--- imach/src/imach.c	2014/01/26 03:57:36	1.142
+++ imach/src/imach.c	2014/01/26 09:45:38	1.143
@@ -1,6 +1,12 @@
-/* $Id: imach.c,v 1.142 2014/01/26 03:57:36 brouard Exp $
+/* $Id: imach.c,v 1.143 2014/01/26 09:45:38 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.143  2014/01/26 09:45:38  brouard
+  Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
+
+  * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
+  (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
+
   Revision 1.142  2014/01/26 03:57:36  brouard
   Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 
@@ -445,11 +451,11 @@ extern int errno;
 #define ODIRSEPARATOR '/'
 #endif
 
-/* $Id: imach.c,v 1.142 2014/01/26 03:57:36 brouard Exp $ */
+/* $Id: imach.c,v 1.143 2014/01/26 09:45:38 brouard Exp $ */
 /* $State: Exp $ */
 
-char version[]="Imach version 0.98nR, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
-char fullversion[]="$Revision: 1.142 $ $Date: 2014/01/26 03:57:36 $"; 
+char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
+char fullversion[]="$Revision: 1.143 $ $Date: 2014/01/26 09:45:38 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -582,8 +588,8 @@ int **codtab; /**< codtab=imatrix(1,100,
 int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double *lsurv, *lpop, *tpop;
 
-double ftol=FTOL; /* Tolerance for computing Max Likelihood */
-double ftolhess; /* Tolerance for computing hessian */
+double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
+double ftolhess; /**< Tolerance for computing hessian */
 
 /**************** split *************************/
 static	int split( char *path, char *dirc, char *name, char *ext, char *finame )
@@ -2203,8 +2209,8 @@ void  freqsummary(char fileres[], int ia
 
   first=1;
 
-  for(k1=1; k1<=j;k1++){
-    for(i1=1; i1<=ncodemax[k1];i1++){
+  for(k1=1; k1<=j;k1++){   /* Loop on covariates */
+    for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
       j1++;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 	scanf("%d", i);*/
@@ -2212,10 +2218,10 @@ void  freqsummary(char fileres[], int ia
 	for (jk=-5; jk<=nlstate+ndeath; jk++)  
 	  for(m=iagemin; m <= iagemax+3; m++)
 	    freq[i][jk][m]=0;
-
-    for (i=1; i<=nlstate; i++)  
-      for(m=iagemin; m <= iagemax+3; m++)
-	prop[i][m]=0;
+      
+      for (i=1; i<=nlstate; i++)  
+	for(m=iagemin; m <= iagemax+3; m++)
+	  prop[i][m]=0;
       
       dateintsum=0;
       k2cpt=0;
@@ -2253,6 +2259,9 @@ void  freqsummary(char fileres[], int ia
 	fprintf(ficresp, "\n#********** Variable "); 
 	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 	fprintf(ficresp, "**********\n#");
+	fprintf(ficlog, "\n#********** Variable "); 
+	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+	fprintf(ficlog, "**********\n#");
       }
       for(i=1; i<=nlstate;i++) 
 	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
@@ -5496,12 +5505,32 @@ run imach with mle=-1 to get a correct t
   m=pow(2,cptcoveff);
  
   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
-    for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
-      for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
-	for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
+    for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
+      for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
+	for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
 	  h++;
 	  if (h>m) 
 	    h=1;
+	  /**< codtab(h,k)  k
+	   *     h     1     2     3     4
+	   *______________________________  
+	   *     1 i=1 1 i=1 1 i=1 1 i=1 1
+	   *     2     2     1     1     1
+	   *     3 i=2 1     2     1     1
+	   *     4     2     2     1     1
+	   *     5 i=3 1 i=2 1     2     1
+	   *     6     2     1     2     1
+	   *     7 i=4 1     2     2     1
+	   *     8     2     2     2     1
+	   *     9 i=5 1 i=3 1 i=2 1     1
+	   *    10     2     1     1     1
+	   *    11 i=6 1     2     1     1
+	   *    12     2     2     1     1
+	   *    13 i=7 1 i=4 1     2     1    
+	   *    14     2     1     2     1
+	   *    15 i=8 1     2     2     1
+	   *    16     2     2     2     1
+	   */
 	  codtab[h][k]=j;
 	  codtab[h][Tvar[k]]=j;
 	  printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
@@ -6081,14 +6110,14 @@ Interval (in months) between two waves:
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
-    i1=cptcoveff;
+    i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
 
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
-      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+      //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
 	k=k+1;
 	/* to clean */
-	printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
+	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
 	fprintf(ficrespl,"\n#******");
 	printf("\n#******");
 	fprintf(ficlog,"\n#******");
@@ -6109,9 +6138,9 @@ Interval (in months) between two waves:
 	  for(i=1; i<=nlstate;i++)
 	    fprintf(ficrespl," %.5f", prlim[i][i]);
 	  fprintf(ficrespl,"\n");
-	}
-      }
-    }
+	} /* Age */
+	/* was end of cptcod */
+    } /* cptcov */
     fclose(ficrespl);
 
     /*------------- h Pij x at various ages ------------*/