--- imach/src/imach.c	2016/09/02 08:49:22	1.246
+++ imach/src/imach.c	2016/09/02 11:11:21	1.247
@@ -1,6 +1,9 @@
-/* $Id: imach.c,v 1.246 2016/09/02 08:49:22 brouard Exp $
+/* $Id: imach.c,v 1.247 2016/09/02 11:11:21 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.247  2016/09/02 11:11:21  brouard
+  *** empty log message ***
+
   Revision 1.246  2016/09/02 08:49:22  brouard
   *** empty log message ***
 
@@ -940,12 +943,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.246 2016/09/02 08:49:22 brouard Exp $ */
+/* $Id: imach.c,v 1.247 2016/09/02 11:11:21 brouard Exp $ */
 /* $State: Exp $ */
 #include "version.h"
 char version[]=__IMACH_VERSION__;
 char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
-char fullversion[]="$Revision: 1.246 $ $Date: 2016/09/02 08:49:22 $"; 
+char fullversion[]="$Revision: 1.247 $ $Date: 2016/09/02 11:11:21 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -2584,6 +2587,7 @@ Earliest age to start was %d-%d=%d, ncvl
   /* If we start from prlim again, prlim tends to a constant matrix */
 
   int i, ii,j,k;
+  int first=0;
   double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **bmij();
@@ -2709,7 +2713,12 @@ Earliest age to start was %d-%d=%d, ncvl
     }
   } /* age loop */
     /* After some age loop it doesn't converge */
-  printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
+  if(first){
+    first=1;
+    printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
+Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
+  }
+  fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
 Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   free_vector(min,1,nlstate);
@@ -3596,10 +3605,11 @@ double funcone( double *x)
       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
+      /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
 	/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 	  and mw[mi+1][i]. dh depends on stepm.*/
 	newm=savm;
-	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
+	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
 	cov[2]=agexact;
 	if(nagesqr==1)
 	  cov[3]= agexact*agexact;
@@ -9877,6 +9887,12 @@ int main(int argc, char *argv[])
   delti=delti3[1][1];
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */
+/* We could also provide initial parameters values giving by simple logistic regression 
+ * only one way, that is without matrix product. We will have nlstate maximizations */
+      /* for(i=1;i<nlstate;i++){ */
+      /* 	/\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
+      /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
+      /* } */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
@@ -10649,6 +10665,10 @@ Please run with mle=-1 to get a correct
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2, Real Maximization */
       /* mlikeli uses func not funcone */
+      /* for(i=1;i<nlstate;i++){ */
+      /* 	/\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
+      /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
+      /* } */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */