--- imach096d/src/imach.c	2001/03/13 18:10:26	1.2
+++ imach096d/src/imach.c	2001/05/02 18:44:18	1.9
@@ -51,6 +51,8 @@
 #define FILENAMELENGTH 80
 /*#define DEBUG*/
 #define windows
+#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 */
@@ -59,15 +61,14 @@
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */
-#define MAXN 80000
+#define MAXN 20000
 #define YEARM 12. /* Number of months per year */
 #define AGESUP 130
 #define AGEBASE 40
 
 
 int nvar;
-static int cptcov;
-int cptcovn;
+int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;
 int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */
@@ -75,9 +76,11 @@ int ncovmodel, ncov;     /* Total number
 
 int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */
+int jmin, jmax; /* min, max spacing between 2 waves */
 int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+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;
@@ -89,9 +92,6 @@ FILE *ficreseij;
  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 
-
-
-
 #define NR_END 1
 #define FREE_ARG char*
 #define FTOL 1.0e-10
@@ -125,18 +125,53 @@ 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 */
+   int	l1, l2;				/* length counters */
+
+   l1 = strlen( path );			/* length of path */
+   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+   s = strrchr( path, '\\' );		/* find last / */
+   if ( s == NULL ) {			/* no directory, so use current */
+#if	defined(__bsd__)		/* get current working directory */
+      extern char	*getwd( );
+
+      if ( getwd( dirc ) == NULL ) {
+#else
+      extern char	*getcwd( );
+
+      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+#endif
+         return( GLOCK_ERROR_GETCWD );
+      }
+      strcpy( name, path );		/* we've got it */
+   } else {				/* strip direcotry from path */
+      s++;				/* after this, the filename */
+      l2 = strlen( s );			/* length of filename */
+      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+      strcpy( name, s );		/* save file name */
+      strncpy( dirc, path, l1 - l2 );	/* now the directory */
+      dirc[l1-l2] = 0;			/* add zero */
+   }
+   l1 = strlen( dirc );			/* length of directory */
+   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+   return( 0 );				/* we're done */
+}
+
 
 /******************************************/
 
@@ -166,25 +201,23 @@ 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;
-  if (t[0]== occ) p=0;
   for(j=0; j<=strlen(t)-1; j++) {
-    if((t[j]!= occ) && (t[j+1]==occ)) p=j+1;
+    if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   }
 
   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]);
   }
 }
 
-
 /********************** nrerror ********************/
 
 void nrerror(char error_text[])
@@ -615,15 +648,27 @@ 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;
@@ -758,9 +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, 
@@ -782,7 +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 */
@@ -792,30 +841,31 @@ double func( double *x)
   /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /*for(i=1;i<imx;i++) 
-printf(" %d\n",s[4][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(mi=1; mi<= wav[i]-1; mi++){
+    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++){
+      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[Tvar[k]][i];
-	      /* printf("k=%d cptcovn=%d %lf\n",k,cptcovn,covar[Tvar[k]][i]);*/
-	    }
-	    }
-	  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
-		       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
-	  savm=oldm;
-	  oldm=newm;
+	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];
+	}
+	
+	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+		     1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+	savm=oldm;
+	oldm=newm;
+	
+	
       } /* end mult */
-   
+      
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
       ipmx +=1;
@@ -827,7 +877,6 @@ printf(" %d\n",s[4][i]);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
-
   return -l;
 }
 
@@ -983,7 +1032,8 @@ double hessii( double x[], double delta,
     }
   }
   delti[theta]=delts;
-  return res;  
+  return res;
+  
 }
 
 double hessij( double x[], double delti[], int thetai,int thetaj)
@@ -1116,13 +1166,14 @@ 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++){
    for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;
-
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+	 scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
 	 for (jk=-1; jk<=nlstate+ndeath; jk++)  
 	   for(m=agemin; m <= agemax+3; m++)
@@ -1131,8 +1182,9 @@ 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++){
@@ -1144,10 +1196,10 @@ 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#");
+	 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#");
+	}
        for(i=1; i<=nlstate;i++) 
 	 fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        fprintf(ficresp, "\n");
@@ -1215,9 +1267,14 @@ void  concatwav(int wav[], int **dh, int
      */
 
   int i, mi, m;
-  int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
-float sum=0.;
+  /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+     double sum=0., jmean=0.;*/
 
+int j, k=0,jk, ju, jl;
+     double sum=0.;
+jmin=1e+5;
+ jmax=-1;
+jmean=0.;
   for(i=1; i<=imx; i++){
     mi=0;
     m=firstpass;
@@ -1248,12 +1305,16 @@ float sum=0.;
       else{
 	if (s[mw[mi+1][i]][i] > nlstate) {
 	  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
-	  if(j=0) j=1;  /* Survives at least one month after exam */
+	  /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/
+	  if(j==0) j=1;  /* Survives at least one month after exam */
+	  k=k+1;
+	  if (j >= jmax) jmax=j;
+	  else if (j <= jmin)jmin=j;
+	  sum=sum+j;
 	}
 	else{
 	  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-	  /*printf("i=%d agevi+1=%lf agevi=%lf j=%d\n", i,agev[mw[mi+1][i]][i],agev[mw[mi][i]][i],j);*/
-
+	  /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/
 	  k=k+1;
 	  if (j >= jmax) jmax=j;
 	  else if (j <= jmin)jmin=j;
@@ -1271,30 +1332,35 @@ float sum=0.;
       }
     }
   }
-  printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);
+  jmean=sum/k;
+  printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 }
 /*********** 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]++; 
+      /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       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; 
 	  ij++;
@@ -1302,9 +1368,25 @@ void tricode(int *Tvar, int **nbcode, in
 	if (ij > ncodemax[j]) break; 
       }  
     } 
-  }   
+  }  
 
