--- imach/src/imach.c	2002/06/10 13:12:49	1.48
+++ imach/src/imach.c	2002/06/20 14:03:39	1.49
@@ -1,4 +1,4 @@
-/* $Id: imach.c,v 1.48 2002/06/10 13:12:49 brouard Exp $
+/* $Id: imach.c,v 1.49 2002/06/20 14:03:39 lievre Exp $
    Interpolated Markov Chain
 
   Short summary of the programme:
@@ -84,7 +84,7 @@
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";
 int erreur; /* Error number */
 int nvar;
-int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
+int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;
 int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */
@@ -1939,7 +1939,7 @@ void varprevlim(char fileres[], double *
 /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 {
-  int i, j,  i1, k1, l1;
+  int i, j=0,  i1, k1, l1, t, tj;
   int k2, l2, j1,  z1;
   int k=0,l, cptcode;
   int first=1;
@@ -2012,37 +2012,43 @@ void varprob(char optionfilefiname[], do
     exit(0);
   }
   else{
-    fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");
-    fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
+    fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
 
   }
+
+ 
   cov[1]=1;
-  j=cptcoveff;
-  if (cptcovn<1) {j=1;ncodemax[1]=1;}
+  tj=cptcoveff;
+  if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   j1=0;
-  for(k1=1; k1<=1;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){ 
-    j1++;
-
-    if  (cptcovn>0) {
-      fprintf(ficresprob, "\n#********** Variable "); 
-      fprintf(ficresprobcov, "\n#********** Variable "); 
-      fprintf(ficgp, "\n#********** Variable "); 
-      fprintf(fichtm, "\n<h4>********** Variable</h4>\n "); 
-      fprintf(ficresprobcor, "\n#********** Variable "); 
-      for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(ficresprob, "**********\n#");
-      for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(ficresprobcov, "**********\n#");
-      for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(ficgp, "**********\n#");
-      for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(ficgp, "**********\n#");
-      for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
-      fprintf(fichtm, "**********\n#");
-    }
-    
+  for(t=1; t<=tj;t++){
+    for(i1=1; i1<=ncodemax[t];i1++){ 
+      j1++;
+      
+      if  (cptcovn>0) {
+	fprintf(ficresprob, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficresprob, "**********\n#");
+	fprintf(ficresprobcov, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficresprobcov, "**********\n#");
+	
+	fprintf(ficgp, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficgp, "**********\n#");
+	
+	
+	fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+	
+	fprintf(ficresprobcor, "\n#********** Variable ");    
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficgp, "**********\n#");    
+      }
+      
       for (age=bage; age<=fage; age ++){ 
 	cov[2]=age;
 	for (k=1; k<=cptcovn;k++) {
@@ -2169,9 +2175,9 @@ void varprob(char optionfilefiname[], do
 		    fprintf(ficgp,"\nset parametric;set nolabel");
 		    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
 		    fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
-		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);
-		    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);
-		    fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);
+		    fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);
+		    fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);
+		    fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);
 		    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
 		    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
 		    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\
@@ -2187,7 +2193,7 @@ void varprob(char optionfilefiname[], do
 		  }/* if first */
 		} /* age mod 5 */
 	      } /* end loop age */
-	      fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);
+	      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);
 	      first=1;
 	    } /*l12 */
 	  } /* k12 */
@@ -2223,7 +2229,7 @@ void printinghtml(char fileres[], char t
     printf("Problem with %s \n",optionfilehtm), exit(0);
   }
 
-   fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
+   fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
@@ -2231,7 +2237,7 @@ void printinghtml(char fileres[], char t
    <a href=\"e%s\">e%s</a> <br>\n</li>", \
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
 
- fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n
+ fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
@@ -2246,7 +2252,7 @@ void printinghtml(char fileres[], char t
 	<br>",fileres,fileres,fileres,fileres);
  else 
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
-fprintf(fichtm," <li>Graphs</li><p>");
+fprintf(fichtm," <li><b>Graphs</b></li><p>");
 
  m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}
@@ -3415,9 +3421,9 @@ Title=%s <br>Datafile=%s Firstpass=%d La
 Total number of observations=%d <br>\n
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
 <hr  size=\"2\" color=\"#EC5E5E\">
- <ul><li>Parameter files<br>\n
+ <ul><li><h4>Parameter files</h4>\n
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
+ - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
   fclose(fichtm);
 
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
@@ -3495,7 +3501,9 @@ Interval (in months) between two waves:
   agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
-  
+
+  /* hstepm=1;   aff par mois*/
+
   k=0;
   for(cptcov=1;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
@@ -3508,6 +3516,9 @@ Interval (in months) between two waves:
 	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
 	  nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 	  nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+
+	  /*	  nhstepm=nhstepm*YEARM; aff par mois*/
+
 	  p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 	  oldm=oldms;savm=savms;
 	  hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
@@ -3517,7 +3528,7 @@ Interval (in months) between two waves:
 	      fprintf(ficrespij," %1d-%1d",i,j);
 	  fprintf(ficrespij,"\n");
 	   for (h=0; h<=nhstepm; h++){
-	    fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+	    fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
 	    for(i=1; i<=nlstate;i++)
 	      for(j=1; j<=nlstate+ndeath;j++)
 		fprintf(ficrespij," %.5f", p3mat[i][j][h]);