version 1.282, 2018/02/27 22:50:02
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version 1.283, 2018/04/19 14:49:16
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.283 2018/04/19 14:49:16 brouard |
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Summary: Some minor bugs fixed |
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Revision 1.282 2018/02/27 22:50:02 brouard |
Revision 1.282 2018/02/27 22:50:02 brouard |
*** empty log message *** |
*** empty log message *** |
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Line 1055 typedef struct {
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Line 1058 typedef struct {
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/* $State$ */ |
/* $State$ */ |
#include "version.h" |
#include "version.h" |
char version[]=__IMACH_VERSION__; |
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 fullversion[]="$Revision$ $Date$"; |
char strstart[80]; |
char strstart[80]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
Line 4368 void freqsummary(char fileres[], double
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Line 4371 void freqsummary(char fileres[], double
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double ***freq; /* Frequencies */ |
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 */ |
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); |
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 **meanqt; |
double *pp, **prop, *posprop, *pospropt; |
double *pp, **prop, *posprop, *pospropt; |
double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0; |
double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0; |
Line 4381 void freqsummary(char fileres[], double
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Line 4384 void freqsummary(char fileres[], double
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pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ |
pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ |
/* prop=matrix(1,nlstate,iagemin,iagemax+3); */ |
/* prop=matrix(1,nlstate,iagemin,iagemax+3); */ |
meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ |
meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ |
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idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ |
meanqt=matrix(1,lastpass,1,nqtveff); |
meanqt=matrix(1,lastpass,1,nqtveff); |
strcpy(fileresp,"P_"); |
strcpy(fileresp,"P_"); |
strcat(fileresp,fileresu); |
strcat(fileresp,fileresu); |
Line 4489 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4493 Title=%s <br>Datafile=%s Firstpass=%d La
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posprop[i]=0; |
posprop[i]=0; |
pospropt[i]=0; |
pospropt[i]=0; |
} |
} |
/* for (z1=1; z1<= nqfveff; z1++) { */ |
for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */ |
/* meanq[z1]+=0.; */ |
idq[z1]+=0.; |
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meanq[z1]+=0.; |
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} |
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/* for (z1=1; z1<= nqtveff; z1++) { */ |
/* for(m=1;m<=lastpass;m++){ */ |
/* for(m=1;m<=lastpass;m++){ */ |
/* meanqt[m][z1]=0.; */ |
/* meanqt[m][z1]=0.; */ |
/* } */ |
/* } */ |
/* } */ |
/* } */ |
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/* dateintsum=0; */ |
/* dateintsum=0; */ |
/* k2cpt=0; */ |
/* k2cpt=0; */ |
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Line 4505 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4511 Title=%s <br>Datafile=%s Firstpass=%d La
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if(j !=0){ |
if(j !=0){ |
if(anyvaryingduminmodel==0){ /* If All fixed covariates */ |
if(anyvaryingduminmodel==0){ /* If All fixed covariates */ |
if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ |
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 *\/ */ |
/* 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 */ |
for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */ |
Line 4571 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4577 Title=%s <br>Datafile=%s Firstpass=%d La
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/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */ |
/* 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 */ |
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 */ |
} |
} |
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for (z1=1; z1<= nqfveff; z1++) { |
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idq[z1]++; |
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meanq[z1]+=covar[ncovcol+z1][iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */ |
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/* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */ |
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} |
} /* end if between passes */ |
} /* end if between passes */ |
if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) { |
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 ?*/ |
dateintsum=dateintsum+k2; /* on all covariates ?*/ |
Line 4618 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4629 Title=%s <br>Datafile=%s Firstpass=%d La
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fprintf(ficresphtmfr, "**********</h3>\n"); |
fprintf(ficresphtmfr, "**********</h3>\n"); |
fprintf(ficlog, "**********\n"); |
fprintf(ficlog, "**********\n"); |
} |
} |
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/* |
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Printing means of quantitative variables if any |
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*/ |
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for (z1=1; z1<= nqfveff; z1++) { |
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fprintf(ficresphtmfr,"V quantitative id %d, number of idividuals= %f, sum=%f", z1, idq[z1], meanq[z1]); |
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fprintf(ficresphtmfr,", mean=%f<p>\n",meanq[z1]/idq[z1]); |
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} |
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/* for (z1=1; z1<= nqtveff; z1++) { */ |
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/* for(m=1;m<=lastpass;m++){ */ |
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/* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */ |
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/* } */ |
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/* } */ |
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fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">"); |
fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">"); |
if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */ |
if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */ |
fprintf(ficresp, " Age"); |
fprintf(ficresp, " Age"); |
Line 4898 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4922 Title=%s <br>Datafile=%s Firstpass=%d La
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fclose(ficresp); |
fclose(ficresp); |
fclose(ficresphtm); |
fclose(ficresphtm); |
fclose(ficresphtmfr); |
fclose(ficresphtmfr); |
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free_vector(idq,1,nqfveff); |
free_vector(meanq,1,nqfveff); |
free_vector(meanq,1,nqfveff); |
free_matrix(meanqt,1,lastpass,1,nqtveff); |
free_matrix(meanqt,1,lastpass,1,nqtveff); |
free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE); |
free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE); |
Line 6865 divided by h: <sub>h</sub>P<sub>ij</sub>
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Line 6890 divided by h: <sub>h</sub>P<sub>ij</sub>
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for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\ |
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. \ |
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 */ |
/* Period (stable) prevalence in each health state */ |
for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
Line 10948 int main(int argc, char *argv[])
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Line 10973 int main(int argc, char *argv[])
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title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ |
title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ |
if (num_filled != 5) { |
if (num_filled != 5) { |
printf("Should be 5 parameters\n"); |
printf("Should be 5 parameters\n"); |
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fprintf(ficlog,"Should be 5 parameters\n"); |
} |
} |
numlinepar++; |
numlinepar++; |
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
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fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
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fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
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fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
} |
} |
/* Second parameter line */ |
/* Second parameter line */ |
while(fgets(line, MAXLINE, ficpar)) { |
while(fgets(line, MAXLINE, ficpar)) { |
/* If line starts with a # it is a comment */ |
/* while(fscanf(ficpar,"%[^\n]", line)) { */ |
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/* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */ |
if (line[0] == '#') { |
if (line[0] == '#') { |
numlinepar++; |
numlinepar++; |
fputs(line,stdout); |
printf("%s",line); |
fputs(line,ficparo); |
fprintf(ficres,"%s",line); |
fputs(line,ficres); |
fprintf(ficparo,"%s",line); |
fputs(line,ficlog); |
fprintf(ficlog,"%s",line); |
continue; |
continue; |
}else |
}else |
break; |
break; |
Line 10970 int main(int argc, char *argv[])
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Line 11000 int main(int argc, char *argv[])
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if (num_filled != 11) { |
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("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); |
printf("but line=%s\n",line); |
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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"); |
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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); |
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); |
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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); |
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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); |
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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*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 */ |
/*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ |
Line 10980 int main(int argc, char *argv[])
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Line 11015 int main(int argc, char *argv[])
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/* If line starts with a # it is a comment */ |
/* If line starts with a # it is a comment */ |
if (line[0] == '#') { |
if (line[0] == '#') { |
numlinepar++; |
numlinepar++; |
fputs(line,stdout); |
printf("%s",line); |
fputs(line,ficparo); |
fprintf(ficres,"%s",line); |
fputs(line,ficres); |
fprintf(ficparo,"%s",line); |
fputs(line,ficlog); |
fprintf(ficlog,"%s",line); |
continue; |
continue; |
}else |
}else |
break; |
break; |
Line 11004 int main(int argc, char *argv[])
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Line 11039 int main(int argc, char *argv[])
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} |
} |
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
printf("model=1+age+%s\n",model);fflush(stdout); |
printf("model=1+age+%s\n",model);fflush(stdout); |
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fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout); |
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fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout); |
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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); */ |
/* 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 *\/ */ |
/* 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); */ |
/* 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(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(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); |
fflush(ficlog); |
/* if(model[0]=='#'|| model[0]== '\0'){ */ |
/* if(model[0]=='#'|| model[0]== '\0'){ */ |
if(model[0]=='#'){ |
if(model[0]=='#'){ |
Line 11872 Please run with mle=-1 to get a correct
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Line 11910 Please run with mle=-1 to get a correct
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printf("\n"); |
printf("\n"); |
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/*--------- results files --------------*/ |
/*--------- 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); */ |
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fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
Line 12740 end:
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Line 12778 end:
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printf("\nType q for exiting: "); fflush(stdout); |
printf("\nType q for exiting: "); fflush(stdout); |
scanf("%s",z); |
scanf("%s",z); |
} |
} |
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printf("End\n"); |
exit(0); |
exit(0); |
} |
} |