-  }
+ for (k=0; k<19; k++) Ndum[k]=0;
+
+ for (i=1; i<=ncovmodel; i++) {
+      ij=Tvar[i];
+      Ndum[ij]++; 
+    }
+
+ ij=1;
+ for (i=1; i<=10; i++) {
+   if((Ndum[i]!=0) && (i<=ncov)){
+     Tvaraff[ij]=i; 
+     ij++;
+   }
+ }
+ 
+    cptcoveff=ij-1;
+}
 
 /*********** Health Expectancies ****************/
 
@@ -1557,7 +1639,7 @@ void varprevlim(char fileres[], double *
 int main()
 {
 
-  int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;
+  int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   double agedeb, agefin,hf;
   double agemin=1.e20, agemax=-1.e20;
 
@@ -1569,7 +1651,7 @@ int main()
   int *indx;
   char line[MAXLINE], linepar[MAXLINE];
   char title[MAXLINE];
-  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
+  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
   char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
@@ -1578,7 +1660,7 @@ int main()
   int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;
   int ju,jl, mi;
-  int i1,j1, k1,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;
@@ -1596,6 +1678,7 @@ int main()
   double *epj, vepp;
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];
+
   char z[1]="c", occ;
 #include <sys/time.h>
 #include <time.h>
@@ -1606,13 +1689,17 @@ int main()
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
 
 
-  printf("\nIMACH, Version 0.63");
+  printf("\nIMACH, Version 0.64b");
   printf("\nEnter the parameter file name: ");
 
 #ifdef windows
   scanf("%s",pathtot);
   getcwd(pathcd, size);
-  cutv(path,optionfile,pathtot,'\\');
+  /*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);
   chdir(path);
   replace(pathc,path);
 #endif
@@ -1651,13 +1738,9 @@ int main()
   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);    
-  if (strlen(model)<=1) cptcovn=0;
-  else {
-    j=0;
-    j=nbocc(model,'+');
-    cptcovn=j+1;
-  }
+  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 */
@@ -1749,7 +1832,6 @@ int main()
   printf("\n");
 
 
-   if(mle==1){
     /*-------- data file ----------*/
     if((ficres =fopen(fileres,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileres);goto end;
@@ -1777,7 +1859,7 @@ int main()
     s=imatrix(1,maxwav+1,1,n);
     adl=imatrix(1,maxwav+1,1,n);    
     tab=ivector(1,NCOVMAX);
-    ncodemax=ivector(1,NCOVMAX);
+    ncodemax=ivector(1,8);
 
     i=1; 
     while (fgets(line, MAXLINE, fic) != NULL)    {
@@ -1802,53 +1884,91 @@ int main()
 	} 
 	num[i]=atol(stra);
 
-	/* 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]));*/
-
-	/*printf("%d %.lf %.lf %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),(covar[3][i]), (covar[4][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]));*/
+	/*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]));*/
 
