--- imach/src/imach.c 2015/11/21 12:41:11 1.211 +++ imach/src/imach.c 2015/12/16 08:52:24 1.215 @@ -1,6 +1,18 @@ -/* $Id: imach.c,v 1.211 2015/11/21 12:41:11 brouard Exp $ +/* $Id: imach.c,v 1.215 2015/12/16 08:52:24 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.215 2015/12/16 08:52:24 brouard + Summary: 0.98r4 working + + Revision 1.214 2015/12/16 06:57:54 brouard + Summary: temporary not working + + Revision 1.213 2015/12/11 18:22:17 brouard + Summary: 0.98r4 + + Revision 1.212 2015/11/21 12:47:24 brouard + Summary: minor typo + Revision 1.211 2015/11/21 12:41:11 brouard Summary: 0.98r3 with some graph of projected cross-sectional @@ -780,12 +792,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.211 2015/11/21 12:41:11 brouard Exp $ */ +/* $Id: imach.c,v 1.215 2015/12/16 08:52:24 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; -char fullversion[]="$Revision: 1.211 $ $Date: 2015/11/21 12:41:11 $"; +char fullversion[]="$Revision: 1.215 $ $Date: 2015/12/16 08:52:24 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -821,7 +833,7 @@ double **matprod2(); /* test */ double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ /*FILE *fic ; */ /* Used in readdata only */ -FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; +FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; FILE *ficlog, *ficrespow; int globpr=0; /* Global variable for printing or not */ double fretone; /* Only one call to likelihood */ @@ -1383,7 +1395,30 @@ char *subdirf3(char fileres[], char *pre strcat(tmpout,fileres); return tmpout; } + +/*************** function subdirfext ***********/ +char *subdirfext(char fileres[], char *preop, char *postop) +{ + + strcpy(tmpout,preop); + strcat(tmpout,fileres); + strcat(tmpout,postop); + return tmpout; +} +/*************** function subdirfext3 ***********/ +char *subdirfext3(char fileres[], char *preop, char *postop) +{ + + /* Caution optionfilefiname is hidden */ + strcpy(tmpout,optionfilefiname); + strcat(tmpout,"/"); + strcat(tmpout,preop); + strcat(tmpout,fileres); + strcat(tmpout,postop); + return tmpout; +} + char *asc_diff_time(long time_sec, char ascdiff[]) { long sec_left, days, hours, minutes; @@ -2220,6 +2255,7 @@ double ***hpxij(double ***po, int nhstep double **out, cov[NCOVMAX+1]; double **newm; double agexact; + double agebegin, ageend; /* Hstepm could be zero and should return the unit matrix */ for (i=1;i<=nlstate+ndeath;i++) @@ -2233,7 +2269,7 @@ double ***hpxij(double ***po, int nhstep newm=savm; /* Covariates have to be included here again */ cov[1]=1.; - agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; + agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */ cov[2]=agexact; if(nagesqr==1) cov[3]= agexact*agexact; @@ -2604,6 +2640,7 @@ double funcone( double *x) int s1, s2; double bbh, survp; double agexact; + double agebegin, ageend; /*extern weight */ /* We are differentiating ll according to initial status */ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ @@ -2622,7 +2659,12 @@ double funcone( double *x) oldm[ii][j]=(ii==j ? 1.0 : 0.0); savm[ii][j]=(ii==j ? 1.0 : 0.0); } - for(d=0; d\nIMaCh PHTM_ %s\n %s
%s \ +
\n\ +Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ + fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); + } + fprintf(ficresphtm,"Current page is file %s
\n\n

Frequencies and prevalence by age at begin of transition

\n",fileresphtm, fileresphtm); + + strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm")); + if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) { + printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); + fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); + fflush(ficlog); + exit(70); + } + else{ + fprintf(ficresphtmfr,"\nIMaCh PHTM_Frequency table %s\n %s
%s \ +
\n\ +Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ + fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); + } + fprintf(ficresphtmfr,"Current page is file %s
\n\n

