--- imach/src/imach.c	2002/03/06 19:02:50	1.29
+++ imach/src/imach.c	2002/03/13 17:19:16	1.34
@@ -1,4 +1,4 @@
-/* $Id: imach.c,v 1.29 2002/03/06 19:02:50 lievre Exp $
+/* $Id: imach.c,v 1.34 2002/03/13 17:19:16 brouard Exp $
    Interpolated Markov Chain
 
   Short summary of the programme:
@@ -82,7 +82,7 @@ int cptcovn, cptcovage=0, cptcoveff=0,cp
 int npar=NPARMAX;
 int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */
-int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int popbased=0;
 
 int *wav; /* Number of waves for this individuual 0 is possible */
@@ -1443,7 +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{
@@ -1451,7 +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;
@@ -1513,7 +1513,7 @@ void tricode(int *Tvar, int **nbcode, in
 
  ij=1;
  for (i=1; i<=10; i++) {
-   if((Ndum[i]!=0) && (i<=ncov)){
+   if((Ndum[i]!=0) && (i<=ncovcol)){
      Tvaraff[ij]=i; 
      ij++;
    }
@@ -1527,7 +1527,7 @@ void tricode(int *Tvar, int **nbcode, in
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)
 {
   /* Health expectancies */
-  int i, j, nhstepm, hstepm, h;
+  int i, j, nhstepm, hstepm, h, nstepm, k;
   double age, agelim,hf;
   double ***p3mat;
   
@@ -1538,40 +1538,44 @@ void evsij(char fileres[], double ***eij
       fprintf(ficreseij," %1d-%1d",i,j);
   fprintf(ficreseij,"\n");
 
-  hstepm=1*YEARM; /*  Every j years of age (in month) */
-  hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
+  k=1;             /* For example stepm=6 months */
+  hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */
+  hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */
+  /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
+     nhstepm is the number of hstepm from age to agelim 
+     nstepm is the number of stepm from age to agelin. 
+     Look at hpijx to understand the reason of that which relies in memory size
+     and note for a fixed period like k years */
+  /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+     survival function given by stepm (the optimization length). Unfortunately it
+     means that if the survival funtion is printed only each two years of age and if
+     you sum them up and add 1 year (area under the trapezoids) you won't get the same 
+     results. So we changed our mind and took the option of the best precision.
+  */
+  hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */ 
 
   agelim=AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /* 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;
-    nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */
+    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
+    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
+    /* if (stepm >= YEARM) hstepm=1;*/
+    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=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=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
 	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
-	  eij[i][j][(int)age] +=(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;
+	  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+	  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
 	}
-    
-    hf=1;
-    if (stepm >= YEARM) hf=stepm/YEARM;
-
-    for(i=1; i<=nlstate;i++)
-      for(j=1; j<=nlstate;j++){
-	if (j==i) eij[i][j][(int)age]= (eij[i][j][(int)age]-0.5*stepm/12./hf);
-	}
-
     fprintf(ficreseij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
-	fprintf(ficreseij," %9.4f", 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);
@@ -1899,7 +1903,7 @@ void printinghtml(char fileres[], char t
     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\"> 
+ fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.8 </font> <hr size=\"2\" color=\"#EC5E5E\"> 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
 
 Total number of observations=%d <br>
@@ -2462,7 +2466,7 @@ int main(int argc, char *argv[])
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
   
 
-  char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";
+  char version[80]="Imach version 0.8, March 2002, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];
 
 
@@ -2523,9 +2527,9 @@ int main(int argc, char *argv[])
   }
   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);
+  fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+  printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+  fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
 while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);
@@ -2682,7 +2686,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
 
 	cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
-	for (j=ncov;j>=1;j--){
+	for (j=ncovcol;j>=1;j--){
 	  cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
 	} 
 	num[i]=atol(stra);
@@ -2751,7 +2755,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	}
 	else {
 	  cutv(strb,stre,strc,'V');
-	  Tvar[i]=ncov+k1;
+	  Tvar[i]=ncovcol+k1;
 	  cutv(strb,strc,strd,'V'); 
 	  Tprod[k1]=i;
 	  Tvard[k1][1]=atoi(strc);
@@ -2759,7 +2763,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 	  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];
+	    covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
 	  k1++;
 	  k2=k2+2;
 	}
@@ -2913,12 +2917,12 @@ 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= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);
+    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
   
 
    jk=1;
-   fprintf(ficres,"# Parameters\n");
-   printf("# Parameters\n");
+   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
    for(i=1,jk=1; i <=nlstate; i++){
      for(k=1; k <=(nlstate+ndeath); k++){
        if (k != i) 
@@ -2940,8 +2944,8 @@ printf("Total number of individuals= %d,
     ftolhess=ftol; /* Usually correct */
     hesscov(matcov, p, npar, delti, ftolhess, func);
  }
-    fprintf(ficres,"# Scales\n");
-    printf("# Scales\n");
+    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+    printf("# Scales (for hessian or gradient estimation)\n");
      for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
 	if (j!=i) {
@@ -2959,8 +2963,8 @@ printf("Total number of individuals= %d,
      }
     
     k=1;
-    fprintf(ficres,"# Covariance\n");
-    printf("# Covariance\n");
+    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
+    printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
       i1=(i-1)/(ncovmodel*nlstate)+1; 
@@ -3171,15 +3175,15 @@ while((c=getc(ficpar))=='#' && c!= EOF){
 
 
   /*---------- Forecasting ------------------*/
-  if(stepm == 1) {
+  if((stepm == 1) && (strcmp(model,".")==0)){
     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);
+    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);
+    printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
   }
   
 
@@ -3239,8 +3243,6 @@ if (popforecast==1) populforecast(filere
       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);
       for(age=bage; age <=fage ;age++){
 	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
@@ -3249,19 +3251,19 @@ if (popforecast==1) populforecast(filere
 	    prlim[i][i]=probs[(int)age][i][k];
 	}
 	
-	fprintf(ficrest," %.0f",age);
+	fprintf(ficrest," %4.0f",age);
 	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
 	  for(i=1, epj[j]=0.;i <=nlstate;i++) {
-	    epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];
+	    epj[j] += prlim[i][i]*eij[i][j][(int)age];
 	  }
 	  epj[nlstate+1] +=epj[j];
 	}
 	for(i=1, vepp=0.;i <=nlstate;i++)
 	  for(j=1;j <=nlstate;j++)
 	    vepp += vareij[i][j][(int)age];
-	fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));
+	fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));
 	for(j=1;j <=nlstate;j++){
-	  fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));
+	  fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));
 	}
 	fprintf(ficrest,"\n");
       }
@@ -3319,7 +3321,7 @@ if (popforecast==1) populforecast(filere
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
 
   if(erreur >0)
-    printf("End of Imach with error %d\n",erreur);
+    printf("End of Imach with error or warning %d\n",erreur);
   else   printf("End of Imach\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */