--- imach/src/imach.c	2016/07/21 08:43:33	1.227
+++ imach/src/imach.c	2016/07/22 17:45:30	1.228
@@ -1,8 +1,8 @@
-/* $Id: imach.c,v 1.227 2016/07/21 08:43:33 brouard Exp $
+/* $Id: imach.c,v 1.228 2016/07/22 17:45:30 brouard Exp $
   $State: Exp $
   $Log: imach.c,v $
-  Revision 1.227  2016/07/21 08:43:33  brouard
-  Summary: 0.99 working (more or less) for Asian Workshop on multitate methods
+  Revision 1.228  2016/07/22 17:45:30  brouard
+  Summary: Fixing some arrays, still debugging
 
   Revision 1.226  2016/07/12 18:42:34  brouard
   Summary: temp
@@ -884,12 +884,12 @@ typedef struct {
 #define ODIRSEPARATOR '\\'
 #endif
 
-/* $Id: imach.c,v 1.227 2016/07/21 08:43:33 brouard Exp $ */
+/* $Id: imach.c,v 1.228 2016/07/22 17:45:30 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: 1.227 $ $Date: 2016/07/21 08:43:33 $"; 
+char fullversion[]="$Revision: 1.228 $ $Date: 2016/07/22 17:45:30 $"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
@@ -1061,7 +1061,9 @@ int *Fixed; /** Fixed[k] 0=fixed, 1 vary
 int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
 int *Tage;
 int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
-int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
 int *Ndum; /** Freq of modality (tricode */
 /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard;
@@ -2946,10 +2948,9 @@ double func( double *x)
   int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;
-  double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */
   int s1, s2;
-  int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */
+  int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
   double bbh, survp;
   long ipmx;
   double agexact;
@@ -2979,7 +2980,7 @@ double func( double *x)
 	cov[++ioffset]=covar[Tvar[k]][i];
       }
       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
-	cov[++ioffset]=coqvar[iqv][i];
+	cov[++ioffset]=coqvar[Tvar[iqv]][i];
       }
 
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
@@ -2996,7 +2997,7 @@ double func( double *x)
       */
       for(mi=1; mi<= wav[i]-1; mi++){
 	for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
-	  cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
+	  cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /* Not sure, Tvar V4+V3+V5 Tvaraff ? */
 	}
 	for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
 	  if(cotqvar[mw[mi][i]][iqtv][i] == -1){
@@ -3275,15 +3276,16 @@ double func( double *x)
 /*************** log-likelihood *************/
 double funcone( double *x)
 {
-  /* Same as likeli but slower because of a lot of printf and if */
+  /* Same as func but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;
-	int ioffset=0;
+  int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;
   double lli; /* Individual log likelihood */
   double llt;
   int s1, s2;
-	int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */
+  int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
+
   double bbh, survp;
   double agexact;
   double agebegin, ageend;
@@ -3309,10 +3311,16 @@ double funcone( double *x)
     
     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
       for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
-	cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];
+	/* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
+	/* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
+	k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */
+	cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
+	printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]);
       }
       for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
-	cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
+	iv=TmodelInvQind[iqtv]; /* Counting the # varying covariate from 1 to ntveff */
+	printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]);
+	cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
       }
       for (ii=1;ii<=nlstate+ndeath;ii++)
 	for (j=1;j<=nlstate+ndeath;j++){
@@ -4713,6 +4721,7 @@ void  concatwav(int wav[], int **dh, int
       ++ij;
       Tvaraff[ij]=Tvar[k]; /*For printing */
       Tmodelind[ij]=k;
+      TmodelInvind[k]=Tvar[k]- ncovcol-nqv;
       if(Fixed[k]!=0)
         anyvaryingduminmodel=1;
     /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
@@ -4732,6 +4741,9 @@ void  concatwav(int wav[], int **dh, int
     Tvaraff[j]=0;
     Tmodelind[j]=0;
   }
+  for(j=ntveff+1; j<= cptcovt; j++){
+    TmodelInvind[j]=0;
+  }
   /* To be sorted */
   ;
 }
@@ -8006,10 +8018,15 @@ Dummy[k] 0=dummy (0 1), 1 quantitative (
       Fixed[k]= 1;
       Dummy[k]= 0;
       ntveff++; /* Only simple time varying dummy variable */
+      printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
+      printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){
 	Fixed[k]= 1;
 	Dummy[k]= 1;
-	nqtveff++;/* Only simple time varying quantitative variable */
+	TmodelInvQind[++nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
+	/* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
+	printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
+      printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
     }else if (Typevar[k] == 1) {  /* product with age */
       if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
 	Fixed[k]= 2;
@@ -9390,6 +9407,12 @@ Please run with mle=-1 to get a correct
 				* Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
 				* 3, 1, 0, 0, 0, 0, 0, 0},
 				* model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
+ TmodelInvind=ivector(1,NCOVMAX);
+  TmodelInvQind=ivector(1,NCOVMAX);/** five the k model position of an
+				* individual quantitative, fixed or varying:
+				* Tmodelqind[1]=1,Tvaraff[1]@9={4,
+				* 3, 1, 0, 0, 0, 0, 0, 0},
+				* model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
 /* Main decodemodel */
 
 
@@ -10540,6 +10563,8 @@ Please run with mle=-1 to get a correct
   free_ivector(invalidvarcomb,1,ncovcombmax);
   free_ivector(Tage,1,NCOVMAX);
   free_ivector(Tmodelind,1,NCOVMAX);
+  free_ivector(TmodelInvind,1,NCOVMAX);
+  free_ivector(TmodelInvQind,1,NCOVMAX);
   
   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
   /* free_imatrix(codtab,1,100,1,10); */