Frequencies of all effective transitions by age at begin of transition

Unknown status is -1
\n",fileresphtmfr, fileresphtmfr); + freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); j1=0; @@ -3212,10 +3290,7 @@ void freqsummary(char fileres[], int ia first=1; - /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ - /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ - /* j1++; */ - for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ + for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */ /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); scanf("%d", i);*/ for (i=-5; i<=nlstate+ndeath; i++) @@ -3229,7 +3304,7 @@ void freqsummary(char fileres[], int ia dateintsum=0; k2cpt=0; - for (i=1; i<=imx; i++) { + for (i=1; i<=imx; i++) { /* For each individual i */ bool=1; if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ for (z1=1; z1<=cptcoveff; z1++) @@ -3242,25 +3317,38 @@ void freqsummary(char fileres[], int ia /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/ } } /* cptcovn > 0 */ - + if (bool==1){ - for(m=firstpass; m<=lastpass; m++){ - k2=anint[m][i]+(mint[m][i]/12.); - /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ - if(agev[m][i]==0) agev[m][i]=iagemax+1; - if(agev[m][i]==1) agev[m][i]=iagemax+2; - if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; + /* for(m=firstpass; m<=lastpass; m++){ */ + for(mi=1; mi=firstpass && m <=lastpass){ + k2=anint[m][i]+(mint[m][i]/12.); + /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ + if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */ + if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */ + if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */ + prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */ if (m1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) { - dateintsum=dateintsum+k2; - k2cpt++; - /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ + /* if(s[m][i]==4 && s[m+1][i]==4) */ + /* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */ + if(s[m][i]==-1) + printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.)); + freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */ + /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */ + freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */ } - /*}*/ + } + if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) { + dateintsum=dateintsum+k2; + k2cpt++; + /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ + } + /*}*/ } /* end m */ } /* end bool */ } /* end i = 1 to imx */ @@ -3269,24 +3357,57 @@ void freqsummary(char fileres[], int ia 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]][codtabm(j1,z1)]); - fprintf(ficresp, "**********\n#"); + fprintf(ficresphtm, "\n

********** Variable "); + fprintf(ficresphtmfr, "\n

********** Variable "); + for (z1=1; z1<=cptcoveff; z1++){ + fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + } + fprintf(ficresp, "**********\n#"); + fprintf(ficresphtm, "**********

