--- imach/src/imach.c	2015/07/16 16:49:02	1.192
+++ imach/src/imach.c	2015/08/04 07:17:42	1.193
@@ -1,6 +1,9 @@
-/* $Id: imach.c,v 1.192 2015/07/16 16:49:02 brouard Exp $
+/* $Id: imach.c,v 1.193 2015/08/04 07:17:42 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.193  2015/08/04 07:17:42  brouard
+  Summary: 0.98q4
+
   Revision 1.192  2015/07/16 16:49:02  brouard
   Summary: Fixing some outputs
 
@@ -693,11 +696,11 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.192 2015/07/16 16:49:02 brouard Exp $ */
+/* $Id: imach.c,v 1.193 2015/08/04 07:17:42 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98q3, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
-char fullversion[]="$Revision: 1.192 $ $Date: 2015/07/16 16:49:02 $"; 
+char version[]="Imach version 0.98q4, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
+char fullversion[]="$Revision: 1.193 $ $Date: 2015/08/04 07:17:42 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -4536,12 +4539,12 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
  }/* End k1 */
  fprintf(fichtm,"</ul>");
 
-
  fprintf(fichtm,"\
 \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);
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
+ - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
 
- fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
+ fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 	 subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
  fprintf(fichtm,"\
  - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
@@ -6561,7 +6564,7 @@ int main(int argc, char *argv[])
 	if(jj==i) continue;
 	j++;
 	fscanf(ficpar,"%1d%1d",&i1,&j1);
-	if ((i1 != i) && (j1 != j)){
+	if ((i1 != i) || (j1 != jj)){
 	  printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
 It might be a problem of design; if ncovcol and the model are correct\n \
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
@@ -6569,8 +6572,8 @@ run imach with mle=-1 to get a correct t
 	}
 	fprintf(ficparo,"%1d%1d",i1,j1);
 	if(mle==1)
-	  printf("%1d%1d",i,j);
-	fprintf(ficlog,"%1d%1d",i,j);
+	  printf("%1d%1d",i,jj);
+	fprintf(ficlog,"%1d%1d",i,jj);
 	for(k=1; k<=ncovmodel;k++){
 	  fscanf(ficpar," %lf",&param[i][j][k]);
 	  if(mle==1){
@@ -7111,9 +7114,10 @@ Interval (in months) between two waves:
     }
     
     printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
-    for (i=1;i<=NDIM;i++) 
+    for (i=1;i<=NDIM;i++) {
       printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-
+      fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
+    }
     lsurv=vector(1,AGESUP);
     lpop=vector(1,AGESUP);
     tpop=vector(1,AGESUP);
@@ -7210,6 +7214,24 @@ Interval (in months) between two waves:
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
+    printf("Parameters and 95%% confidence intervals\n");
+    fprintf(ficlog, "Parameters, T and confidence intervals\n");
+    for(i=1,jk=1; i <=nlstate; i++){
+      for(k=1; k <=(nlstate+ndeath); k++){
+	if (k != i) {
+	  printf("%d%d ",i,k);
+	  fprintf(ficlog,"%d%d ",i,k);
+	  for(j=1; j <=ncovmodel; j++){
+	    printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
+	    fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
+	    jk++; 
+	  }
+	  printf("\n");
+	  fprintf(ficlog,"\n");
+	}
+      }
+    }
+
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
@@ -7366,6 +7388,7 @@ Interval (in months) between two waves:
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
     
     fscanf(ficpar,"pop_based=%d\n",&popbased);
+    fprintf(ficlog,"pop_based=%d\n",popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);