eij, ***vareij;
-  double **varpl; /* Variances of prevalence limits by age */
-  double *epj, vepp;
-  double kk1, kk2;
-  double *popeffectif,*popcount;
-  double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;
-  double yp,yp1,yp2;
+/******************* 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[],char rfileres[] ){
+  int jj1, k1, i1, cpt;
+  FILE *fichtm;
+  /*char optionfilehtm[FILENAMELENGTH];*/
 
-  char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";
-  char *alph[]={"a","a","b","c","d","e"}, str[4];
+  strcpy(optionfilehtm,optionfile);
+  strcat(optionfilehtm,".htm");
+  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtm), exit(0);
+  }
 
+ fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\"> 
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
 
-  char z[1]="c", occ;
-#include <sys/time.h>
-#include <time.h>
-  char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+Total number of observations=%d <br>
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
+<hr  size=\"2\" color=\"#EC5E5E\"> 
+<li>Outputs files<br><br>\n
+        - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
+- Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
+        - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
+        - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
+        - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
+        - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
+        - 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>
+        - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
+        - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>
+        - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>
+	<br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
  
-  /* long total_usecs;
-  struct timeval start_time, end_time;
-  
-  gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+fprintf(fichtm," <li>Graphs</li><p>");
 
+ m=cptcoveff;
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 
-  printf("\n%s",version);
-  if(argc <=1){
-    printf("\nEnter the parameter file name: ");
-    scanf("%s",pathtot);
-  }
-  else{
-    strcpy(pathtot,argv[1]);
-  }
-  /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
-  /*cygwin_split_path(pathtot,path,optionfile);
-    printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
-  /* cutv(path,optionfile,pathtot,'\\');*/
+ jj1=0;
+ for(k1=1; k1<=m;k1++){
+   for(i1=1; i1<=ncodemax[k1];i1++){
+       jj1++;
+       if (cptcovn > 0) {
+	 fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+	 for (cpt=1; cpt<=cptcoveff;cpt++) 
+	   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+	 fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+       }
+       fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
+<img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
+       for(cpt=1; cpt<nlstate;cpt++){
+	 fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
+<img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+       }
+    for(cpt=1; cpt<=nlstate;cpt++) {
+       fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+interval) in state (%d): v%s%d%d.gif <br>
+<img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
+     }
+     for(cpt=1; cpt<=nlstate;cpt++) {
+        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
+<img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+     }
+     fprintf(fichtm,"\n<br>- Total life expectancy by age and
+health expectancies in states (1) and (2): e%s%d.gif<br>
+<img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+fprintf(fichtm,"\n</body>");
+   }
+   }
+fclose(fichtm);
+}
 
-  split(pathtot,path,optionfile,optionfilext,optionfilefiname);
-   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
-  chdir(path);
-  replace(pathc,path);
+/******************* Gnuplot file **************/
+void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){
 
-/*-------- arguments in the command line --------*/
+  int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
 
-  strcpy(fileres,"r");
-  strcat(fileres, optionfilefiname);
-  strcat(fileres,".txt");    /* Other files have txt extension */
+  strcpy(optionfilegnuplot,optionfilefiname);
+  strcat(optionfilegnuplot,".plt");
+  if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+    printf("Problem with file %s",optionfilegnuplot);
+  }
 
-  /*---------arguments file --------*/
+#ifdef windows
+    fprintf(ficgp,"cd \"%s\" \n",pathc);
+#endif
+m=pow(2,cptcoveff);
+  
+ /* 1eme*/
+  for (cpt=1; cpt<= nlstate ; cpt ++) {
+   for (k1=1; k1<= m ; k1 ++) {
 
-  if((ficpar=fopen(optionfile,"r"))==NULL)    {
-    printf("Problem with optionfile %s\n",optionfile);
-    goto end;
-  }
+#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);
+#endif
+#ifdef unix
+fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
+#endif
 
-  strcpy(filereso,"o");
-  strcat(filereso,fileres);
-  if((ficparo=fopen(filereso,"w"))==NULL) {
-    printf("Problem with Output resultfile: %s\n", filereso);goto end;
+for (i=1; i<= nlstate ; i ++) {
+  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}
+    fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
+    for (i=1; i<= nlstate ; i ++) {
+  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+} 
+  fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
+     for (i=1; i<= nlstate ; i ++) {
+  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}  
+     fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+#ifdef unix
+fprintf(ficgp,"\nset ter gif small size 400,300");
+#endif
+fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
+   }
   }
+  /*2 eme*/
 
