--- imach/src/imach.c	2018/04/27 14:27:04	1.286
+++ imach/src/imach.c	2018/05/01 17:57:25	1.287
@@ -1,6 +1,9 @@
-/* $Id: imach.c,v 1.286 2018/04/27 14:27:04 brouard Exp $
+/* $Id: imach.c,v 1.287 2018/05/01 17:57:25 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
+  Revision 1.287  2018/05/01 17:57:25  brouard
+  Summary: Bug fixed by providing frequencies only for non missing covariates
+
   Revision 1.286  2018/04/27 14:27:04  brouard
   Summary: some minor bugs
 
@@ -1063,12 +1066,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.286 2018/04/27 14:27:04 brouard Exp $ */
+/* $Id: imach.c,v 1.287 2018/05/01 17:57:25 brouard Exp $ */
 /* $State: Exp $ */
 #include "version.h"
 char version[]=__IMACH_VERSION__;
 char copyright[]="April 2018,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: 1.286 $ $Date: 2018/04/27 14:27:04 $"; 
+char fullversion[]="$Revision: 1.287 $ $Date: 2018/05/01 17:57:25 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -5366,7 +5369,6 @@ void  concatwav(int wav[], int **dh, int
        nbcode[k][j]=0; /* Valgrind */
 
    /* Loop on covariates without age and products and no quantitative variable */
-   /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
@@ -5384,7 +5386,11 @@ void  concatwav(int wav[], int **dh, int
 	     modmaxcovj=ij; 
 	   else if (ij < modmincovj) 
 	     modmincovj=ij; 
-	   if ((ij < -1) && (ij > NCOVMAX)){
+	   if (ij <0 || ij >1 ){
+	     printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
+	     fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
+	   }
+	   if ((ij < -1) || (ij > NCOVMAX)){
 	     printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
 	     exit(1);
 	   }else
@@ -5430,12 +5436,18 @@ void  concatwav(int wav[], int **dh, int
 	 /* nbcode[Tvar[j]][3]=2; */
 	 /* To be continued (not working yet). */
 	 ij=0; /* ij is similar to i but can jump over null modalities */
-	 for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+
+	 /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+	 /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
+	 /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
+	  * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
+	 /*, could be restored in the future */
+	 for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
 	   if (Ndum[i] == 0) { /* If nobody responded to this modality k */
 	     break;
 	   }
 	   ij++;
-	   nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
+	   nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
 	   cptcode = ij; /* New max modality for covar j */
 	 } /* end of loop on modality i=-1 to 1 or more */
 	 break;
@@ -5451,21 +5463,7 @@ void  concatwav(int wav[], int **dh, int
 	 break;
        } /* end switch */
      } /* end dummy test */
-    
-     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
-     /* 	/\*recode from 0 *\/ */
-     /* 				     k is a modality. If we have model=V1+V1*sex  */
-     /* 				     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
-     /* 				  But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
-     /* 	} */
-     /* 	/\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
-     /* 	if (ij > ncodemax[j]) { */
-     /* 	  printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */
-     /* 	  fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
-     /* 	  break; */
-     /* 	} */
-     /*   }  /\* end of loop on modality k *\/ */
-   } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
+   } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
   
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
    /* Look at fixed dummy (single or product) covariates to check empty modalities */