\n"); + fprintf(ficresphtmfr, "**********\n"); fprintf(ficlog, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficlog, "**********\n#"); + fprintf(ficlog, "**********\n"); } - for(i=1; i<=nlstate;i++) + fprintf(ficresphtm,""); + for(i=1; i<=nlstate;i++) { fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); + fprintf(ficresphtm, "",i,i); + } fprintf(ficresp, "\n"); + fprintf(ficresphtm, "\n"); + /* Header of frequency table by age */ + fprintf(ficresphtmfr,"
AgePrev(%d)N(%d)N
"); + fprintf(ficresphtmfr," "); + for(jk=-1; jk <=nlstate+ndeath; jk++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(jk!=0 && m!=0) + fprintf(ficresphtmfr," ",jk,m); + } + } + fprintf(ficresphtmfr, "\n"); + + /* For each age */ for(i=iagemin; i <= iagemax+3; i++){ - if(i==iagemax+3){ + fprintf(ficresphtm,""); + if(i==iagemax+1){ + fprintf(ficlog,"1"); + fprintf(ficresphtmfr," "); + }else if(i==iagemax+2){ + fprintf(ficlog,"0"); + fprintf(ficresphtmfr," "); + }else if(i==iagemax+3){ fprintf(ficlog,"Total"); + fprintf(ficresphtmfr," "); }else{ if(first==1){ first=0; printf("See log file for details...\n"); } + fprintf(ficresphtmfr," ",i); fprintf(ficlog,"Age %d", i); } for(jk=1; jk <=nlstate ; jk++){ @@ -3329,32 +3450,47 @@ void freqsummary(char fileres[], int ia if( i <= iagemax){ if(pos>=1.e-5){ fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); + fprintf(ficresphtm,"",i,prop[jk][i]/posprop, prop[jk][i],posprop); /*probs[i][jk][j1]= pp[jk]/pos;*/ /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ } - else + else{ fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); + fprintf(ficresphtm,"",i, prop[jk][i],posprop); + } } } - for(jk=-1; jk <=nlstate+ndeath; jk++) - for(m=-1; m <=nlstate+ndeath; m++) - if(freq[jk][m][i] !=0 ) { - if(first==1) - printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); + for(jk=-1; jk <=nlstate+ndeath; jk++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(freq[jk][m][i] !=0 ) { /* minimizing output */ + if(first==1){ + printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); + } fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); } - if(i <= iagemax) + if(jk!=0 && m!=0) + fprintf(ficresphtmfr," ",freq[jk][m][i]); + } + } + fprintf(ficresphtmfr,"\n "); + if(i <= iagemax){ fprintf(ficresp,"\n"); + fprintf(ficresphtm,"\n"); + } if(first==1) printf("Others in log...\n"); fprintf(ficlog,"\n"); } /* end loop i */ + fprintf(ficresphtm,"
Age%d%d
0
Unknown
Total
%d%d%.5f%.0f%.0f%dNaNq%.0f%.0f%.0f
\n"); + fprintf(ficresphtmfr,"\n"); /*}*/ } /* end j1 */ dateintmean=dateintsum/k2cpt; fclose(ficresp); + fclose(ficresphtm); + fclose(ficresphtmfr); free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); free_vector(pp,1,nlstate); free_matrix(prop,1,nlstate,iagemin, iagemax+3); @@ -3370,6 +3506,9 @@ void prevalence(double ***probs, double */ int i, m, jk, j1, bool, z1,j; + int mi; /* Effective wave */ + int iage; + double agebegin, ageend; double **prop; double posprop; @@ -3389,54 +3528,57 @@ void prevalence(double ***probs, double first=1; for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ - /*for(i1=1; i1<=ncodemax[k1];i1++){ - j1++;*/ - - for (i=1; i<=nlstate; i++) - for(m=iagemin; m <= iagemax+3; m++) - prop[i][m]=0.0; - - for (i=1; i<=imx; i++) { /* Each individual */ - bool=1; - if (cptcovn>0) { - for (z1=1; z1<=cptcoveff; z1++) - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) - bool=0; - } - if (bool==1) { - for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ + for (i=1; i<=nlstate; i++) + for(iage=iagemin; iage <= iagemax+3; iage++) + prop[i][iage]=0.0; + + for (i=1; i<=imx; i++) { /* Each individual */ + 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]][codtabm(j1,z1)]) + bool=0; + } + if (bool==1) { + /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */ + for(mi=1; mi=firstpass && m <=lastpass){ y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ if(agev[m][i]==0) agev[m][i]=iagemax+1; if(agev[m][i]==1) agev[m][i]=iagemax+2; if((int)agev[m][i] iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); - if (s[m][i]>0 && s[m][i]<=nlstate) { + if (s[m][i]>0 && s[m][i]<=nlstate) { /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/ - prop[s[m][i]][(int)agev[m][i]] += weight[i]; - prop[s[m][i]][iagemax+3] += weight[i]; - } - } + prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */ + prop[s[m][i]][iagemax+3] += weight[i]; + } /* end valid statuses */ + } /* end selection of dates */ } /* end selection of waves */ - } - } - for(i=iagemin; i <= iagemax+3; i++){ - for(jk=1,posprop=0; jk <=nlstate ; jk++) { - posprop += prop[jk][i]; - } - - for(jk=1; jk <=nlstate ; jk++){ - if( i <= iagemax){ - if(posprop>=1.e-5){ - probs[i][jk][j1]= prop[jk][i]/posprop; - } else{ - if(first==1){ - first=0; - printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]); - } + } /* end effective waves */ + } /* end bool */ + } + for(i=iagemin; i <= iagemax+3; i++){ + for(jk=1,posprop=0; jk <=nlstate ; jk++) { + posprop += prop[jk][i]; + } + + for(jk=1; jk <=nlstate ; jk++){ + if( i <= iagemax){ + if(posprop>=1.e-5){ + probs[i][jk][j1]= prop[jk][i]/posprop; + } else{ + if(first==1){ + first=0; + printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]); } - } - }/* end jk */ - }/* end i */ + } + } + }/* end jk */ + }/* end i */ /*} *//* end i1 */ } /* end j1 */ @@ -3459,17 +3601,18 @@ void concatwav(int wav[], int **dh, int int i, mi, m; /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; double sum=0., jmean=0.;*/ - int first; + int first, firstwo; int j, k=0,jk, ju, jl; double sum=0.; first=0; + firstwo=0; jmin=100000; jmax=-1; jmean=0.; - for(i=1; i<=imx; i++){ + for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ mi=0; m=firstpass; - while(s[m][i] <= nlstate){ + while(s[m][i] <= nlstate){ /* a live state */ if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) mw[++mi][i]=m; if(m >=lastpass) @@ -3477,13 +3620,26 @@ void concatwav(int wav[], int **dh, int else m++; }/* end while */ - if (s[m][i] > nlstate){ + if (s[m][i] > nlstate){ /* In a death state */ mi++; /* Death is another wave */ /* if(mi==0) never been interviewed correctly before death */ /* Only death is a correct wave */ mw[mi][i]=m; + }else if (andc[i] != 9999) { /* A death occured after lastpass */ + m++; + mi++; + s[m][i]=nlstate+1; /* We are setting the status to the last of non live state */ + mw[mi][i]=m; + nbwarn++; + if(firstwo==0){ + printf("Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m); + fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m); + firstwo=1; + } + if(firstwo==1){ + fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m); + } } - wav[i]=mi; if(mi==0){ nbwarn++; @@ -3496,7 +3652,9 @@ void concatwav(int wav[], int **dh, int } } /* end mi==0 */ } /* End individuals */ + /* wav and mw are no more changed */ + for(i=1; i<=imx; i++){ for(mi=1; mi
  • Result files (first order: no variance)\n \
  • Result files (second order (variance)\n \ "); - fprintf(fichtm,"