-  /* Reads comments: lines beginning with '#' */
-  while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
+  for (k1=1; k1<= m ; k1 ++) { 
+    fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
+    
+    for (i=1; i<= nlstate+1 ; i ++) {
+      k=2*i;
+      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+      for (j=1; j<= nlstate+1 ; j ++) {
+  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}   
+      if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+      else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+    fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+      for (j=1; j<= nlstate+1 ; j ++) {
+	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+	else fprintf(ficgp," \%%*lf (\%%*lf)");
+}   
+      fprintf(ficgp,"\" t\"\" w l 0,");
+     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+      for (j=1; j<= nlstate+1 ; j ++) {
+  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+  else fprintf(ficgp," \%%*lf (\%%*lf)");
+}   
+      if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+      else fprintf(ficgp,"\" t\"\" w l 0,");
+    }
+    fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
   }
-  ungetc(c,ficpar);
+ 
+  /*3eme*/
 
-  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);
-  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);
-  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);
-while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
-  
-   
-  covar=matrix(0,NCOVMAX,1,n); 
-  cptcovn=0; 
-  if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+  for (k1=1; k1<= m ; k1 ++) { 
+    for (cpt=1; cpt<= nlstate ; cpt ++) {
+      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);
+      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,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
+    }
+    }
+ 
+  /* CV preval stat */
+    for (k1=1; k1<= m ; k1 ++) { 
+    for (cpt=1; cpt<nlstate ; cpt ++) {
+      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);
 
