version 1.303, 2021/02/11 19:50:15
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version 1.313, 2022/04/11 15:57:42
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.313 2022/04/11 15:57:42 brouard |
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* imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed |
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Revision 1.312 2022/04/05 21:24:39 brouard |
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*** empty log message *** |
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Revision 1.311 2022/04/05 21:03:51 brouard |
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Summary: Fixed quantitative covariates |
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Fixed covariates (dummy or quantitative) |
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with missing values have never been allowed but are ERRORS and |
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program quits. Standard deviations of fixed covariates were |
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wrongly computed. Mean and standard deviations of time varying |
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covariates are still not computed. |
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Revision 1.310 2022/03/17 08:45:53 brouard |
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Summary: 99r25 |
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Improving detection of errors: result lines should be compatible with |
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the model. |
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Revision 1.309 2021/05/20 12:39:14 brouard |
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Summary: Version 0.99r24 |
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Revision 1.308 2021/03/31 13:11:57 brouard |
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Summary: Version 0.99r23 |
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* imach.c (Module): Still bugs in the result loop. Thank to Holly Benett |
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Revision 1.307 2021/03/08 18:11:32 brouard |
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Summary: 0.99r22 fixed bug on result: |
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Revision 1.306 2021/02/20 15:44:02 brouard |
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Summary: Version 0.99r21 |
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* imach.c (Module): Fix bug on quitting after result lines! |
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(Module): Version 0.99r21 |
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Revision 1.305 2021/02/20 15:28:30 brouard |
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* imach.c (Module): Fix bug on quitting after result lines! |
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Revision 1.304 2021/02/12 11:34:20 brouard |
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* imach.c (Module): The use of a Windows BOM (huge) file is now an error |
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Revision 1.303 2021/02/11 19:50:15 brouard |
Revision 1.303 2021/02/11 19:50:15 brouard |
* (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed. |
* (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed. |
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Line 1133 typedef struct {
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Line 1178 typedef struct {
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/* $State$ */ |
/* $State$ */ |
#include "version.h" |
#include "version.h" |
char version[]=__IMACH_VERSION__; |
char version[]=__IMACH_VERSION__; |
char copyright[]="May 2019,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020"; |
char copyright[]="March 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021, INED 2000-2021"; |
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 1550 char *cutl(char *blocc, char *alocc, cha
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Line 1595 char *cutl(char *blocc, char *alocc, cha
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{ |
{ |
/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' |
/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' |
and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') |
and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') |
gives blocc="abcdef" and alocc="ghi2j". |
gives alocc="abcdef" and blocc="ghi2j". |
If occ is not found blocc is null and alocc is equal to in. Returns blocc |
If occ is not found blocc is null and alocc is equal to in. Returns blocc |
*/ |
*/ |
char *s, *t; |
char *s, *t; |
Line 3817 double funcone( double *x)
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Line 3862 double funcone( double *x)
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/* Fixed */ |
/* Fixed */ |
/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */ |
/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */ |
/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */ |
/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */ |
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */ |
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */ |
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/ |
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/ |
/* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */ |
/* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */ |
/* cov[2+6]=covar[Tvar[6]][i]; */ |
/* cov[2+6]=covar[Tvar[6]][i]; */ |
Line 4672 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4717 Title=%s <br>Datafile=%s Firstpass=%d La
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if(s[m][iind]==-1) |
if(s[m][iind]==-1) |
printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.)); |
printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.)); |
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */ |
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */ |
for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */ |
for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */ |
idq[z1]=idq[z1]+weight[iind]; |
if(!isnan(covar[ncovcol+z1][iind])){ |
meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */ |
idq[z1]=idq[z1]+weight[iind]; |
stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */ |
meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */ |
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/* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/ |
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stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */ |
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} |
} |
} |
/* if((int)agev[m][iind] == 55) */ |
/* if((int)agev[m][iind] == 55) */ |
/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */ |
/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */ |
Line 4738 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4786 Title=%s <br>Datafile=%s Firstpass=%d La
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Printing means of quantitative variables if any |
Printing means of quantitative variables if any |
*/ |
*/ |
for (z1=1; z1<= nqfveff; z1++) { |
for (z1=1; z1<= nqfveff; z1++) { |
fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]); |
fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]); |
fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]); |
fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]); |
if(weightopt==1){ |
if(weightopt==1){ |
printf(" Weighted mean and standard deviation of"); |
printf(" Weighted mean and standard deviation of"); |
fprintf(ficlog," Weighted mean and standard deviation of"); |
fprintf(ficlog," Weighted mean and standard deviation of"); |
fprintf(ficresphtmfr," Weighted mean and standard deviation of"); |
fprintf(ficresphtmfr," Weighted mean and standard deviation of"); |
} |
} |
printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1])); |
/* mu = \frac{w x}{\sum w} |
fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1])); |
var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2 |
fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1])); |
*/ |
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printf(" fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); |
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fprintf(ficlog," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); |
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fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1])); |
} |
} |
/* for (z1=1; z1<= nqtveff; z1++) { */ |
/* for (z1=1; z1<= nqtveff; z1++) { */ |
/* for(m=1;m<=lastpass;m++){ */ |
/* for(m=1;m<=lastpass;m++){ */ |
Line 5250 void concatwav(int wav[], int **dh, int
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Line 5301 void concatwav(int wav[], int **dh, int
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for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ |
for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ |
mi=0; /* First valid wave */ |
mi=0; /* First valid wave */ |
mli=0; /* Last valid wave */ |
mli=0; /* Last valid wave */ |
m=firstpass; |
m=firstpass; /* Loop on waves */ |
while(s[m][i] <= nlstate){ /* a live state */ |
while(s[m][i] <= nlstate){ /* a live state or unknown state */ |
if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */ |
if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */ |
mli=m-1;/* mw[++mi][i]=m-1; */ |
mli=m-1;/* mw[++mi][i]=m-1; */ |
}else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */ |
}else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */ |
mw[++mi][i]=m; |
mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition */ |
mli=m; |
mli=m; |
} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */ |
} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */ |
if(m < lastpass){ /* m < lastpass, standard case */ |
if(m < lastpass){ /* m < lastpass, standard case */ |
m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */ |
m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */ |
} |
} |
else{ /* m >= lastpass, eventual special issue with warning */ |
else{ /* m = lastpass, eventual special issue with warning */ |
#ifdef UNKNOWNSTATUSNOTCONTRIBUTING |
#ifdef UNKNOWNSTATUSNOTCONTRIBUTING |
break; |
break; |
#else |
#else |
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ |
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* case -2 (vital status unknown is warned later */ |
if(firsthree == 0){ |
