--- imach096d/src/imach.c	2001/05/02 17:42:45	1.5
+++ imach096d/src/imach.c	2001/05/02 17:50:24	1.7
@@ -54,8 +54,6 @@
 #define	GLOCK_ERROR_NOPATH		-1	/* empty path */
 #define	GLOCK_ERROR_GETCWD		-2	/* cannot get cwd */
 
-
-
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 
@@ -71,7 +69,7 @@
 
 int nvar;
 static int cptcov;
-int cptcovn;
+int cptcovn, cptcovage=0, cptcoveff=0;
 int npar=NPARMAX;
 int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */
@@ -93,9 +91,6 @@ FILE *ficreseij;
  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 
-
-
-
 #define NR_END 1
 #define FREE_ARG char*
 #define FTOL 1.0e-10
@@ -129,19 +124,19 @@ int stepm;
 /* Stepm, step in month: minimum step interpolation*/
 
 int m,nb;
-int *num, firstpass=0, lastpass=4,*cod, *ncodemax;
+int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij;
 
 double *weight;
 int **s; /* Status */
 double *agedc, **covar, idx;
-int **nbcode, *Tcode, *Tvar, **codtab;
+int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 double ftolhess; /* Tolerance for computing hessian */
 
-
+/**************** split *************************/
 static	int split( char *path, char *dirc, char *name )
 {
    char	*s;				/* pointer */
@@ -205,7 +200,7 @@ int nbocc(char *s, char occ)
 
 void cutv(char *u,char *v, char*t, char occ)
 {
-  int i,lg,j,p;
+  int i,lg,j,p=0;
   i=0;
   for(j=0; j<=strlen(t)-1; j++) {
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
@@ -214,8 +209,8 @@ void cutv(char *u,char *v, char*t, char
   lg=strlen(t);
   for(j=0; j<p; j++) {
     (u[j] = t[j]);
-    u[p]='\0';
   }
+     u[p]='\0';
 
    for(j=0; j<= lg; j++) {
     if (j>=(p+1))(v[j-p-1] = t[j]);
@@ -652,15 +647,28 @@ double **prevalim(double **prlim, int nl
     for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }
-  /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+
+   cov[1]=1.;
+ 
+ /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     newm=savm;
     /* Covariates have to be included here again */
-    cov[1]=1.;
-    cov[2]=agefin;
-    if (cptcovn>0){
-      for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}
-    }
+     cov[2]=agefin;
+  
+      for (k=1; k<=cptcovn;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]);*/
+      }
+      for (k=1; k<=cptcovage;k++)
+	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+      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]]];
+
+      /*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]);*/
+
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 
     savm=oldm;
@@ -795,9 +803,13 @@ double ***hpxij(double ***po, int nhstep
       /* Covariates have to be included here again */
       cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
-      if (cptcovn>0){
-      for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];
-    }
+      for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+for (k=1; k<=cptcovage;k++)
+	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+   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]]];
+
+
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
@@ -819,7 +831,7 @@ double ***hpxij(double ***po, int nhstep
 /*************** log-likelihood *************/
 double func( double *x)
 {
-  int i, ii, j, k, mi, d;
+  int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double **out;
   double sw; /* Sum of weights */
@@ -831,19 +843,24 @@ double func( double *x)
   /*for(i=1;i<imx;i++) 
 printf(" %d\n",s[4][i]);
   */
+  cov[1]=1.;
 
   for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+    for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
       for (ii=1;ii<=nlstate+ndeath;ii++)
 	for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(d=0; d<dh[mi][i]; d++){
-	newm=savm;
-	  cov[1]=1.;
-	  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
-	  if (cptcovn>0){
-	    for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];
-	    }
+	      newm=savm;
+	      cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	      for (kk=1; kk<=cptcovage;kk++) {
+		 cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+		 /*printf("%d %d",kk,Tage[kk]);*/
+	      }
+	      /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/
+	      /*cov[3]=pow(cov[2],2)/1000.;*/
+
 	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 	  savm=oldm;
@@ -1152,7 +1169,7 @@ void  freqsummary(char fileres[], int ag
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   j1=0;
 