-  ncovmodel=2+cptcovn;
-  nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
-  
-  /* Read guess parameters */
+      for (i=1; i< nlstate ; i ++)
+	fprintf(ficgp,"+$%d",k+i+1);
+      fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+      
+      l=3+(nlstate+ndeath)*cpt;
+      fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+      for (i=1; i< nlstate ; i ++) {
+	l=3+(nlstate+ndeath)*cpt;
+	fprintf(ficgp,"+$%d",l+i+1);
+      }
+      fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
+      fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
+    } 
+  }  
+  
+  /* proba elementaires */
+   for(i=1,jk=1; i <=nlstate; i++){
+    for(k=1; k <=(nlstate+ndeath); k++){
+      if (k != i) {
+	for(j=1; j <=ncovmodel; j++){
+	
+	  fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+	  jk++; 
+	  fprintf(ficgp,"\n");
+	}
+      }
+    }
+    }
+
+    for(jk=1; jk <=m; jk++) {
+  fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);
+   i=1;
+   for(k2=1; k2<=nlstate; k2++) {
+     k3=i;
+     for(k=1; k<=(nlstate+ndeath); k++) {
+       if (k != k2){
+    	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+ij=1;
+	for(j=3; j <=ncovmodel; j++) {
+	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+	    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+	    ij++;
+	  }
+	  else
+	  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+	}
+	  fprintf(ficgp,")/(1");
+	
+	for(k1=1; k1 <=nlstate; k1++){   
+	  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+ij=1;
+	  for(j=3; j <=ncovmodel; j++){
+	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+	    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+	    ij++;
+	  }
+	  else
+	    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+	  }
+	  fprintf(ficgp,")");
+	}
+	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+	i=i+ncovmodel;
+       }
+     }
+   }
+   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
+   }
+   
+  fclose(ficgp);
+}  /* end gnuplot */
+
+
+/*************** Moving average **************/
+void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){
+
+  int i, cpt, cptcod;
+    for (agedeb=agemin; agedeb<=fage; agedeb++)
+      for (i=1; i<=nlstate;i++)
+	for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
+	  mobaverage[(int)agedeb][i][cptcod]=0.;
+    
+    for (agedeb=agemin+4; agedeb<=fage; agedeb++){
+      for (i=1; i<=nlstate;i++){
+	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+	  for (cpt=0;cpt<=4;cpt++){
+	    mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
+	  }
+	  mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
+	}
+      }
+    }
+    
+}
+
+
+/************** 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){
+  
+  int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+  int *popage;
+  double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+  double *popeffectif,*popcount;
+  double ***p3mat;
+  char fileresf[FILENAMELENGTH];
+
+ agelim=AGESUP;
+calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+
+  prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+ 
+ 
+  strcpy(fileresf,"f"); 
+  strcat(fileresf,fileres);
+  if((ficresf=fopen(fileresf,"w"))==NULL) {
+    printf("Problem with forecast resultfile: %s\n", fileresf);
+  }
+  printf("Computing forecasting: result on file '%s' \n", fileresf);
+
+  if (cptcoveff==0) ncodemax[cptcoveff]=1;
+
+  if (mobilav==1) {
+    mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    movingaverage(agedeb, fage, agemin, mobaverage);
+  }
+
+  stepsize=(int) (stepm+YEARM-1)/YEARM;
+  if (stepm<=12) stepsize=1;
+  
+  agelim=AGESUP;
+  
+  hstepm=1;
+  hstepm=hstepm/stepm; 
+  yp1=modf(dateintmean,&yp);
+  anprojmean=yp;
+  yp2=modf((yp1*12),&yp);
+  mprojmean=yp;
+  yp1=modf((yp2*30.5),&yp);
+  jprojmean=yp;
+  if(jprojmean==0) jprojmean=1;
+  if(mprojmean==0) jprojmean=1;
+  
+  fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
+  
+  for(cptcov=1;cptcov<=i2;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      k=k+1;
+      fprintf(ficresf,"\n#******");
+      for(j=1;j<=cptcoveff;j++) {
+	fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      }
+      fprintf(ficresf,"******\n");
+      fprintf(ficresf,"# StartingAge FinalAge");
+      for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+      
+      
+      for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
+	fprintf(ficresf,"\n");
+	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--){ 
+	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
+	  nhstepm = nhstepm/hstepm; 
+	  
+	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	  oldm=oldms;savm=savms;
+	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
+	
+	  for (h=0; h<=nhstepm; h++){
+	    if (h==(int) (calagedate+YEARM*cpt)) {
+	      fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
+	    } 
+	    for(j=1; j<=nlstate+ndeath;j++) {
+	      kk1=0.;kk2=0;
+	      for(i=1; i<=nlstate;i++) {	      
+		if (mobilav==1) 
+		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+		else {
+		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+		}
+		
+	      }
+	      if (h==(int)(calagedate+12*cpt)){
+		fprintf(ficresf," %.3f", kk1);
+	     		
+	      }
+	    }
+	  }
+	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	}
+      }
+    }
+  }
+       
+  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+  fclose(ficresf);
+}
+/************** 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){
+  
+  int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+  int *popage;
+  double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+  double *popeffectif,*popcount;
+  double ***p3mat,***tabpop,***tabpopprev;
+  char filerespop[FILENAMELENGTH];
+
+  tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  agelim=AGESUP;
+  calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+  
+  prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+  
+  
+  strcpy(filerespop,"pop"); 
+  strcat(filerespop,fileres);
+  if((ficrespop=fopen(filerespop,"w"))==NULL) {
+    printf("Problem with forecast resultfile: %s\n", filerespop);
+  }
+  printf("Computing forecasting: result on file '%s' \n", filerespop);
+
+  if (cptcoveff==0) ncodemax[cptcoveff]=1;
+
+  if (mobilav==1) {
+    mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+    movingaverage(agedeb, fage, agemin, mobaverage);
+  }
+
+  stepsize=(int) (stepm+YEARM-1)/YEARM;
+  if (stepm<=12) stepsize=1;
+  
+  agelim=AGESUP;
+  
+  hstepm=1;
+  hstepm=hstepm/stepm; 
+  
+  if (popforecast==1) {
+    if((ficpop=fopen(popfile,"r"))==NULL) {
+      printf("Problem with population file : %s\n",popfile);exit(0);
+    } 
+    popage=ivector(0,AGESUP);
+    popeffectif=vector(0,AGESUP);
+    popcount=vector(0,AGESUP);
+    
+    i=1;   
+    while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+   
+    imx=i;
+    for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+  }
+
