Changes index.htm: title, model, ...

diff --git a/src/imach.c b/src/imach.c
index e3169cf15438d21959675700c080606c512d710d..50abd3dfb9d2d5e761bdc723aef0a09ce6036b5d 100644 (file)
--- a/src/imach.c
+++ b/src/imach.c
@@ -68,8 +68,7 @@
 \r
 \r
 int nvar;\r
-static int cptcov;\r
-int cptcovn, cptcovage=0, cptcoveff=0;\r
+int cptcovn, cptcovage=0, cptcoveff=0,cptcov;\r
 int npar=NPARMAX;\r
 int nlstate=2; /* Number of live states */\r
 int ndeath=1; /* Number of dead states */\r
@@ -77,9 +76,11 @@ int ncovmodel, ncov;     /* Total number of covariables including constant a12*1
 \r
 int *wav; /* Number of waves for this individuual 0 is possible */\r
 int maxwav; /* Maxim number of waves */\r
+int jmin, jmax; /* min, max spacing between 2 waves */\r
 int mle, weightopt;\r
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */\r
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */\r
+double jmean; /* Mean space between 2 waves */\r
 double **oldm, **newm, **savm; /* Working pointers to matrices */\r
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */\r
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;\r
@@ -666,7 +667,6 @@ double **prevalim(double **prlim, int nlstate, double x[], double age, double **
        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];\r
 \r
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/\r
-\r
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/\r
 \r
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);\r
@@ -841,34 +841,31 @@ double func( double *x)
   /* We are differentiating ll according to initial status */\r
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/\r
   /*for(i=1;i<imx;i++) \r
-printf(" %d\n",s[4][i]);\r
+    printf(" %d\n",s[4][i]);\r
   */\r
   cov[1]=1.;\r
 \r
   for(k=1; k<=nlstate; k++) ll[k]=0.;\r
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
-       for(mi=1; mi<= wav[i]-1; mi++){\r
+    for(mi=1; mi<= wav[i]-1; mi++){\r
       for (ii=1;ii<=nlstate+ndeath;ii++)\r
        for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
-            for(d=0; d<dh[mi][i]; d++){\r
-             newm=savm;\r
-             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
-             for (kk=1; kk<=cptcovage;kk++) {\r
-                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
-                /*printf("%d %d",kk,Tage[kk]);*/\r
-             }\r
-             /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/\r
-             /*cov[3]=pow(cov[2],2)/1000.;*/\r
-\r
-         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
-                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
-         savm=oldm;\r
-         oldm=newm;\r
-\r
-\r
+      for(d=0; d<dh[mi][i]; d++){\r
+       newm=savm;\r
+       cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
+       for (kk=1; kk<=cptcovage;kk++) {\r
+         cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
+       }\r
+       \r
+       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
+                    1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+       savm=oldm;\r
+       oldm=newm;\r
+       \r
+       \r
       } /* end mult */\r
-   \r
+      \r
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);\r
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/\r
       ipmx +=1;\r
@@ -1175,7 +1172,8 @@ void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev
   for(k1=1; k1<=j;k1++){\r
    for(i1=1; i1<=ncodemax[k1];i1++){\r
        j1++;\r
-\r
+       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);\r
+        scanf("%d", i);*/\r
         for (i=-1; i<=nlstate+ndeath; i++)  \r
         for (jk=-1; jk<=nlstate+ndeath; jk++)  \r
           for(m=agemin; m <= agemax+3; m++)\r
@@ -1185,7 +1183,8 @@ void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev
         bool=1;\r
         if  (cptcovn>0) {\r
           for (z1=1; z1<=cptcoveff; z1++) \r