 	i=i+1;
       }
     } 
-    /*scanf("%d",i);*/
 
+    /*scanf("%d",i);*/
   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 ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+      printf("Error. Non available option model=%s ",model);
+      goto end;
     }
-    else {
-      for(i=j; i>=1;i--){
-	cutv(stra,strb,modelsav,'+');
-	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];
+    
+    for(i=(j+1); i>=1;i--){
+      cutv(stra,strb,modelsav,'+');
+      if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); 
+      /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+      /*scanf("%d",i);*/
+      if (strchr(strb,'*')) {
+	cutv(strd,strc,strb,'*');
+	if (strcmp(strc,"age")==0) {
+	  cptcovprod--;
+	  cutv(strb,stre,strd,'V');
+	  Tvar[i]=atoi(stre);
+	  cptcovage++;
+	    Tage[cptcovage]=i;
+	    /*printf("stre=%s ", stre);*/
+	}
+	else if (strcmp(strd,"age")==0) {
+	  cptcovprod--;
+	  cutv(strb,stre,strc,'V');
+	  Tvar[i]=atoi(stre);
+	  cptcovage++;
+	  Tage[cptcovage]=i;
 	}
 	else {
-	  cutv(strd,strc,strb,'V');
-	  Tvar[i+1]=atoi(strc);
+	  cutv(strb,stre,strc,'V');
+	  Tvar[i]=ncov+k1;
+	  cutv(strb,strc,strd,'V'); 
+	  Tprod[k1]=i;
+	  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;
 	}
-	strcpy(modelsav,stra);  
       }
-      /*cutv(strd,strc,stra,'V');*/
-      Tvar[1]=atoi(strc);
+      else {
+	/*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+       /*  scanf("%d",i);*/
+      cutv(strd,strc,strb,'V');
+      Tvar[i]=atoi(strc);
+      }
+      strcpy(modelsav,stra);  
+      /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+	scanf("%d",i);*/
     }
-  }
-  /*printf("tvar=%d ",Tvar[1]);*/
-  /*scanf("%d ",i);*/
+}
+  
+  /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],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;
     }
@@ -1858,23 +1978,22 @@ int main()
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=1; (m<= maxwav); m++){
-	if (mint[m][i]==99 || anint[m][i]==9999) s[m][i]=-1;  
 	if(s[m][i] >0){
 	  if (s[m][i] == nlstate+1) {
 	    if(agedc[i]>0)
 	      if(moisdc[i]!=99 && andc[i]!=9999)
 	      agev[m][i]=agedc[i];
-	    else{
+	    else {
+	      if (andc[i]!=9999){
 	      printf("Warning negative age at death: %d line:%d\n",num[i],i);
 	      agev[m][i]=-1;
+	      }
 	    }
 	  }
 	  else if(s[m][i] !=9){ /* Should no more exist */
 	    agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
-	    if(mint[m][i]==99 || anint[m][i]==9999){
+	    if(mint[m][i]==99 || anint[m][i]==9999)
 	      agev[m][i]=1;
-	      /* printf("i=%d m=%d agev=%lf \n",i,m, agev[m][i]);    */ 
-	    }
 	    else if(agev[m][i] <agemin){ 
 	      agemin=agev[m][i];
 	      /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
@@ -1925,19 +2044,19 @@ 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(0,NCOVMAX,0,NCOVMAX); 
+      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;
 	 } 
@@ -1945,13 +2064,14 @@ 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'. */
@@ -1966,9 +2086,10 @@ 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) */
-    /*scanf("%d",i);*/
-    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);
@@ -1992,10 +2113,11 @@ 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++){
@@ -2050,6 +2172,8 @@ 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) {
@@ -2058,7 +2182,7 @@ 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 ++) {
@@ -2157,41 +2281,61 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
   }
 
   /* proba elementaires */
-  for(i=1,jk=1; i <=nlstate; i++){
+   for(i=1,jk=1; i <=nlstate; i++){
     for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {
-	/*  fprintf(ficgp,"%1d%1d ",i,k);*/
 	for(j=1; j <=ncovmodel; j++){
-	  fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);
+	  /*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);
-  for(i=1; i <=nlstate; i++) {
-    for(k=1; k <=(nlstate+ndeath); k++){
-      if (k != i) {
-	fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);
-	for(j=3; j <=ncovmodel; j++) 
-	  fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	fprintf(ficgp,")/(1");
-	for(k1=1; k1 <=(nlstate+ndeath); k1++) 
-	  if (k1 != i) {
-	    fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);
-	    for(j=3; j <=ncovmodel; j++)
-	      fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
-	    fprintf(ficgp,")");
+   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++;
 	  }
-	fprintf(ficgp,") t \"p%d%d\" ", i,k);
-      if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
-      }
-    }
-  }
-fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
+	  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);
    
 chdir(path);
@@ -2209,7 +2353,7 @@ chdir(path);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
-   }
+    /*  }*/
    
    /*________fin mle=1_________*/
    
@@ -2230,11 +2374,18 @@ chdir(path);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
 /*--------- index.htm --------*/
 
-  if((fichtm=fopen("index.htm","w"))==NULL)    {
-    printf("Problem with index.htm \n");goto end;
+  strcpy(optionfilehtm,optionfile);
+  strcat(optionfilehtm,".htm");
+  if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
+    printf("Problem with %s \n",optionfilehtm);goto end;
   }
 
- fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n
+ fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </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>
@@ -2243,11 +2394,11 @@ chdir(path);
         - 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><br>",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><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);
 
- fprintf(fichtm," <li>Graphs</li>\n<p>");
+ fprintf(fichtm," <li>Graphs</li><p>");
 
- m=cptcovn;
+ m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 
  j1=0;
@@ -2255,10 +2406,10 @@ chdir(path);
    for(i1=1; i1<=ncodemax[k1];i1++){
        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]]);
-	 fprintf(fichtm," ************\n<hr>");
+	 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);     
@@ -2306,16 +2457,16 @@ 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++){
@@ -2348,8 +2499,8 @@ 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 */
@@ -2407,17 +2558,17 @@ 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");
 
@@ -2478,8 +2629,8 @@ 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);
@@ -2518,7 +2669,8 @@ strcpy(fileresvpl,"vpl");
 #ifdef windows
  chdir(pathcd);
 #endif 
- system("wgnuplot ../gp37mgw/graph.plt");
+ /*system("wgnuplot graph.plt");*/
+ system("../gp37mgw/wgnuplot graph.plt");
 
 #ifdef windows
   while (z[0] != 'q') {