--- imach/src/imach.c	2006/01/05 20:23:19	1.105
+++ imach/src/imach.c	2006/01/19 13:24:36	1.106
@@ -1,6 +1,9 @@
-/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $
+/* $Id: imach.c,v 1.106 2006/01/19 13:24:36 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.106  2006/01/19 13:24:36  brouard
+  Some cleaning and links added in html output
+
   Revision 1.105  2006/01/05 20:23:19  lievre
   *** empty log message ***
 
@@ -221,6 +224,7 @@
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 #include <unistd.h>
 
 /* #include <sys/time.h> */
@@ -259,11 +263,11 @@
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $ */
+/* $Id: imach.c,v 1.106 2006/01/19 13:24:36 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.105 $ $Date: 2006/01/05 20:23:19 $"; 
+char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
+char fullversion[]="$Revision: 1.106 $ $Date: 2006/01/19 13:24:36 $"; 
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
@@ -2556,7 +2560,7 @@ void varevsij(char optionfilefiname[], d
   }  
   fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\n# Routine varevsij");
- fprintf(fichtm, "#Local time at start: %s", strstart);
+  /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 /*   } */
@@ -3199,7 +3203,10 @@ void printinghtml(char fileres[], char t
 		  double jprev2, double mprev2,double anprev2){
   int jj1, k1, i1, cpt;
 
-   fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
+   fprintf(fichtm,"<ul><li><a> href="#firstorder">Result files (first order: no variance)</a>\n \
+   <li><a> href="#secondorder">Result files (second order (variance)</a>\n \
+</ul>");
+   fprintf(fichtm,"<ul><li><h4><a name="firstorder">Result files (first order: no variance)</a></h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
 	   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
    fprintf(fichtm,"\
@@ -3250,7 +3257,7 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
 
 
  fprintf(fichtm,"\
-\n<br><li><h4> Result files (second order: variances)</h4>\n\
+\n<br><li><h4> <a name="secondorder">Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
 
  fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
@@ -4009,7 +4016,7 @@ void printinghtmlmort(char fileres[], ch
 
 fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
 
- fprintf(fichtm,"\nAge   lx     qx    dx    Lx     Tx     e(x)<br>");
+ fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
 
  for (k=agegomp;k<(agemortsup-2);k++) 
    fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
@@ -4504,12 +4511,12 @@ int main(int argc, char *argv[])
      if (s[4][i]==9)  s[4][i]=-1; 
      printf("%ld %.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]));}*/
   
- for (i=1; i<=imx; i++)
+  /* for (i=1; i<=imx; i++) */
  
    /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
      else weight[i]=1;*/
 
-  /* Calculation of the number of parameter from char model*/
+  /* Calculation of the number of parameters from char model */
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
   Tprod=ivector(1,15); 
   Tvaraff=ivector(1,15);