-  j=cptcovn;
+  j=cptcoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}
 
   for(k1=1; k1<=j;k1++){
@@ -1167,8 +1184,8 @@ void  freqsummary(char fileres[], int ag
        for (i=1; i<=imx; i++) {
 	 bool=1;
 	 if  (cptcovn>0) {
-	   for (z1=1; z1<=cptcovn; z1++) 
-	     if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=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-1; m++){
@@ -1180,10 +1197,10 @@ void  freqsummary(char fileres[], int ag
 	 }
        }
         if  (cptcovn>0) {
-	 fprintf(ficresp, "\n#Variable"); 
-	 for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);
+	 fprintf(ficresp, "\n#********** Variable "); 
+	 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++) 
 	 fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        fprintf(ficresp, "\n");
@@ -1310,35 +1327,57 @@ float sum=0.;
 /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)
 {
-  int Ndum[80],ij, k, j, i;
+  int Ndum[20],ij=1, k, j, i;
   int cptcode=0;
-  for (k=0; k<79; k++) Ndum[k]=0;
+  cptcoveff=0; 
+ 
+  for (k=0; k<19; k++) Ndum[k]=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;
-  
-  for (j=1; j<=cptcovn; j++) {
+
+  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for (i=1; i<=imx; i++) {
       ij=(int)(covar[Tvar[j]][i]);
       Ndum[ij]++; 
       if (ij > cptcode) cptcode=ij; 
     }
+
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/
     for (i=0; i<=cptcode; i++) {
       if(Ndum[i]!=0) ncodemax[j]++;
     }
-  
     ij=1; 
+
     for (i=1; i<=ncodemax[j]; i++) {
-      for (k=0; k<=79; k++) {
+      for (k=0; k<=19; k++) {
 	if (Ndum[k] != 0) {
 	  nbcode[Tvar[j]][ij]=k; 
+	  /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/
 	  ij++;
 	}
 	if (ij > ncodemax[j]) break; 
       }  
     } 
-  }   
-
-  }
+  }  
+ for (i=1; i<=10; i++) {
+      ij=Tvar[i];
+      Ndum[ij]++; 
+    }
+ ij=1;
+ for (i=1; i<=cptcovn; i++) {
+   if((Ndum[i]!=0) && (i<=ncov)){
+     Tvaraff[i]=ij; 
+   ij++;
+   }
+ }
+ 
+ for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+   if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];
+   /*printf("j=%d %d\n",j,Tvar[j]);*/
+ }
+ 
+ /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);
+    scanf("%d",i);*/
+}
 
 /*********** Health Expectancies ****************/
 
@@ -1612,7 +1651,7 @@ int main()
   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;
+  int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
   
   int hstepm, nhstepm;
@@ -1690,7 +1729,7 @@ split(pathtot, path,optionfile);
   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);
 
-  covar=matrix(1,NCOVMAX,1,n);    
+  covar=matrix(0,NCOVMAX,1,n);    
   if (strlen(model)<=1) cptcovn=0;
   else {
     j=0;
@@ -1788,7 +1827,6 @@ split(pathtot, path,optionfile);
   printf("\n");
 
 
-   if(mle==1){
     /*-------- data file ----------*/
     if((ficres =fopen(fileres,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileres);goto end;
@@ -1851,29 +1889,91 @@ split(pathtot, path,optionfile);
   imx=i-1; /* Number of individuals */
 
   /* Calculation of the number of parameter from char model*/
-  Tvar=ivector(1,8);    
+  Tvar=ivector(1,15); 
+  Tprod=ivector(1,15); 
+  Tvaraff=ivector(1,15); 
+  Tvard=imatrix(1,15,1,2);
+  Tage=ivector(1,15);      
    
   if (strlen(model) >1){
-    j=0;
+    j=0, j1=0, k1=1, k2=1;
     j=nbocc(model,'+');
+    j1=nbocc(model,'*');
     cptcovn=j+1;
+    cptcovprod=j1;
     
