--- imach/src/imach.c	2001/05/02 18:44:18	1.9
+++ imach/src/imach.c	2002/02/20 16:57:00	1.12
@@ -8,7 +8,7 @@
   Health expectancies are computed from the transistions observed between 
   waves and are computed for each degree of severity of disability (number
   of life states). More degrees you consider, more time is necessary to
-  reach the Maximum Likelihood of the parameters involved in the model.
+  reach the Maximum Likelihood of the parameters involved in the model. 
   The simplest model is the multinomial logistic model where pij is
   the probabibility to be observed in state j at the second wave conditional
   to be observed in state i at the first wave. Therefore the model is:
@@ -22,7 +22,7 @@
   delay between waves is not identical for each individual, or if some 
   individual missed an interview, the information is not rounded or lost, but
   taken into account using an interpolation or extrapolation.
-  hPijx is the probability to be
+  hPijx is the probability to be 
   observed in state i at age x+h conditional to the observed state i at age 
   x. The delay 'h' can be split into an exact number (nh*stepm) of 
   unobserved intermediate  states. This elementary transition (by month or 
@@ -693,7 +693,7 @@ double **prevalim(double **prlim, int nl
   }
 }
 
-/*************** transition probabilities **********/ 
+/*************** transition probabilities ***************/ 
 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {
@@ -716,9 +716,11 @@ double **pmij(double **ps, double *cov,
 	s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 	/*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       }
-      ps[i][j]=s2;
+      ps[i][j]=(s2);
     }
   }
+    /*ps[3][2]=1;*/
+
   for(i=1; i<= nlstate; i++){
      s1=0;
     for(j=1; j<i; j++)
@@ -740,6 +742,7 @@ double **pmij(double **ps, double *cov,
     }
   }
 
+
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     for(jj=1; jj<= nlstate+ndeath; jj++){
      printf("%lf ",ps[ii][jj]);
@@ -804,9 +807,9 @@ double ***hpxij(double ***po, int nhstep
       cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-for (k=1; k<=cptcovage;k++)
+      for (k=1; k<=cptcovage;k++)
 	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
-   for (k=1; k<=cptcovprod;k++)
+      for (k=1; k<=cptcovprod;k++)
 	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 
 
@@ -913,7 +916,6 @@ void hesscov(double **matcov, double p[]
   void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;
 
-
   hess=matrix(1,npar,1,npar);
 
   printf("\nCalculation of the hessian matrix. Wait...\n");
@@ -921,14 +923,16 @@ void hesscov(double **matcov, double p[]
     printf("%d",i);fflush(stdout);
     hess[i][i]=hessii(p,ftolhess,i,delti);
     /*printf(" %f ",p[i]);*/
+    /*printf(" %lf ",hess[i][i]);*/
   }
-
+  
   for (i=1;i<=npar;i++) {
     for (j=1;j<=npar;j++)  {
       if (j>i) { 
 	printf(".%d%d",i,j);fflush(stdout);
 	hess[i][j]=hessij(p,delti,i,j);
-	hess[j][i]=hess[i][j];
+	hess[j][i]=hess[i][j];    
+	/*printf(" %lf ",hess[i][j]);*/
       }
     }
   }
@@ -1032,7 +1036,7 @@ double hessii( double x[], double delta,
     }
   }
   delti[theta]=delts;
-  return res;
+  return res; 
   
 }
 
@@ -1270,11 +1274,11 @@ void  concatwav(int wav[], int **dh, int
   /* 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.;
+  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;
@@ -1304,20 +1308,22 @@ jmean=0.;
 	dh[mi][i]=1;
       else{
 	if (s[mw[mi+1][i]][i] > nlstate) {
+	  if (agedc[i] < 2*AGESUP) {
 	  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
-	  /*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;
+	  if (j <= jmin) jmin=j;
 	  sum=sum+j;
+	  /* if (j<10) printf("j=%d num=%d ",j,i); */
+	  }
 	}
 	else{
 	  j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-	  /*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;
+	  /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 	  sum=sum+j;
 	}
 	jk= j/stepm;
@@ -1334,7 +1340,7 @@ jmean=0.;
   }
   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)
 {
@@ -1372,7 +1378,7 @@ void tricode(int *Tvar, int **nbcode, in
 
  for (k=0; k<19; k++) Ndum[k]=0;
 
- for (i=1; i<=ncovmodel; i++) {
+ for (i=1; i<=ncovmodel-2; i++) {
       ij=Tvar[i];
       Ndum[ij]++; 
     }
@@ -1447,7 +1453,7 @@ void varevsij(char fileres[], double ***
   double **dnewm,**doldm;
   int i, j, nhstepm, hstepm, h;
   int k, cptcode;
-   double *xp;
+  double *xp;
   double **gp, **gm;
   double ***gradg, ***trgradg;
   double ***p3mat;
@@ -1662,7 +1668,7 @@ int main()
   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 hstepm, nhstepm;
   double bage, fage, age, agelim, agebase;
   double ftolpl=FTOL;
@@ -1676,7 +1682,7 @@ int main()
   double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;
-  char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";
+  char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];
 
   char z[1]="c", occ;
@@ -1771,7 +1777,8 @@ split(pathtot, path,optionfile);
       fprintf(ficparo,"\n");
     }
   
-  npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+    npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+
   p=param[1][1];
   
   /* Reads comments: lines beginning with '#' */
@@ -1861,7 +1868,7 @@ split(pathtot, path,optionfile);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
 
-    i=1; 
+    i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
 	
@@ -1883,16 +1890,24 @@ split(pathtot, path,optionfile);
 	  cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 	} 
 	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]));*/
+	
+	/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+	  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])); ij=ij+1;}*/
 
 	i=i+1;
       }
     } 
-
-    /*scanf("%d",i);*/
+    /* printf("ii=%d", ij);
+       scanf("%d",i);*/
   imx=i-1; /* Number of individuals */
 
+  /* for (i=1; i<=imx; i++){
+    if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+    if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+    if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+  }
+  for (i=1; i<=imx; 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]));*/
+
   /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,15); 
   Tprod=ivector(1,15); 
@@ -1974,6 +1989,13 @@ split(pathtot, path,optionfile);
     }
     /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
+
+   for (i=1; i<=imx; i++) 
+     for(m=2; (m<= maxwav); m++)
+       if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
+	 anint[m][i]=9999;
+	 s[m][i]=-1;
+       }
     
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
@@ -2082,7 +2104,7 @@ printf("Total number of individuals= %d,
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-    
+     
     /* 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) */
@@ -2665,12 +2687,15 @@ strcpy(fileresvpl,"vpl");
   /*printf("Total time was %d uSec.\n", total_usecs);*/
   /*------ End -----------*/
 
+
  end:
 #ifdef windows
  chdir(pathcd);
 #endif 
  /*system("wgnuplot graph.plt");*/
- system("../gp37mgw/wgnuplot graph.plt");
+ /*system("../gp37mgw/wgnuplot graph.plt");*/
+ /*system("cd ../gp37mgw");*/
+ system("..\\gp37mgw\\wgnuplot graph.plt");
 
 #ifdef windows
   while (z[0] != 'q') {
@@ -2680,7 +2705,7 @@ strcpy(fileresvpl,"vpl");
     if (z[0] == 'c') system("./imach");
     else if (z[0] == 'e') {
       chdir(path);
-      system("index.htm");
+      system(optionfilehtm);
     }
     else if (z[0] == 'q') exit(0);
   }