-            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;\r
+            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) \r
+              bool=0;\r
         }\r
          if (bool==1) {\r
           for(m=firstpass; m<=lastpass-1; m++){\r
@@ -1199,8 +1198,8 @@ void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev
         if  (cptcovn>0) {\r
         fprintf(ficresp, "\n#********** Variable "); \r
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
-       }\r
        fprintf(ficresp, "**********\n#");\r
+       }\r
        for(i=1; i<=nlstate;i++) \r
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);\r
        fprintf(ficresp, "\n");\r
@@ -1268,9 +1267,14 @@ void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **
      */\r
 \r
   int i, mi, m;\r
-  int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;\r
-float sum=0.;\r
-\r
+  /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;\r
+     double sum=0., jmean=0.;*/\r
+\r
+int j, k=0,jk, ju, jl;\r
+     double sum=0.;\r
+jmin=1e+5;\r
+ jmax=-1;\r
+jmean=0.;\r
   for(i=1; i<=imx; i++){\r
     mi=0;\r
     m=firstpass;\r
@@ -1301,10 +1305,16 @@ float sum=0.;
       else{\r
        if (s[mw[mi+1][i]][i] > nlstate) {\r
          j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); \r
-         if(j=0) j=1;  /* Survives at least one month after exam */\r
+         /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/\r
+         if(j==0) j=1;  /* Survives at least one month after exam */\r
+         k=k+1;\r
+         if (j >= jmax) jmax=j;\r
+         else if (j <= jmin)jmin=j;\r
+         sum=sum+j;\r
        }\r
        else{\r
          j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));\r
+         /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/\r
          k=k+1;\r
          if (j >= jmax) jmax=j;\r
          else if (j <= jmin)jmin=j;\r
@@ -1322,7 +1332,8 @@ float sum=0.;
       }\r
     }\r
   }\r
-  printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);\r
+  jmean=sum/k;\r
+  printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);\r
 }\r
 /*********** Tricode ****************************/\r
 void tricode(int *Tvar, int **nbcode, int imx)\r
@@ -1338,45 +1349,43 @@ void tricode(int *Tvar, int **nbcode, int imx)
     for (i=1; i<=imx; i++) {\r
       ij=(int)(covar[Tvar[j]][i]);\r
       Ndum[ij]++; \r
+      /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/\r
       if (ij > cptcode) cptcode=ij; \r
     }\r
 \r
-    /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/\r
     for (i=0; i<=cptcode; i++) {\r
       if(Ndum[i]!=0) ncodemax[j]++;\r
     }\r
     ij=1; \r
 \r
+\r
     for (i=1; i<=ncodemax[j]; i++) {\r
       for (k=0; k<=19; k++) {\r
        if (Ndum[k] != 0) {\r
          nbcode[Tvar[j]][ij]=k; \r
-         /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/\r
          ij++;\r
        }\r
        if (ij > ncodemax[j]) break; \r
       }  \r
     } \r
   }  \r
- for (i=1; i<=10; i++) {\r
+\r
+ for (k=0; k<19; k++) Ndum[k]=0;\r
+\r
+ for (i=1; i<=ncovmodel; i++) {\r
       ij=Tvar[i];\r
       Ndum[ij]++; \r
     }\r
+\r
  ij=1;\r
- for (i=1; i<=cptcovn; i++) {\r
+ for (i=1; i<=10; i++) {\r
    if((Ndum[i]!=0) && (i<=ncov)){\r
-     Tvaraff[i]=ij; \r
-   ij++;\r
+     Tvaraff[ij]=i; \r
+     ij++;\r
    }\r
  }\r
  \r
- for (j=1; j<=(cptcovn+2*cptcovprod); j++) {\r
-   if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];\r
-   /*printf("j=%d %d\n",j,Tvar[j]);*/\r
- }\r
- \r
- /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);\r
-    scanf("%d",i);*/\r
+    cptcoveff=ij-1;\r
 }\r
 \r
 /*********** Health Expectancies ****************/\r
@@ -1630,7 +1639,7 @@ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], dou
 int main()\r
 {\r
 \r
-  int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;\r
+  int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;\r
   double agedeb, agefin,hf;\r
   double agemin=1.e20, agemax=-1.e20;\r