     strcpy(modelsav,model); 
-    if (j==0) {
-      cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);
+   if (j==0) {
+      if (j1==0){
+	cutv(stra,strb,modelsav,'V');
+	Tvar[1]=atoi(strb);
+      }
+      else if (j1==1) {
+	cutv(stra,strb,modelsav,'*');
+	Tage[1]=1; cptcovage++;
+	if (strcmp(stra,"age")==0) {
+	  cptcovprod--;
+	  cutv(strd,strc,strb,'V');
+	  Tvar[1]=atoi(strc);
+	}
+	else if (strcmp(strb,"age")==0) {
+	  cptcovprod--;
+	  cutv(strd,strc,stra,'V');
+	  Tvar[1]=atoi(strc);
+	}
+	else {
+	  cutv(strd,strc,strb,'V');
+	  cutv(stre,strd,stra,'V');
+	  Tvar[1]=ncov+1;
+	  for (k=1; k<=lastobs;k++) 
+	      covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];
+	}
+	/*printf("%s %s %s\n", stra,strb,modelsav);
+printf("%d ",Tvar[1]);
+scanf("%d",i);*/
+      }
     }
-    else {
+   else {
       for(i=j; i>=1;i--){
 	cutv(stra,strb,modelsav,'+');
+	/*printf("%s %s %s\n", stra,strb,modelsav);
+	  scanf("%d",i);*/
 	if (strchr(strb,'*')) {
 	  cutv(strd,strc,strb,'*');
-	  cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;
-	  cutv(strb,strc,strd,'V'); 
-	  for (k=1; k<=lastobs;k++) 
-	    covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+	  if (strcmp(strc,"age")==0) {
+	    cptcovprod--;
+	    cutv(strb,stre,strd,'V');
+	    Tvar[i+1]=atoi(stre);
+	    cptcovage++;
+	    Tage[cptcovage]=i+1;
+	    printf("stre=%s ", stre);
+	  }
+	  else if (strcmp(strd,"age")==0) {
+	    cptcovprod--;
+	    cutv(strb,stre,strc,'V');
+	    Tvar[i+1]=atoi(stre);
+	    cptcovage++;
+	    Tage[cptcovage]=i+1;
+	  }
+	  else {
+	    cutv(strb,stre,strc,'V');
+	    Tvar[i+1]=ncov+k1;
+	    cutv(strb,strc,strd,'V'); 
+	    Tprod[k1]=i+1;
+	    Tvard[k1][1]=atoi(strc);
+	    Tvard[k1][2]=atoi(stre);
+	    Tvar[cptcovn+k2]=Tvard[k1][1];
+	    Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
+	    for (k=1; k<=lastobs;k++) 
+	      covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+	    k1++;
+	    k2=k2+2;
+	  }
 	}
-	else {cutv(strd,strc,strb,'V');
-	Tvar[i+1]=atoi(strc);
+	else {
+	  cutv(strd,strc,strb,'V');
+	  /* printf("%s %s %s", strd,strc,strb);*/
+	  Tvar[i+1]=atoi(strc);
 	}
 	strcpy(modelsav,stra);   
       }
@@ -1881,10 +1981,14 @@ split(pathtot, path,optionfile);
       Tvar[1]=atoi(strc);
     }
   }
-  /*printf("tvar=%d ",Tvar[1]);
-  scanf("%d ",i);*/ 
+  /* for (i=1; i<=5; i++)
+     printf("i=%d %d ",i,Tvar[i]);*/
+  /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/
+ /*printf("cptcovprod=%d ", cptcovprod);*/
+  /*  scanf("%d ",i);*/
     fclose(fic);
 
+    /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
@@ -1958,19 +2062,19 @@ printf("Total number of individuals= %d,
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
 
 
-Tcode=ivector(1,100);
-   nbcode=imatrix(1,nvar,1,8);  
-   ncodemax[1]=1;
-   if (cptcovn > 0) tricode(Tvar,nbcode,imx);
- 
+      Tcode=ivector(1,100);
+      nbcode=imatrix(1,nvar,1,8); 
+      ncodemax[1]=1;
+      if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+      
    codtab=imatrix(1,100,1,10);
    h=0;
-   m=pow(2,cptcovn);
+   m=pow(2,cptcoveff);
  
-   for(k=1;k<=cptcovn; k++){
+   for(k=1;k<=cptcoveff; k++){
      for(i=1; i <=(m/pow(2,k));i++){
        for(j=1; j <= ncodemax[k]; j++){
-	 for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){
+	 for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
 	   h++;
 	   if (h>m) h=1;codtab[h][k]=j;
 	 } 
@@ -1978,13 +2082,14 @@ Tcode=ivector(1,100);
      }
    } 
 
+
    /*for(i=1; i <=m ;i++){ 
      for(k=1; k <=cptcovn; k++){
-       printf("i=%d k=%d %d ",i,k,codtab[i][k]);
+       printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
      }
      printf("\n");
-   }*/
-   /*scanf("%d",i);*/
+   }
+   scanf("%d",i);*/
     
    /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
@@ -1999,9 +2104,10 @@ Tcode=ivector(1,100);
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-    
-    mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
 
+    if(mle==1){
+    mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+    }
     