+  for(cptcov=1;cptcov<=i2;cptcov++){
+   for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+      k=k+1;
+      fprintf(ficrespop,"\n#******");
+      for(j=1;j<=cptcoveff;j++) {
+	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      }
+      fprintf(ficrespop,"******\n");
+      fprintf(ficrespop,"# Age");
+      for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+      if (popforecast==1)  fprintf(ficrespop," [Population]");
+      
+      for (cpt=0; cpt<=0;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--){ 
+	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
+	  nhstepm = nhstepm/hstepm; 
+	  
+	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	  oldm=oldms;savm=savms;
+	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
+	
+	  for (h=0; h<=nhstepm; h++){
+	    if (h==(int) (calagedate+YEARM*cpt)) {
+	      fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+	    } 
+	    for(j=1; j<=nlstate+ndeath;j++) {
+	      kk1=0.;kk2=0;
+	      for(i=1; i<=nlstate;i++) {	      
+		if (mobilav==1) 
+		  kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+		else {
+		  kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+		}
+	      }
+	      if (h==(int)(calagedate+12*cpt)){
+		tabpop[(int)(agedeb)][j][cptcod]=kk1;
+		  /*fprintf(ficrespop," %.3f", kk1);
+		    if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+	      }
+	    }
+	    for(i=1; i<=nlstate;i++){
+	      kk1=0.;
+		for(j=1; j<=nlstate;j++){
+		  kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
+		}
+		  tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+	    }
+
+	    if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) 
+	      fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+	  }
+	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	}
+      }
+ 
+  /******/
+
+      for (cpt=1; cpt<=(anpyram1-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--){ 
+	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
+	  nhstepm = nhstepm/hstepm; 
+	  
+	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	  oldm=oldms;savm=savms;
+	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
+	  for (h=0; h<=nhstepm; h++){
+	    if (h==(int) (calagedate+YEARM*cpt)) {
+	      fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+	    } 
+	    for(j=1; j<=nlstate+ndeath;j++) {
+	      kk1=0.;kk2=0;
+	      for(i=1; i<=nlstate;i++) {	      
+		kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	
+	      }
+	      if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);	
+	    }
+	  }
+	  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+	}
+      }
+   } 
+  }
+ 
+  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+  if (popforecast==1) {
+    free_ivector(popage,0,AGESUP);
+    free_vector(popeffectif,0,AGESUP);
+    free_vector(popcount,0,AGESUP);
+  }
+  free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+  fclose(ficrespop);
+}
+
+/***********************************************/
+/**************** Main Program *****************/
+/***********************************************/
+
+int main(int argc, char *argv[])
+{
+
+  int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+  double agedeb, agefin,hf;
+  double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+
+  double fret;
+  double **xi,tmp,delta;
+
+  double dum; /* Dummy variable */
+  double ***p3mat;
+  int *indx;
+  char line[MAXLINE], linepar[MAXLINE];
+  char title[MAXLINE];
+  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+  char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+  
+  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+
+  char filerest[FILENAMELENGTH];
+  char fileregp[FILENAMELENGTH];
+  char popfile[FILENAMELENGTH];
+  char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
+  int firstobs=1, lastobs=10;
+  int sdeb, sfin; /* Status at beginning and end */
+  int c,  h , cpt,l;
+  int ju,jl, mi;
+  int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+  int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; 
+  int mobilav=0,popforecast=0;
+  int hstepm, nhstepm;
+  double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;
+
+  double bage, fage, age, agelim, agebase;
+  double ftolpl=FTOL;
+  double **prlim;
+  double *severity;
+  double ***param; /* Matrix of parameters */
+  double  *p;
+  double **matcov; /* Matrix of covariance */
+  double ***delti3; /* Scale */
+  double *delti; /* Scale */
+  double ***eij, ***vareij;
+  double **varpl; /* Variances of prevalence limits by age */
+  double *epj, vepp;
+  double kk1, kk2;
+  double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+  
+
+  char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";
+  char *alph[]={"a","a","b","c","d","e"}, str[4];
+
+
+  char z[1]="c", occ;
+#include <sys/time.h>
+#include <time.h>
+  char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+ 
+  /* long total_usecs;
+  struct timeval start_time, end_time;
+  
+  gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+
+
+  printf("\n%s",version);
+  if(argc <=1){
+    printf("\nEnter the parameter file name: ");
+    scanf("%s",pathtot);
+  }
+  else{
+    strcpy(pathtot,argv[1]);
+  }
+  /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
+  /*cygwin_split_path(pathtot,path,optionfile);
+    printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+  /* cutv(path,optionfile,pathtot,'\\');*/
+
+  split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+  chdir(path);
+  replace(pathc,path);
+
+/*-------- arguments in the command line --------*/
+
+  strcpy(fileres,"r");
+  strcat(fileres, optionfilefiname);
+  strcat(fileres,".txt");    /* Other files have txt extension */
+
+  /*---------arguments file --------*/
+
+  if((ficpar=fopen(optionfile,"r"))==NULL)    {
+    printf("Problem with optionfile %s\n",optionfile);
+    goto end;
+  }
+
+  strcpy(filereso,"o");
+  strcat(filereso,fileres);
+  if((ficparo=fopen(filereso,"w"))==NULL) {
+    printf("Problem with Output resultfile: %s\n", filereso);goto end;
+  }
+
+  /* Reads comments: lines beginning with '#' */
+  while((c=getc(ficpar))=='#' && c!= EOF){
+    ungetc(c,ficpar);
+    fgets(line, MAXLINE, ficpar);
+    puts(line);
+    fputs(line,ficparo);
+  }
+  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);
+  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);
+  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);
+while((c=getc(ficpar))=='#' && c!= EOF){
+    ungetc(c,ficpar);
+    fgets(line, MAXLINE, ficpar);
+    puts(line);
+    fputs(line,ficparo);
+  }
+  ungetc(c,ficpar);
+  
+   
+  covar=matrix(0,NCOVMAX,1,n); 
+  cptcovn=0; 
+  if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+
+  ncovmodel=2+cptcovn;
+  nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+  
+  /* Read guess parameters */
   /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
@@ -2103,12 +2627,17 @@ while((c=getc(ficpar))=='#' && c!= EOF){
   printf("\n");
 