 \r
@@ -1729,13 +1738,9 @@ split(pathtot, path,optionfile);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);\r
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);\r
 \r
-  covar=matrix(0,NCOVMAX,1,n);    \r
-  if (strlen(model)<=1) cptcovn=0;\r
-  else {\r
-    j=0;\r
-    j=nbocc(model,'+');\r
-    cptcovn=j+1;\r
-  }\r
+  covar=matrix(0,NCOVMAX,1,n); \r
+  cptcovn=0; \r
+  if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;\r
 \r
   ncovmodel=2+cptcovn;\r
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */\r
@@ -1902,90 +1907,65 @@ split(pathtot, path,optionfile);
     cptcovn=j+1;\r
     cptcovprod=j1;\r
     \r
+    \r
     strcpy(modelsav,model); \r
-   if (j==0) {\r
-      if (j1==0){\r
-       cutv(stra,strb,modelsav,'V');\r
-       Tvar[1]=atoi(strb);\r
-      }\r
-      else if (j1==1) {\r
-       cutv(stra,strb,modelsav,'*');\r
-       Tage[1]=1; cptcovage++;\r
-       if (strcmp(stra,"age")==0) {\r
+    if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){\r
+      printf("Error. Non available option model=%s ",model);\r
+      goto end;\r
+    }\r
+    \r
+    for(i=(j+1); i>=1;i--){\r
+      cutv(stra,strb,modelsav,'+');\r
+      if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); \r
+      /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/\r
+      /*scanf("%d",i);*/\r
+      if (strchr(strb,'*')) {\r
+       cutv(strd,strc,strb,'*');\r
+       if (strcmp(strc,"age")==0) {\r
          cptcovprod--;\r
-         cutv(strd,strc,strb,'V');\r
-         Tvar[1]=atoi(strc);\r
+         cutv(strb,stre,strd,'V');\r
+         Tvar[i]=atoi(stre);\r
+         cptcovage++;\r
+           Tage[cptcovage]=i;\r
+           /*printf("stre=%s ", stre);*/\r
        }\r
-       else if (strcmp(strb,"age")==0) {\r
+       else if (strcmp(strd,"age")==0) {\r
          cptcovprod--;\r
-         cutv(strd,strc,stra,'V');\r
-         Tvar[1]=atoi(strc);\r
+         cutv(strb,stre,strc,'V');\r
+         Tvar[i]=atoi(stre);\r
+         cptcovage++;\r
+         Tage[cptcovage]=i;\r
        }\r
        else {\r
-         cutv(strd,strc,strb,'V');\r
-         cutv(stre,strd,stra,'V');\r
-         Tvar[1]=ncov+1;\r
+         cutv(strb,stre,strc,'V');\r
+         Tvar[i]=ncov+k1;\r
+         cutv(strb,strc,strd,'V'); \r
+         Tprod[k1]=i;\r
+         Tvard[k1][1]=atoi(strc);\r
+         Tvard[k1][2]=atoi(stre);\r
+         Tvar[cptcovn+k2]=Tvard[k1][1];\r
+         Tvar[cptcovn+k2+1]=Tvard[k1][2]; \r
          for (k=1; k<=lastobs;k++) \r
-             covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];\r
+           covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];\r
+         k1++;\r
+         k2=k2+2;\r
        }\r
-       /*printf("%s %s %s\n", stra,strb,modelsav);\r
-printf("%d ",Tvar[1]);\r
-scanf("%d",i);*/\r
       }\r
-    }\r
-   else {\r
-      for(i=j; i>=1;i--){\r
-       cutv(stra,strb,modelsav,'+');\r
-       /*printf("%s %s %s\n", stra,strb,modelsav);\r
-         scanf("%d",i);*/\r
-       if (strchr(strb,'*')) {\r
-         cutv(strd,strc,strb,'*');\r
-         if (strcmp(strc,"age")==0) {\r
-           cptcovprod--;\r
-           cutv(strb,stre,strd,'V');\r
-           Tvar[i+1]=atoi(stre);\r
-           cptcovage++;\r
-           Tage[cptcovage]=i+1;\r
-           printf("stre=%s ", stre);\r
-         }\r
-         else if (strcmp(strd,"age")==0) {\r
-           cptcovprod--;\r
-           cutv(strb,stre,strc,'V');\r
-           Tvar[i+1]=atoi(stre);\r
-           cptcovage++;\r
-           Tage[cptcovage]=i+1;\r
-         }\r
-         else {\r
-           cutv(strb,stre,strc,'V');\r
-           Tvar[i+1]=ncov+k1;\r
-           cutv(strb,strc,strd,'V'); \r
-           Tprod[k1]=i+1;\r
-           Tvard[k1][1]=atoi(strc);\r
-           Tvard[k1][2]=atoi(stre);\r
-           Tvar[cptcovn+k2]=Tvard[k1][1];\r
-           Tvar[cptcovn+k2+1]=Tvard[k1][2]; \r
-           for (k=1; k<=lastobs;k++) \r