     /*--------- results files --------------*/
     fprintf(ficres,"\ntitle=%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);
@@ -2025,10 +2131,11 @@ Tcode=ivector(1,100);
 	 }
      }
    }
-
+ if(mle==1){
     /* Computing hessian and covariance matrix */
     ftolhess=ftol; /* Usually correct */
     hesscov(matcov, p, npar, delti, ftolhess, func);
+ }
     fprintf(ficres,"# Scales\n");
     printf("# Scales\n");
      for(i=1,jk=1; i <=nlstate; i++){
@@ -2083,6 +2190,8 @@ Tcode=ivector(1,100);
 
     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);
+
+   
 /*------------ gnuplot -------------*/
 chdir(pathcd);
   if((ficgp=fopen("graph.plt","w"))==NULL) {
@@ -2091,7 +2200,7 @@ chdir(pathcd);
 #ifdef windows
   fprintf(ficgp,"cd \"%s\" \n",pathc);
 #endif
-m=pow(2,cptcovn);
+m=pow(2,cptcoveff);
   
  /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {
@@ -2212,26 +2321,38 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
      for(k=1; k<=(nlstate+ndeath); k++) {
        if (k != k2){
     	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
-
-	for(j=3; j <=ncovmodel; j++) 
-	  fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	fprintf(ficgp,")/(1");
-
-	for(k1=1; k1 <=nlstate+1; k1=k1+2){   
-	    fprintf(ficgp,"+exp(p%d+p%d*x",k1+k3-1,k1+k3);
-
-	    for(j=3; j <=ncovmodel; j++)
-	      fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	    fprintf(ficgp,")");
+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;
+	i=i+ncovmodel;
        }
      }
    }
-  fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
-   }
+   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk); 
+  }
    
   fclose(ficgp);
    
@@ -2250,7 +2371,7 @@ chdir(path);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
-   }
+    /*  }*/
    
    /*________fin mle=1_________*/
    
@@ -2288,7 +2409,7 @@ chdir(path);
 
  fprintf(fichtm," <li>Graphs</li>\n<p>");
 
- m=cptcovn;
+ m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 
  j1=0;
@@ -2297,8 +2418,8 @@ chdir(path);
        j1++;
        if (cptcovn > 0) {
 	 fprintf(fichtm,"<hr>************ Results for covariates");
-	 for (cpt=1; cpt<=cptcovn;cpt++) 
-	   fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);
+	 for (cpt=1; cpt<=cptcoveff;cpt++) 
+	   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
 	 fprintf(fichtm," ************\n<hr>");
        }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
@@ -2347,16 +2468,16 @@ fclose(fichtm);
   agebase=agemin;
   agelim=agemax;
   ftolpl=1.e-10;
-  i1=cptcovn;
+  i1=cptcoveff;
   if (cptcovn < 1){i1=1;}
 
   for(cptcov=1;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 	k=k+1;
 	/*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
-	fprintf(ficrespl,"\n#****** ");
-	for(j=1;j<=cptcovn;j++) 
-	  fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
+	fprintf(ficrespl,"\n#******");
+	for(j=1;j<=cptcoveff;j++) 
+	  fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 	fprintf(ficrespl,"******\n");
 	
 	for (age=agebase; age<=agelim; age++){
@@ -2389,8 +2510,8 @@ fclose(fichtm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;
 	fprintf(ficrespij,"\n#****** ");
-	for(j=1;j<=cptcovn;j++) 
-	  fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
+	for(j=1;j<=cptcoveff;j++) 
+	  fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
 	fprintf(ficrespij,"******\n");
 	
 	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
@@ -2448,17 +2569,17 @@ fclose(fichtm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;
       fprintf(ficrest,"\n#****** ");
-      for(j=1;j<=cptcovn;j++) 
-	fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
+      for(j=1;j<=cptcoveff;j++) 
+	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficrest,"******\n");
 
       fprintf(ficreseij,"\n#****** ");
-      for(j=1;j<=cptcovn;j++) 
+      for(j=1;j<=cptcoveff;j++) 
 	fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
       fprintf(ficreseij,"******\n");
 
       fprintf(ficresvij,"\n#****** ");
-      for(j=1;j<=cptcovn;j++) 
+      for(j=1;j<=cptcoveff;j++) 
 	fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
       fprintf(ficresvij,"******\n");
 
@@ -2519,8 +2640,8 @@ strcpy(fileresvpl,"vpl");
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
      k=k+1;
      fprintf(ficresvpl,"\n#****** ");
-     for(j=1;j<=cptcovn;j++) 
-       fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);
+     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);