 
-    /*-------- data file ----------*/
-    if((ficres =fopen(fileres,"w"))==NULL) {
-      printf("Problem with resultfile: %s\n", fileres);goto end;
+    /*-------- Rewriting paramater file ----------*/
+     strcpy(rfileres,"r");    /* "Rparameterfile */
+     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);
     
+    /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
     }
@@ -2381,7 +2910,7 @@ printf("Total number of individuals= %d,
     }
     
     /*--------- 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 ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);
   
 
    jk=1;
@@ -2410,287 +2939,72 @@ printf("Total number of individuals= %d,
  }
     fprintf(ficres,"# Scales\n");
     printf("# Scales\n");
-     for(i=1,jk=1; i <=nlstate; i++){
-      for(j=1; j <=nlstate+ndeath; j++){
-	if (j!=i) {
-	  fprintf(ficres,"%1d%1d",i,j);
-	  printf("%1d%1d",i,j);
-	  for(k=1; k<=ncovmodel;k++){
-	    printf(" %.5e",delti[jk]);
-	    fprintf(ficres," %.5e",delti[jk]);
-	    jk++;
-	  }
-	  printf("\n");
-	  fprintf(ficres,"\n");
-	}
-      }
-     }
-    
-    k=1;
-    fprintf(ficres,"# Covariance\n");
-    printf("# Covariance\n");
-    for(i=1;i<=npar;i++){
-      /*  if (k>nlstate) k=1;
-      i1=(i-1)/(ncovmodel*nlstate)+1; 
-      fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
-      printf("%s%d%d",alph[k],i1,tab[i]);*/
-      fprintf(ficres,"%3d",i);
-      printf("%3d",i);
-      for(j=1; j<=i;j++){
-	fprintf(ficres," %.5e",matcov[i][j]);
-	printf(" %.5e",matcov[i][j]);
-      }
-      fprintf(ficres,"\n");
-      printf("\n");
-      k++;
-    }
-    
-    while((c=getc(ficpar))=='#' && c!= EOF){
-      ungetc(c,ficpar);
-      fgets(line, MAXLINE, ficpar);
-      puts(line);
-      fputs(line,ficparo);
-    }
-    ungetc(c,ficpar);
-  
-    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
-    
-    if (fage <= 2) {
-      bage = agemin;
-      fage = agemax;
-    }
-    
-    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,agemax,bage,fage);
-    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
- 
-    while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
-  
-  fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
-  fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
- fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
-     
-  while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
- 
-
-   dateprev1=anprev1+mprev1/12.+jprev1/365.;
-   dateprev2=anprev2+mprev2/12.+jprev2/365.;
-
-  fscanf(ficpar,"pop_based=%d\n",&popbased);
-   fprintf(ficparo,"pop_based=%d\n",popbased);   
-   fprintf(ficres,"pop_based=%d\n",popbased);   
-
-  while((c=getc(ficpar))=='#' && c!= EOF){
-    ungetc(c,ficpar);
-    fgets(line, MAXLINE, ficpar);
-    puts(line);
-    fputs(line,ficparo);
-  }
-  ungetc(c,ficpar);
-  fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
-fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
-fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
-
- freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);
-
-    
-    /*------------ gnuplot -------------*/
-    /*chdir(pathcd);*/
-    strcpy(optionfilegnuplot,optionfilefiname);
-    strcat(optionfilegnuplot,".plt");
-    if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
-      printf("Problem with file %s",optionfilegnuplot);goto end;
-    }
-#ifdef windows
-    fprintf(ficgp,"cd \"%s\" \n",pathc);
-#endif
-m=pow(2,cptcoveff);
-  
- /* 1eme*/
-  for (cpt=1; cpt<= nlstate ; cpt ++) {
-   for (k1=1; k1<= m ; k1 ++) {
-
-#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);
-#endif
-#ifdef unix
-fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);
-#endif
-
-for (i=1; i<= nlstate ; i ++) {
-  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}
-    fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
-    for (i=1; i<= nlstate ; i ++) {
-  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-} 
-  fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
-     for (i=1; i<= nlstate ; i ++) {
-  if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}  
-     fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
-#ifdef unix
-fprintf(ficgp,"\nset ter gif small size 400,300");
-#endif
-fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-   }
-  }
-  /*2 eme*/
-
-  for (k1=1; k1<= m ; k1 ++) { 
-    fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);
-    
-    for (i=1; i<= nlstate+1 ; i ++) {
-      k=2*i;
-      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
-      for (j=1; j<= nlstate+1 ; j ++) {
-  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}   
-      if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
-      else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
-    fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
-      for (j=1; j<= nlstate+1 ; j ++) {