-             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];\r
-           k1++;\r
-           k2=k2+2;\r
-         }\r
-       }\r
-       else {\r
-         cutv(strd,strc,strb,'V');\r
-         /* printf("%s %s %s", strd,strc,strb);*/\r
-         Tvar[i+1]=atoi(strc);\r
-       }\r
-       strcpy(modelsav,stra);   \r
+      else {\r
+       /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/\r
+       /*  scanf("%d",i);*/\r
+      cutv(strd,strc,strb,'V');\r
+      Tvar[i]=atoi(strc);\r
       }\r
-      cutv(strd,strc,stra,'V');\r
-      Tvar[1]=atoi(strc);\r
+      strcpy(modelsav,stra);  \r
+      /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);\r
+       scanf("%d",i);*/\r
     }\r
-  }\r
-  /* for (i=1; i<=5; i++)\r
-     printf("i=%d %d ",i,Tvar[i]);*/\r
-  /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/\r
- /*printf("cptcovprod=%d ", cptcovprod);*/\r
-  /*  scanf("%d ",i);*/\r
+}\r
+  \r
+  /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);\r
+  printf("cptcovprod=%d ", cptcovprod);\r
+  scanf("%d ",i);*/\r
     fclose(fic);\r
 \r
     /*  if(mle==1){*/\r
@@ -2003,9 +1983,11 @@ scanf("%d",i);*/
            if(agedc[i]>0)\r
              if(moisdc[i]!=99 && andc[i]!=9999)\r
              agev[m][i]=agedc[i];\r
-           else{\r
+           else {\r
+             if (andc[i]!=9999){\r
              printf("Warning negative age at death: %d line:%d\n",num[i],i);\r
              agev[m][i]=-1;\r
+             }\r
            }\r
          }\r
          else if(s[m][i] !=9){ /* Should no more exist */\r
@@ -2063,7 +2045,7 @@ printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx,
 \r
 \r
       Tcode=ivector(1,100);\r
-      nbcode=imatrix(1,nvar,1,8); \r
+      nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); \r
       ncodemax[1]=1;\r
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);\r
       \r
@@ -2396,7 +2378,12 @@ chdir(path);
     printf("Problem with index.htm \n");goto end;\r
   }\r
 \r
- fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n\r
+ fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64a </font> <hr size=\"2\" color=\"#EC5E5E\"> \r
+Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\r
+Total number of observations=%d <br>\r
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\r
+<hr  size=\"2\" color=\"#EC5E5E\"> \r
+<li>Outputs files<br><br>\n\r
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n\r
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\r
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\r
@@ -2405,9 +2392,9 @@ chdir(path);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>\r
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\r
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\r
-        - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);\r
+        - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);\r
 \r
- fprintf(fichtm," <li>Graphs</li>\n<p>");\r
+ fprintf(fichtm," <li>Graphs</li><p>");\r
 \r
  m=cptcoveff;\r
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}\r
@@ -2417,10 +2404,10 @@ chdir(path);
    for(i1=1; i1<=ncodemax[k1];i1++){\r
        j1++;\r
        if (cptcovn > 0) {\r
-        fprintf(fichtm,"<hr>************ Results for covariates");\r
+        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");\r
         for (cpt=1; cpt<=cptcoveff;cpt++) \r
           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);\r
-        fprintf(fichtm," ************\n<hr>");\r
+        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");\r
        }\r
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>\r
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);     \r
@@ -2680,7 +2667,8 @@ strcpy(fileresvpl,"vpl");
 #ifdef windows\r
  chdir(pathcd);\r
 #endif \r
- system("wgnuplot graph.plt");\r
+ /*system("wgnuplot graph.plt");*/\r
+ system("../gp37mgw/wgnuplot graph.plt");\r
 \r
 #ifdef windows\r
   while (z[0] != 'q') {\r