--- imach/src/imach.c	2016/09/07 14:10:18	1.248
+++ imach/src/imach.c	2016/09/07 17:14:18	1.249
@@ -1,6 +1,9 @@
-/* $Id: imach.c,v 1.248 2016/09/07 14:10:18 brouard Exp $
+/* $Id: imach.c,v 1.249 2016/09/07 17:14:18 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.249  2016/09/07 17:14:18  brouard
+  Summary: Starting values from frequencies
+
   Revision 1.248  2016/09/07 14:10:18  brouard
   *** empty log message ***
 
@@ -946,12 +949,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.248 2016/09/07 14:10:18 brouard Exp $ */
+/* $Id: imach.c,v 1.249 2016/09/07 17:14:18 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: 1.248 $ $Date: 2016/09/07 14:10:18 $"; 
+char fullversion[]="$Revision: 1.249 $ $Date: 2016/09/07 17:14:18 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -4249,7 +4252,6 @@ Title=%s <br>Datafile=%s Firstpass=%d La
   j=cptcoveff;  /* Only dummy covariates of the model */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
-  first=1;
   
   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
      reference=low_education V1=0,V2=0
@@ -4257,7 +4259,11 @@ Title=%s <br>Datafile=%s Firstpass=%d La
      high_educ               V1=0 V2=1
      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
   */
-  
+  dateintsum=0;
+  k2cpt=0;
+
+  for (j = 0; j <= cptcoveff; j+=cptcoveff){   
+  first=1;
   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
     posproptt=0.;
     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
@@ -4280,11 +4286,13 @@ Title=%s <br>Datafile=%s Firstpass=%d La
     /*   } */
     /* } */
     
-    dateintsum=0;
-    k2cpt=0;
+    /* dateintsum=0; */
+    /* k2cpt=0; */
+
     /* For that combination of covariate j1, we count and print the frequencies in one pass */
     for (iind=1; iind<=imx; iind++) { /* For each individual iind */
       bool=1;
+      if(j !=0){
       if(anyvaryingduminmodel==0){ /* If All fixed covariates */
 	if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
 	  /* for (z1=1; z1<= nqfveff; z1++) {   */
@@ -4307,16 +4315,18 @@ Title=%s <br>Datafile=%s Firstpass=%d La
 	  } /* end z1 */
 	} /* cptcovn > 0 */
       } /* end any */
+      }/* end j==0 */
       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
 	/* for(m=firstpass; m<=lastpass; m++){ */
 	for(mi=1; mi<wav[iind];mi++){ /* For that wave */
 	  m=mw[mi][iind];
+	  if(j!=0){
 	  if(anyvaryingduminmodel==1){ /* Some are varying covariates */
 	    for (z1=1; z1<=cptcoveff; z1++) {
 	      if( Fixed[Tmodelind[z1]]==1){
 		iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
 		if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
-		  bool=0;
+		  bool=0; /* not selected */
 	      }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
 		if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
 		  bool=0;
@@ -4324,6 +4334,7 @@ Title=%s <br>Datafile=%s Firstpass=%d La
 	      }
 	    }
 	  }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
+	  } /* end j==0 */
 	  /* bool =0 we keep that guy which corresponds to the combination of dummy values */
 	  if(bool==1){
 	    /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
@@ -4347,8 +4358,8 @@ Title=%s <br>Datafile=%s Firstpass=%d La
 		freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
 	      }
 	    } /* end if between passes */  
-	    if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
-	      dateintsum=dateintsum+k2;
+	    if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
+	      dateintsum=dateintsum+k2; /* on all covariates ?*/
 	      k2cpt++;
 	      /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
 	    }
@@ -4362,7 +4373,7 @@ Title=%s <br>Datafile=%s Firstpass=%d La
     
     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     pstamp(ficresp);
-    if  (cptcoveff>0){
+    if  (cptcoveff>0 && j!=0){
       fprintf(ficresp, "\n#********** Variable "); 
       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
@@ -4528,6 +4539,20 @@ Title=%s <br>Datafile=%s Firstpass=%d La
     }
     fprintf(ficresphtmfr,"</table>\n");
   } /* end selected combination of covariate j1 */
+  if(j==0){ /* We can estimate starting values from the occurences in each case */
+    for(jk=-1; jk <=nlstate+ndeath; jk++){
+      for(m=-1; m <=nlstate+ndeath; m++){
+	/* param[i]|j][k]= freq[jk][m][iagemax+3] */
+	if(freq[jk][m][iage] !=0 ) { /* minimizing output */
+	  if(first==1){
+	    printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
+	  }
+	  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
+	}
+      }
+    } /* end loop jk */
+  }
+  } /* end j */
   dateintmean=dateintsum/k2cpt; 
   
   fclose(ficresp);