-	if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-	else fprintf(ficgp," \%%*lf (\%%*lf)");
-}   
-      fprintf(ficgp,"\" t\"\" w l 0,");
-     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
-      for (j=1; j<= nlstate+1 ; j ++) {
-  if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
-  else fprintf(ficgp," \%%*lf (\%%*lf)");
-}   
-      if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
-      else fprintf(ficgp,"\" t\"\" w l 0,");
-    }
-    fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
-  }
- 
-  /*3eme*/
-
-  for (k1=1; k1<= m ; k1 ++) { 
-    for (cpt=1; cpt<= nlstate ; cpt ++) {
-      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);
-      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,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-    }
-  }
- 
-  /* CV preval stat */
-  for (k1=1; k1<= m ; k1 ++) { 
-    for (cpt=1; cpt<nlstate ; cpt ++) {
-      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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
-      for (i=1; i< nlstate ; i ++)
-	fprintf(ficgp,"+$%d",k+i+1);
-      fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-      
-      l=3+(nlstate+ndeath)*cpt;
-      fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
-      for (i=1; i< nlstate ; i ++) {
-	l=3+(nlstate+ndeath)*cpt;
-	fprintf(ficgp,"+$%d",l+i+1);
-      }
-      fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
-      fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
-    } 
-  }  
-
-  /* proba elementaires */
-   for(i=1,jk=1; i <=nlstate; i++){
-    for(k=1; k <=(nlstate+ndeath); k++){
-      if (k != i) {
-	for(j=1; j <=ncovmodel; j++){
-	  /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
-	  /*fprintf(ficgp,"%s",alph[1]);*/
-	  fprintf(ficgp,"p%d=%f ",jk,p[jk]);
-	  jk++; 
-	  fprintf(ficgp,"\n");
-	}
-      }
-    }
-    }
-
-  for(jk=1; jk <=m; jk++) {
-  fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
-   i=1;
-   for(k2=1; k2<=nlstate; k2++) {
-     k3=i;
-     for(k=1; k<=(nlstate+ndeath); k++) {
-       if (k != k2){
-    	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-ij=1;
-	for(j=3; j <=ncovmodel; j++) {
-	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-	    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-	    ij++;
-	  }
-	  else
-	  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	}
-	  fprintf(ficgp,")/(1");
-	
-	for(k1=1; k1 <=nlstate; k1++){   
-	  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
-ij=1;
-	  for(j=3; j <=ncovmodel; j++){
-	  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
-	    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
-	    ij++;
-	  }
-	  else
-	    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+     for(i=1,jk=1; i <=nlstate; i++){
+      for(j=1; j <=nlstate+ndeath; j++){
+	if (j!=i) {
+	  fprintf(ficres,"%1d%1d",i,j);
+	  printf("%1d%1d",i,j);
+	  for(k=1; k<=ncovmodel;k++){
+	    printf(" %.5e",delti[jk]);
+	    fprintf(ficres," %.5e",delti[jk]);
+	    jk++;
 	  }
-	  fprintf(ficgp,")");
+	  printf("\n");
+	  fprintf(ficres,"\n");
 	}
-	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
-	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-	i=i+ncovmodel;
-       }
+      }
      }
-   }
-   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
+    
+    k=1;
+    fprintf(ficres,"# Covariance\n");
+    printf("# Covariance\n");
+    for(i=1;i<=npar;i++){
+      /*  if (k>nlstate) k=1;
+      i1=(i-1)/(ncovmodel*nlstate)+1; 
+      fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+      printf("%s%d%d",alph[k],i1,tab[i]);*/
+      fprintf(ficres,"%3d",i);
+      printf("%3d",i);
+      for(j=1; j<=i;j++){
+	fprintf(ficres," %.5e",matcov[i][j]);
+	printf(" %.5e",matcov[i][j]);
+      }
+      fprintf(ficres,"\n");
+      printf("\n");
+      k++;
+    }
+    
+    while((c=getc(ficpar))=='#' && c!= EOF){
+      ungetc(c,ficpar);
+      fgets(line, MAXLINE, ficpar);
+      puts(line);
+      fputs(line,ficparo);
+    }
+    ungetc(c,ficpar);
+  
+    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);
+    
+    if (fage <= 2) {
+      bage = agemin;
+      fage = agemaxpar;
+    }
+    
+    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(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);
+ 
+    while((c=getc(ficpar))=='#' && c!= EOF){
+    ungetc(c,ficpar);
+    fgets(line, MAXLINE, ficpar);
+    puts(line);
+    fputs(line,ficparo);
   }
-   
-  fclose(ficgp);
-  /* end gnuplot */
-   
-chdir(path);
-   
-    free_ivector(wav,1,imx);
-    free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
-    free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
-    free_ivector(num,1,n);
-    free_vector(agedc,1,n);
-    /*free_matrix(covar,1,NCOVMAX,1,n);*/
-    fclose(ficparo);
-    fclose(ficres);
-    /*  }*/
-   
-   /*________fin mle=1_________*/
-   
-
+  ungetc(c,ficpar);
   
-    /* No more information from the sample is required now */
-  /* Reads comments: lines beginning with '#' */
+  fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
+  fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+ fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+     
   while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
@@ -2698,74 +3012,62 @@ chdir(path);
     fputs(line,ficparo);
   }
   ungetc(c,ficpar);
-  
-  fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
-  printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
-  fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
-/*--------- index.htm --------*/
+ 
 
-  strcpy(optionfilehtm,optionfile);
-  strcat(optionfilehtm,".htm");
-  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
-    printf("Problem with %s \n",optionfilehtm);goto end;
+   dateprev1=anprev1+mprev1/12.+jprev1/365.;
+   dateprev2=anprev2+mprev2/12.+jprev2/365.;
+
+  fscanf(ficpar,"pop_based=%d\n",&popbased);
+  fprintf(ficparo,"pop_based=%d\n",popbased);   
+  fprintf(ficres,"pop_based=%d\n",popbased);   
+  
+  while((c=getc(ficpar))=='#' && c!= EOF){
+    ungetc(c,ficpar);
+    fgets(line, MAXLINE, ficpar);
+    puts(line);
+    fputs(line,ficparo);
   }
+  ungetc(c,ficpar);
 
- fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\"> 
-Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
-Total number of observations=%d <br>
-Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
-<hr  size=\"2\" color=\"#EC5E5E\"> 
-<li>Outputs files<br><br>\n
-        - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
-- Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
-        - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
-        - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
-        - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
-        - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
-        - 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>
-        - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
-        - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
-<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);
+  fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
+fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
+fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
 
- fprintf(fichtm," <li>Graphs</li><p>");
 
- m=cptcoveff;
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+while((c=getc(ficpar))=='#' && c!= EOF){
+    ungetc(c,ficpar);
+    fgets(line, MAXLINE, ficpar);
+    puts(line);
+    fputs(line,ficparo);
+  }
+  ungetc(c,ficpar);
 
- j1=0;
- for(k1=1; k1<=m;k1++){
-   for(i1=1; i1<=ncodemax[k1];i1++){
-       j1++;
-       if (cptcovn > 0) {
-	 fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
-	 for (cpt=1; cpt<=cptcoveff;cpt++) 
-	   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
-	 fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
-       }
-       fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
-<img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);     
-       for(cpt=1; cpt<nlstate;cpt++){
-	 fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>
-<img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-       }
-    for(cpt=1; cpt<=nlstate;cpt++) {
-       fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
-interval) in state (%d): v%s%d%d.gif <br>
-<img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
-     }
-     for(cpt=1; cpt<=nlstate;cpt++) {
-        fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
-<img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
-     }
-     fprintf(fichtm,"\n<br>- Total life expectancy by age and
-health expectancies in states (1) and (2): e%s%d.gif<br>
-<img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);
-fprintf(fichtm,"\n</body>");
-   }
- }
-fclose(fichtm);
+  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+  fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+  fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+
+/*------------ gnuplot -------------*/
+ printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);
+ 
+/*------------ free_vector  -------------*/
+ chdir(path);
+ 
+ free_ivector(wav,1,imx);
+ free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+ free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
+ free_ivector(num,1,n);
+ free_vector(agedc,1,n);
+ /*free_matrix(covar,1,NCOVMAX,1,n);*/
+ fclose(ficparo);
+ fclose(ficres);
+
+/*--------- index.htm --------*/
+
+  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);
 
+  
   /*--------------- Prevalence limit --------------*/
   
   strcpy(filerespl,"pl");
@@ -2787,7 +3089,7 @@ fclose(fichtm);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   k=0;
   agebase=agemin;
-  agelim=agemax;
+  agelim=agemaxpar;
   ftolpl=1.e-10;
   i1=cptcoveff;
   if (cptcovn < 1){i1=1;}
@@ -2864,152 +3166,19 @@ fclose(fichtm);
 
   fclose(ficrespij);
 
-  if(stepm == 1) {
-  /*---------- Forecasting ------------------*/
-  calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
-
-  /*printf("calage= %f", calagedate);*/
-  
-  prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
-
-
-  strcpy(fileresf,"f"); 
-  strcat(fileresf,fileres);
-  if((ficresf=fopen(fileresf,"w"))==NULL) {
-    printf("Problem with forecast resultfile: %s\n", fileresf);goto end;
-  }
-  printf("Computing forecasting: result on file '%s' \n", fileresf);
-
-  free_matrix(mint,1,maxwav,1,n);
-  free_matrix(anint,1,maxwav,1,n);
-  free_matrix(agev,1,maxwav,1,imx);
-  /* Mobile average */
-
-  if (cptcoveff==0) ncodemax[cptcoveff]=1;
-
-  if (mobilav==1) {
-    mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-    for (agedeb=bage+3; agedeb<=fage-2; agedeb++)
-      for (i=1; i<=nlstate;i++)
-	for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
-	  mobaverage[(int)agedeb][i][cptcod]=0.;
-    
-    for (agedeb=bage+4; agedeb<=fage; agedeb++){
-      for (i=1; i<=nlstate;i++){
-	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-	  for (cpt=0;cpt<=4;cpt++){
-	    mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];
-	  }
-	  mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;
-	}
-      }
-    }   
-  }
-
-  stepsize=(int) (stepm+YEARM-1)/YEARM;
-  if (stepm<=12) stepsize=1;
-
-  agelim=AGESUP;
-  /*hstepm=stepsize*YEARM; *//* Every year of age */
-  hstepm=1;
-  hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */ 
-  yp1=modf(dateintmean,&yp);
-  anprojmean=yp;
-  yp2=modf((yp1*12),&yp);
-  mprojmean=yp;
-  yp1=modf((yp2*30.5),&yp);
-  jprojmean=yp;
-  if(jprojmean==0) jprojmean=1;
-  if(mprojmean==0) jprojmean=1;
-
-  fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
-
-  if (popforecast==1) {
-    if((ficpop=fopen(popfile,"r"))==NULL)    {
-      printf("Problem with population file : %s\n",popfile);goto end;
-    } 
-    popage=ivector(0,AGESUP);
-    popeffectif=vector(0,AGESUP);
-    popcount=vector(0,AGESUP);
-
-    i=1;   
-    while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)
-      {
-	i=i+1;
-      }
-    imx=i;
-    
-    for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
-  }
-
-  for(cptcov=1;cptcov<=i1;cptcov++){
-    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
-      k=k+1;
-      fprintf(ficresf,"\n#******");
-      for(j=1;j<=cptcoveff;j++) {
-	fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-      }
-      fprintf(ficresf,"******\n");
-      fprintf(ficresf,"# StartingAge FinalAge");
-      for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
-      if (popforecast==1)  fprintf(ficresf," [Population]");
-   
-      for (cpt=0; cpt<4;cpt++) { 
-	fprintf(ficresf,"\n");
-	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
-
-	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */
-	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
-	nhstepm = nhstepm/hstepm; 
-	/*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/
-
-	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-	oldm=oldms;savm=savms;
-	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
-	
-	for (h=0; h<=nhstepm; h++){
-	  if (h==(int) (calagedate+YEARM*cpt)) {
-	    fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);
-	  } 
-	  for(j=1; j<=nlstate+ndeath;j++) {
-	    kk1=0.;kk2=0;
-	    for(i=1; i<=nlstate;i++) {	      
-	      if (mobilav==1) 
-		kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
-	      else {
-		kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
-	        /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/
-	      }
 