    • Result files (first order: no variance)

      \n \ - - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s
      \n ", - jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); + fprintf(fichtm,"

      • Result files (first order: no variance)

        \n"); + fprintf(fichtm,"
      • - Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file)
        \n", + jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm")); + fprintf(fichtm,"
      • - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s (html file) ", + jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm")); + fprintf(fichtm,", %s (text file)
        \n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_")); fprintf(fichtm,"\ - Estimated transition probabilities over %d (stepm) months: %s
        \n ", stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_")); @@ -4886,8 +5047,8 @@ divided by h: hPij if(prevfcast==1){ /* Projection of prevalence up to period (stable) prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
        \n- Projection of prevalece up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
        \ -", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1); + fprintf(fichtm,"
        \n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
        \ +", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1); } } @@ -5006,15 +5167,15 @@ true period expectancies (those weighted /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */ /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */ fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); - fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); + fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); - fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); + fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); for (i=1; i<= nlstate ; i ++) { fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i); fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk)); - fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1); + fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1); for (j=2; j<= nlstate+ndeath ; j ++) { - fprintf(ficgp,",\\\n \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j); + fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j); } fprintf(ficgp,";\nset out; unset ylabel;\n"); } @@ -5536,6 +5697,8 @@ void prevforecast(char fileres[], double in each health status at the date of interview (if between dateprev1 and dateprev2). We still use firstpass and lastpass as another selection. */ + /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */ + /* firstpass, lastpass, stepm, weightopt, model); */ prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); strcpy(fileresf,"F_"); @@ -5544,8 +5707,8 @@ void prevforecast(char fileres[], double printf("Problem with forecast resultfile: %s\n", fileresf); fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf); } - printf("Computing forecasting: result on file '%s' \n", fileresf); - fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf); + printf("Computing forecasting: result on file '%s', please wait... \n", fileresf); + fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf); if (cptcoveff==0) ncodemax[cptcoveff]=1; @@ -5640,6 +5803,9 @@ void prevforecast(char fileres[], double if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); fclose(ficresf); + printf("End of Computing forecasting \n"); + fprintf(ficlog,"End of Computing forecasting\n"); + } /************** Forecasting *****not tested NB*************/ @@ -6479,12 +6645,12 @@ int calandcheckages(int imx, int maxwav, for (i=1; i<=imx; i++) { agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); for(m=firstpass; (m<= lastpass); m++){ - if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ + if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */ if (s[m][i] >= nlstate+1) { if(agedc[i]>0){ if((int)moisdc[i]!=99 && (int)andc[i]!=9999){ agev[m][i]=agedc[i]; - /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ }else { if ((int)andc[i]!=9999){ nbwarn++; @@ -6494,7 +6660,7 @@ int calandcheckages(int imx, int maxwav, } } } /* agedc > 0 */ - } + } /* end if */ else if(s[m][i] !=9){ /* Standard case, age in fractional years but with the precision of a month */ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); @@ -6510,17 +6676,23 @@ int calandcheckages(int imx, int maxwav, } /*agev[m][i]=anint[m][i]-annais[i];*/ /* agev[m][i] = age[i]+2*m;*/ - } + } /* en if 9*/ else { /* =9 */ + /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */ agev[m][i]=1; s[m][i]=-1; } } - else /*= 0 Unknown */ + else if(s[m][i]==0) /*= 0 Unknown */ agev[m][i]=1; - } - + else{ + printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); + fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]); + agev[m][i]=0; + } + } /* End for lastpass */ } + for (i=1; i<=imx; i++) { for(m=firstpass; (m<=lastpass); m++){ if (s[m][i] > (nlstate+ndeath)) { @@ -7519,19 +7691,32 @@ Please run with mle=-1 to get a correct free_vector(annais,1,n); /* free_matrix(mint,1,maxwav,1,n); free_matrix(anint,1,maxwav,1,n);*/ - free_vector(moisdc,1,n); - free_vector(andc,1,n); + /* free_vector(moisdc,1,n); */ + /* free_vector(andc,1,n); */ /* */ wav=ivector(1,imx); - dh=imatrix(1,lastpass-firstpass+1,1,imx); - bh=imatrix(1,lastpass-firstpass+1,1,imx); - mw=imatrix(1,lastpass-firstpass+1,1,imx); + /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */ + /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */ + /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */ + dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/ + bh=imatrix(1,lastpass-firstpass+2,1,imx); + mw=imatrix(1,lastpass-firstpass+2,1,imx); /* Concatenates waves */ + /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. + Death is a valid wave (if date is known). + mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i + dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] + and mw[mi+1][i]. dh depends on stepm. + */ + concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); /* */ + free_vector(moisdc,1,n); + free_vector(andc,1,n); + /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); @@ -7584,7 +7769,7 @@ Please run with mle=-1 to get a correct * 15 i=8 1 2 2 2 * 16 2 2 2 2 */ - /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? + /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */ /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4 * and the value of each covariate? * V1=1, V2=1, V3=2, V4=1 ? @@ -7705,7 +7890,7 @@ Title=%s
        Datafile=%s Firstpass=%d La optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(fichtm,"\n\n\nIMaCh %s\n IMaCh for Interpolated Markov Chain
        \nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015
        \ + fprintf(fichtm,"\n\n\nIMaCh %s\n IMaCh for Interpolated Markov Chain
        \nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
        \
        \n\ IMaCh-%s
        %s         \
        \n\ @@ -7735,7 +7920,8 @@ Title=%s
        Datafile=%s Firstpass=%d La /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ + firstpass, lastpass, stepm, weightopt, model); fprintf(fichtm,"\n"); fprintf(fichtm,"
        Total number of observations=%d
        \n\ @@ -8266,15 +8452,15 @@ Please run with mle=-1 to get a correct printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\ model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \ - jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); + jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); /*------------ free_vector -------------*/ /* chdir(path); */ - free_ivector(wav,1,imx); - free_imatrix(dh,1,lastpass-firstpass+1,1,imx); - free_imatrix(bh,1,lastpass-firstpass+1,1,imx); - free_imatrix(mw,1,lastpass-firstpass+1,1,imx); + /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */ + /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */ + /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */ + /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */ free_lvector(num,1,n); free_vector(agedc,1,n); /*free_matrix(covar,0,NCOVMAX,1,n);*/ @@ -8334,6 +8520,11 @@ Please run with mle=-1 to get a correct /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\ ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); */ + free_ivector(wav,1,imx); + free_imatrix(dh,1,lastpass-firstpass+2,1,imx); + free_imatrix(bh,1,lastpass-firstpass+2,1,imx); + free_imatrix(mw,1,lastpass-firstpass+2,1,imx); + if (mobilav!=0) { mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);