Summary: 0.98q5 Flavia

diff --git a/src/imach.c b/src/imach.c
index 588eaa1979ffd00c891366e80efc5cc264e7a0c0..9f608c68e0078479ea165f4e07905db4040fa01d 100644 (file)
--- a/src/imach.c
+++ b/src/imach.c
@@ -1,6 +1,9 @@
 /* $Id$
   $State$
   $Log$
+  Revision 1.197  2015/09/01 18:24:39  brouard
+  *** empty log message ***
+
   Revision 1.196  2015/08/18 23:17:52  brouard
   Summary: 0.98q5
 
@@ -1908,13 +1911,13 @@ double **prevalim(double **prlim, int nlstate, double x[], double age, double **
     if(nagesqr==1)
       cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {
-      cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
-      /*      printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
+      cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
+      /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
     }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-    for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
+    for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2];
     for (k=1; k<=cptcovprod;k++) /* Useless */
-      cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+      cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
     
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
@@ -2087,12 +2090,12 @@ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, in
       if(nagesqr==1)
        cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++) 
-       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
        /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
+       cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
-       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
 
 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
@@ -2963,13 +2966,13 @@ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **ag
        bool=1;
        if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
          for (z1=1; z1<=cptcoveff; z1++)       
-            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
+            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */
               bool=0;
-              /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
-                bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
-                j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
-              /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
+              /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
+                bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
+                j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
+              /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
             } 
        }
  
@@ -2998,10 +3001,10 @@ void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **ag
       pstamp(ficresp);
       if  (cptcovn>0) {
        fprintf(ficresp, "\n#********** Variable "); 
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(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]]);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(ficlog, "**********\n#");
       }
       for(i=1; i<=nlstate;i++) 
@@ -3129,7 +3132,7 @@ void prevalence(double ***probs, double agemin, double agemax, int **s, double *
        bool=1;
        if  (cptcovn>0) {
          for (z1=1; z1<=cptcoveff; z1++) 
-           if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
+           if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
              bool=0;
        } 
        if (bool==1) { 
@@ -4255,23 +4258,23 @@ To be simple, these graphs help to understand the significativity of each parame
     /*j1++;*/
       if  (cptcovn>0) {
        fprintf(ficresprob, "\n#********** Variable "); 
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(ficresprob, "**********\n#\n");
        fprintf(ficresprobcov, "\n#********** Variable "); 
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(ficresprobcov, "**********\n#\n");
        
        fprintf(ficgp, "\n#********** Variable "); 
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(ficgp, "**********\n#\n");
        
        
        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
        
        fprintf(ficresprobcor, "\n#********** Variable ");    
-       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
        fprintf(ficresprobcor, "**********\n#");    
       }
       
@@ -4284,7 +4287,7 @@ To be simple, these graphs help to understand the significativity of each parame
        if(nagesqr==1)
          cov[3]= age*age;
        for (k=1; k<=cptcovn;k++) {
-         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4
                                                         * 1  1 1 1 1
                                                         * 2  2 1 1 1
                                                         * 3  1 2 1 1
@@ -4292,9 +4295,9 @@ To be simple, these graphs help to understand the significativity of each parame
          /* nbcode[1][1]=0 nbcode[1][2]=1;*/
        }
        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
-       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
+       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2];
        for (k=1; k<=cptcovprod;k++)
-         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];
        
     
        for(theta=1; theta <=npar; theta++){
@@ -4531,8 +4534,8 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
      if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){ 
-        fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
-        printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
+        fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
+        printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
        }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
@@ -4614,7 +4617,7 @@ See page 'Matrix of variance-covariance of one-step probabilities' below. \n", r
      if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++) 
-        fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+        fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }
      for(cpt=1; cpt<=nlstate;cpt++) {
@@ -4825,12 +4828,12 @@ plot [%.f:%.f]  ", ageminpar, agemaxpar);
               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
               if(ij <=cptcovage) { /* Bug valgrind */
                 if((j-2)==Tage[ij]) { /* Bug valgrind */
-                  fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                  fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
                   ij++;
                 }
               }
               else
-                fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
             }
             fprintf(ficgp,")/(1");
             
@@ -4844,12 +4847,12 @@ plot [%.f:%.f]  ", ageminpar, agemaxpar);
               for(j=3; j <=ncovmodel-nagesqr; j++){
                 if(ij <=cptcovage) { /* Bug valgrind */
                   if((j-2)==Tage[ij]) { /* Bug valgrind */
-                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
                     ij++;
                   }
                 }
                 else
-                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
               }
               fprintf(ficgp,")");
             }
@@ -4976,7 +4979,7 @@ void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1,
       k=k+1;
       fprintf(ficresf,"\n#******");
       for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       fprintf(ficresf,"******\n");
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");
@@ -5000,7 +5003,7 @@ void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1,
            if (h*hstepm/YEARM*stepm ==yearp) {
               fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++) 
-                fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+                fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
            } 
            for(j=1; j<=nlstate+ndeath;j++) {
@@ -5098,7 +5101,7 @@ void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,do
       k=k+1;
       fprintf(ficrespop,"\n#******");
       for(j=1;j<=cptcoveff;j++) {
-       fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }
       fprintf(ficrespop,"******\n");
       fprintf(ficrespop,"# Age");
@@ -5755,9 +5758,9 @@ int decodemodel ( char model[], int lastobs) /**< This routine decode the model
       /*       k=1 Tvar[1]=2 (from V2) */
       /*       k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
-      /*       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+      /*       cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       /*       } */
-      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
+      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
@@ -6168,14 +6171,14 @@ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxp
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
        k=k+1;
        /* to clean */
-       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
+       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
        fprintf(ficrespl,"\n#******");
        printf("\n#******");
        fprintf(ficlog,"\n#******");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
-         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
        fprintf(ficrespl,"******\n");
        printf("******\n");
@@ -6183,7 +6186,7 @@ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxp
 
        fprintf(ficrespl,"#Age ");
        for(j=1;j<=cptcoveff;j++) {
-         fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+         fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
        }
        for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
        fprintf(ficrespl,"\n");
@@ -6193,7 +6196,7 @@ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxp
          prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
          fprintf(ficrespl,"%.0f ",age );
          for(j=1;j<=cptcoveff;j++)
-           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          for(i=1; i<=nlstate;i++)
            fprintf(ficrespl," %.5f", prlim[i][i]);
          fprintf(ficrespl,"\n");
@@ -6240,7 +6243,7 @@ int hPijx(double *p, int bage, int fage){
     for (k=1; k <= (int) pow(2,cptcoveff); k++){
       fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) 
-       fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+       fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       fprintf(ficrespij,"******\n");
       
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
@@ -6912,7 +6915,7 @@ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numline
   /* 1 to ncodemax[j] is the maximum value of this jth covariate */
 
   codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
-  /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
+  /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;