Summary: Some minor bugs fixed

diff --git a/src/imach.c b/src/imach.c
index 1770218c653377a10ee845a7b7e17917151e91ae..f343fa44a6b9199271d4c178805714f4a4fc4deb 100644 (file)
--- a/src/imach.c
+++ b/src/imach.c
@@ -1,6 +1,9 @@
 /* $Id$
   $State$
   $Log$
+  Revision 1.282  2018/02/27 22:50:02  brouard
+  *** empty log message ***
+
   Revision 1.281  2018/02/27 19:25:23  brouard
   Summary: Adding second argument for quitting
 
@@ -1052,7 +1055,7 @@ typedef struct {
 /* $State$ */
 #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 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[]="$Revision$ $Date$"; 
 char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];
@@ -4365,7 +4368,7 @@ void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int
   double ***freq; /* Frequencies */
   double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
   int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
-  double *meanq;
+  double *meanq, *idq;
   double **meanqt;
   double *pp, **prop, *posprop, *pospropt;
   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
@@ -4378,6 +4381,7 @@ void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int
   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
+  idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
   meanqt=matrix(1,lastpass,1,nqtveff);
   strcpy(fileresp,"P_");
   strcat(fileresp,fileresu);
@@ -4486,13 +4490,15 @@ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age
        posprop[i]=0;
        pospropt[i]=0;
       }
-      /* for (z1=1; z1<= nqfveff; z1++) {   */
-      /*   meanq[z1]+=0.; */
+      for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
+        idq[z1]+=0.;
+        meanq[z1]+=0.;
+      }
+      /* for (z1=1; z1<= nqtveff; z1++) { */
       /*   for(m=1;m<=lastpass;m++){ */
-      /*       meanqt[m][z1]=0.; */
-      /*   } */
-      /* } */
-      
+      /*         meanqt[m][z1]=0.; */
+      /*       } */
+      /* }       */
       /* dateintsum=0; */
       /* k2cpt=0; */
       
@@ -4502,7 +4508,7 @@ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age
        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++) {   */
+             /* for (z1=1; z1<= nqfveff; z1++) { */
              /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
              /* } */
              for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
@@ -4568,6 +4574,11 @@ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age
                  /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                  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 */
                }
+               for (z1=1; z1<= nqfveff; z1++) {
+                 idq[z1]++;
+                 meanq[z1]+=covar[ncovcol+z1][iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
+                 /* meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
+               }
              } /* end if between passes */  
              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 ?*/
@@ -4615,6 +4626,19 @@ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age
        fprintf(ficresphtmfr, "**********</h3>\n");
        fprintf(ficlog, "**********\n");
       }
+           /*
+             Printing means of quantitative variables if any
+           */
+           for (z1=1; z1<= nqfveff; z1++) {
+             fprintf(ficresphtmfr,"V quantitative id %d, number of idividuals= %f, sum=%f", z1, idq[z1], meanq[z1]);
+             fprintf(ficresphtmfr,", mean=%f<p>\n",meanq[z1]/idq[z1]);
+           }
+           /* for (z1=1; z1<= nqtveff; z1++) { */
+           /*  for(m=1;m<=lastpass;m++){ */
+           /*    fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
+           /*   } */
+           /* } */
+
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
         fprintf(ficresp, " Age");
@@ -4895,6 +4919,7 @@ Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age
   fclose(ficresp);
   fclose(ficresphtm);
   fclose(ficresphtmfr);
+  free_vector(idq,1,nqfveff);
   free_vector(meanq,1,nqfveff);
   free_matrix(meanqt,1,lastpass,1,nqtveff);
   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
@@ -6862,7 +6887,7 @@ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-
      for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.    \
- <a href=\"%s_%d-%d-%d.svg\">%s_%d%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+ <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
      }
      /* Period (stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){
@@ -10945,19 +10970,24 @@ int main(int argc, char *argv[])
                        title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
     if (num_filled != 5) {
       printf("Should be 5 parameters\n");
+      fprintf(ficlog,"Should be 5 parameters\n");
     }
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
+    fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
   }
   /* Second parameter line */
   while(fgets(line, MAXLINE, ficpar)) {
-    /* If line starts with a # it is a comment */
+    /* while(fscanf(ficpar,"%[^\n]", line)) { */
+    /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
     if (line[0] == '#') {
       numlinepar++;
-      fputs(line,stdout);
-      fputs(line,ficparo);
-      fputs(line,ficres);
-      fputs(line,ficlog);
+      printf("%s",line);
+      fprintf(ficres,"%s",line);
+      fprintf(ficparo,"%s",line);
+      fprintf(ficlog,"%s",line);
       continue;
     }else
       break;
@@ -10967,8 +10997,13 @@ int main(int argc, char *argv[])
     if (num_filled != 11) {
       printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
       printf("but line=%s\n",line);
+      fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
+      fprintf(ficlog,"but line=%s\n",line);
     }
     printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+    fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+    fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+    fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
   }
   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
@@ -10977,10 +11012,10 @@ int main(int argc, char *argv[])
     /* If line starts with a # it is a comment */
     if (line[0] == '#') {
       numlinepar++;
-      fputs(line,stdout);
-      fputs(line,ficparo);
-      fputs(line,ficres);
-      fputs(line,ficlog);
+      printf("%s",line);
+      fprintf(ficres,"%s",line);
+      fprintf(ficparo,"%s",line);
+      fprintf(ficlog,"%s",line);
       continue;
     }else
       break;
@@ -11001,12 +11036,15 @@ int main(int argc, char *argv[])
     }
     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
     printf("model=1+age+%s\n",model);fflush(stdout);
+    fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
+    fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
+    fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
   }
   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
   /* numlinepar=numlinepar+3; /\* In general *\/ */
   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
-  fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
-  fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+  /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
+  /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
   fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){
@@ -11869,7 +11907,7 @@ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpa
     printf("\n");
     
     /*--------- results files --------------*/
-    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
+    /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
     
     
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
@@ -12737,5 +12775,6 @@ end:
     printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);
   }
+  printf("End\n");
   exit(0);
 }