--- imach/src/imach.c	2001/03/13 18:10:26	1.2
+++ imach/src/imach.c	2001/05/02 17:21:42	1.3
@@ -59,7 +59,7 @@
 #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
@@ -168,9 +168,8 @@ void cutv(char *u,char *v, char*t, char
 {
   int i,lg,j,p;
   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);
@@ -184,7 +183,6 @@ void cutv(char *u,char *v, char*t, char
   }
 }
 
-
 /********************** nrerror ********************/
 
 void nrerror(char error_text[])
@@ -805,15 +803,14 @@ printf(" %d\n",s[4][i]);
 	  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]);*/
-	    }
+	    for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];
 	    }
 	  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]]);
@@ -827,7 +824,6 @@ 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 +979,8 @@ double hessii( double x[], double delta,
     }
   }
   delti[theta]=delts;
-  return res;  
+  return res;
+  
 }
 
 double hessij( double x[], double delti[], int thetai,int thetaj)
@@ -1252,8 +1249,6 @@ float sum=0.;
 	}
 	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);*/
-
 	  k=k+1;
 	  if (j >= jmax) jmax=j;
 	  else if (j <= jmin)jmin=j;
@@ -1777,7 +1772,7 @@ 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)    {
@@ -1802,17 +1797,15 @@ 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 %.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]),  (mint[5][i]), (anint[5][i]), (s[5][i]),  (mint[6][i]), (anint[6][i]), (s[6][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);    
    
@@ -1820,7 +1813,7 @@ int main()
     j=0;
     j=nbocc(model,'+');
     cptcovn=j+1;
- 
+    
     strcpy(modelsav,model); 
     if (j==0) {
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);
@@ -1835,18 +1828,17 @@ int main()
 	  for (k=1; k<=lastobs;k++) 
 	    covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
 	}
-	else {
-	  cutv(strd,strc,strb,'V');
-	  Tvar[i+1]=atoi(strc);
+	else {cutv(strd,strc,strb,'V');
+	Tvar[i+1]=atoi(strc);
 	}
-	strcpy(modelsav,stra);  
+	strcpy(modelsav,stra);   
       }
-      /*cutv(strd,strc,stra,'V');*/
+      cutv(strd,strc,stra,'V');
       Tvar[1]=atoi(strc);
     }
   }
-  /*printf("tvar=%d ",Tvar[1]);*/
-  /*scanf("%d ",i);*/
+  /*printf("tvar=%d ",Tvar[1]);
+  scanf("%d ",i);*/ 
     fclose(fic);
 
     if (weightopt != 1) { /* Maximisation without weights*/
@@ -1858,7 +1850,6 @@ 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)
@@ -1871,10 +1862,8 @@ int main()
 	  }
 	  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);*/
@@ -1950,13 +1939,17 @@ Tcode=ivector(1,100);
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);
      }
      printf("\n");
-   }
-  scanf("%d",i);*/
+   }*/
+   /*scanf("%d",i);*/
     
    /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
 
+
+  /*scanf("%d ",i);*/
+
+
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
@@ -1966,7 +1959,7 @@ 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);
 
     
@@ -2125,7 +2118,7 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
  
   /*3eme*/
 
-  for (k1=1; k1<= m ; k1 ++) { 
+   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);
@@ -2134,10 +2127,10 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
       } 
       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 (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);
@@ -2155,7 +2148,7 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
       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++){
@@ -2192,9 +2185,10 @@ fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
   }
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
   }
-  fclose(ficgp);
-   
-chdir(path);
+ 
+ fclose(ficgp);
+
+    chdir(path);
     free_matrix(agev,1,maxwav,1,imx);
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
@@ -2225,6 +2219,7 @@ chdir(path);
   }
   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);
@@ -2273,7 +2268,7 @@ interval) in state (%d): v%s%d%d.gif <br
      }
      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);
+<img src=\"ex%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>
@@ -2461,7 +2456,7 @@ fclose(fichtm);
   fclose(ficrest);
   fclose(ficpar);
   free_vector(epj,1,nlstate+1);
-  /*  scanf("%d ",i); */
+  /*scanf("%d ",i); */
 
   /*------- Variance limit prevalence------*/   
 
@@ -2518,7 +2513,7 @@ strcpy(fileresvpl,"vpl");
 #ifdef windows
  chdir(pathcd);
 #endif 
- system("wgnuplot ../gp37mgw/graph.plt");
+ system("wgnuplot graph.plt");
 
 #ifdef windows
   while (z[0] != 'q') {