-	      if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];
-	    }
-	 
-	    if (h==(int)(calagedate+12*cpt)){
-	      fprintf(ficresf," %.3f", kk1);
-	     
-	      if (popforecast==1) fprintf(ficresf," [%.f]", kk2);
-	    }
-	  }
-	}
-	/*	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/
-      }
-      }
-    }
-  }
-  /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-  if (popforecast==1) {
-    free_ivector(popage,0,AGESUP);
-    free_vector(popeffectif,0,AGESUP);
-    free_vector(popcount,0,AGESUP);
-  }
-  free_imatrix(s,1,maxwav+1,1,n);
-  free_vector(weight,1,n);*/
-  fclose(ficresf);
-  }/* End forecasting */
+  /*---------- Forecasting ------------------*/
+  if((stepm == 1) && (model==".")){
+    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);
+    free_matrix(mint,1,maxwav,1,n);
+    free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
+    free_vector(weight,1,n);}
   else{
     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);
   }
+  
 
   /*---------- Health expectancies and variances ------------*/
 
@@ -3059,12 +3228,14 @@ fclose(fichtm);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);  
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;
-      varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
-      
+       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+    
+
+ 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
       fprintf(ficrest,"\n");
-	
+
       hf=1;
       if (stepm >= YEARM) hf=stepm/YEARM;
       epj=vector(1,nlstate+1);
@@ -3093,20 +3264,16 @@ fclose(fichtm);
       }
     }
   }
-	
-       
-
 
- fclose(ficreseij);
- fclose(ficresvij);
+  fclose(ficreseij);
+  fclose(ficresvij);
   fclose(ficrest);
   fclose(ficpar);
   free_vector(epj,1,nlstate+1);
-  /*  scanf("%d ",i); */
-
+  
   /*------- Variance limit prevalence------*/   
 
-strcpy(fileresvpl,"vpl");
+  strcpy(fileresvpl,"vpl");
   strcat(fileresvpl,fileres);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
@@ -3114,19 +3281,19 @@ strcpy(fileresvpl,"vpl");
   }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
 
- k=0;
- for(cptcov=1;cptcov<=i1;cptcov++){
-   for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
-     k=k+1;
-     fprintf(ficresvpl,"\n#****** ");
-     for(j=1;j<=cptcoveff;j++) 
-       fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-     fprintf(ficresvpl,"******\n");
-     
-     varpl=matrix(1,nlstate,(int) bage, (int) fage);
-     oldm=oldms;savm=savms;
+  k=0;
+  for(cptcov=1;cptcov<=i1;cptcov++){
+    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+      k=k+1;
+      fprintf(ficresvpl,"\n#****** ");
+      for(j=1;j<=cptcoveff;j++) 
+	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+      fprintf(ficresvpl,"******\n");
+      
+      varpl=matrix(1,nlstate,(int) bage, (int) fage);
+      oldm=oldms;savm=savms;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
-   }
+    }
  }
 
   fclose(ficresvpl);
@@ -3145,7 +3312,7 @@ strcpy(fileresvpl,"vpl");
  
   free_matrix(matcov,1,npar,1,npar);
   free_vector(delti,1,npar);
-  
+  free_matrix(agev,1,maxwav,1,imx);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 
   if(erreur >0)