if(firsthree == 0){ |
printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); |
printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); |
firsthree=1; |
firsthree=1; |
} |
} |
fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); |
fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); |
mw[++mi][i]=m; |
mw[++mi][i]=m; /* Valid transition with unknown status */ |
mli=m; |
mli=m; |
} |
} |
if(s[m][i]==-2){ /* Vital status is really unknown */ |
if(s[m][i]==-2){ /* Vital status is really unknown */ |
nbwarn++; |
nbwarn++; |
if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */ |
if((int)anint[m][i] == 9999){ /* Has the vital status really been verified?not a transition */ |
printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); |
printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); |
fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); |
fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); |
} |
} |
Line 5301 void concatwav(int wav[], int **dh, int
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Line 5352 void concatwav(int wav[], int **dh, int
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#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE |
#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE |
else if ((int) andc[i] != 9999) { /* Date of death is known */ |
else if ((int) andc[i] != 9999) { /* Date of death is known */ |
if ((int)anint[m][i]!= 9999) { /* date of last interview is known */ |
if ((int)anint[m][i]!= 9999) { /* date of last interview is known */ |
if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */ |
if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */ |
nbwarn++; |
nbwarn++; |
if(firstfiv==0){ |
if(firstfiv==0){ |
printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
firstfiv=1; |
firstfiv=1; |
}else{ |
}else{ |
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
} |
} |
}else{ /* Death occured afer last wave potential bias */ |
s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */ |
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}else{ /* Month of Death occured afer last wave month, potential bias */ |
nberr++; |
nberr++; |
if(firstwo==0){ |
if(firstwo==0){ |
printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); |
printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
firstwo=1; |
firstwo=1; |
} |
} |
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); |
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
} |
} |
}else{ /* if date of interview is unknown */ |
}else{ /* if date of interview is unknown */ |
/* death is known but not confirmed by death status at any wave */ |
/* death is known but not confirmed by death status at any wave */ |
if(firstfour==0){ |
if(firstfour==0){ |
printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); |
printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
firstfour=1; |
firstfour=1; |
} |
} |
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); |
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); |
} |
} |
} /* end if date of death is known */ |
} /* end if date of death is known */ |
#endif |
#endif |
wav[i]=mi; /* mi should be the last effective wave (or mli) */ |
wav[i]=mi; /* mi should be the last effective wave (or mli), */ |
/* wav[i]=mw[mi][i]; */ |
/* wav[i]=mw[mi][i]; */ |
if(mi==0){ |
if(mi==0){ |
nbwarn++; |
nbwarn++; |
if(first==0){ |
if(first==0){ |
Line 5463 void concatwav(int wav[], int **dh, int
|
Line 5515 void concatwav(int wav[], int **dh, int
|
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ |
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ |
switch(Fixed[k]) { |
switch(Fixed[k]) { |
case 0: /* Testing on fixed dummy covariate, simple or product of fixed */ |
case 0: /* Testing on fixed dummy covariate, simple or product of fixed */ |
|
modmaxcovj=0; |
|
modmincovj=0; |
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/ |
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/ |
ij=(int)(covar[Tvar[k]][i]); |
ij=(int)(covar[Tvar[k]][i]); |
/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i |
/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i |
Line 5476 void concatwav(int wav[], int **dh, int
|
Line 5530 void concatwav(int wav[], int **dh, int
|
else if (ij < modmincovj) |
else if (ij < modmincovj) |
modmincovj=ij; |
modmincovj=ij; |
if (ij <0 || ij >1 ){ |
if (ij <0 || ij >1 ){ |
printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i); |
printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i); |
fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i); |
fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i); |
|
fflush(ficlog); |
|
exit(1); |
} |
} |
if ((ij < -1) || (ij > NCOVMAX)){ |
if ((ij < -1) || (ij > NCOVMAX)){ |
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); |
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); |
Line 5552 void concatwav(int wav[], int **dh, int
|
Line 5608 void concatwav(int wav[], int **dh, int
|
break; |
break; |
} /* end switch */ |
} /* end switch */ |
} /* end dummy test */ |
} /* end dummy test */ |
|
if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */ |
|
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/ |
|
if(isnan(covar[Tvar[k]][i])){ |
|
printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i); |
|
fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i); |
|
fflush(ficlog); |
|
exit(1); |
|
} |
|
} |
|
} |
} /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/ |
} /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/ |
|
|
for (k=-1; k< maxncov; k++) Ndum[k]=0; |
for (k=-1; k< maxncov; k++) Ndum[k]=0; |
Line 9255 int readdata(char datafile[], int firsto
|
Line 9321 int readdata(char datafile[], int firsto
|
else if( line[0] == (char)0xFF && line[1] == (char)0xFE) |
else if( line[0] == (char)0xFF && line[1] == (char)0xFE) |
{ |
{ |
noffset=noffset+2; |
noffset=noffset+2; |
printf("# Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout); |
printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout); |
fprintf(ficlog,"# Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile); |
fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile); |
fflush(ficlog); return 1; |
fflush(ficlog); return 1; |
} |
} |
else if( line[0] == 0 && line[1] == 0) |
else if( line[0] == 0 && line[1] == 0) |
{ |
{ |
if( line[2] == (char)0xFE && line[3] == (char)0xFF){ |
if( line[2] == (char)0xFE && line[3] == (char)0xFF){ |
noffset=noffset+4; |
noffset=noffset+4; |
printf("# Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout); |
printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout); |
fprintf(ficlog,"# Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile); |
fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile); |
fflush(ficlog); return 1; |
fflush(ficlog); return 1; |
} |
} |
} else{ |
} else{ |
Line 9476 int readdata(char datafile[], int firsto
|
Line 9542 int readdata(char datafile[], int firsto
|
cutv(stra, strb, line, ' '); |
cutv(stra, strb, line, ' '); |
if(strb[0]=='.') { /* Missing value */ |
if(strb[0]=='.') { /* Missing value */ |
lval=-1; |
lval=-1; |
|
coqvar[iv][i]=NAN; |
|
covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */ |
}else{ |
}else{ |
errno=0; |
errno=0; |
/* what_kind_of_number(strb); */ |
/* what_kind_of_number(strb); */ |
Line 9579 int decoderesult ( char resultline[], in
|
Line 9647 int decoderesult ( char resultline[], in
|
char stra[80], strb[80], strc[80], strd[80],stre[80]; |
char stra[80], strb[80], strc[80], strd[80],stre[80]; |
|
|
removefirstspace(&resultline); |
removefirstspace(&resultline); |
printf("decoderesult:%s\n",resultline); |
|
|
|
if (strstr(resultline,"v") !=0){ |
if (strstr(resultline,"v") !=0){ |
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline); |
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline); |
Line 9594 int decoderesult ( char resultline[], in
|
Line 9661 int decoderesult ( char resultline[], in
|
TKresult[nres]=0; /* Combination for the nresult and the model */ |
TKresult[nres]=0; /* Combination for the nresult and the model */ |
return (0); |
return (0); |
} |
} |
|
|
if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */ |
if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */ |
printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); |
printf("ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs); |
fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); |
fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs); |
} |
} |
for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */ |
for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */ |
if(nbocc(resultsav,'=') >1){ |
if(nbocc(resultsav,'=') >1){ |
cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' |
cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' |
resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */ |
resultsav= V4=1 V5=25.1 V3=0 stra= V5=25.1 V3=0 strb= V4=1 */ |
cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */ |
cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */ |
}else |
}else |
cutl(strc,strd,resultsav,'='); |
cutl(strc,strd,resultsav,'='); |
Line 9627 int decoderesult ( char resultline[], in
|
Line 9693 int decoderesult ( char resultline[], in
|
} |
} |
} |
} |
if(match == 0){ |
if(match == 0){ |
printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); |
printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model); |
|
fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model); |
|
return 1; |
} |
} |
} |
} |
} |
} |
Line 9644 int decoderesult ( char resultline[], in
|
Line 9712 int decoderesult ( char resultline[], in
|
} |
} |
if(match == 0){ |
if(match == 0){ |
printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); |
printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); |
|
fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model); |
|
return 1; |
}else if(match > 1){ |
}else if(match > 1){ |
printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); |
printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); |
|
fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model); |
|
return 1; |
} |
} |
} |
} |
|
|
Line 12405 Please run with mle=-1 to get a correct
|
Line 12477 Please run with mle=-1 to get a correct
|
} |
} |
|
|
/* Results */ |
/* Results */ |
|
endishere=0; |
nresult=0; |
nresult=0; |
|
parameterline=0; |
do{ |
do{ |
if(!fgets(line, MAXLINE, ficpar)){ |
if(!fgets(line, MAXLINE, ficpar)){ |
endishere=1; |
endishere=1; |
parameterline=14; |
parameterline=15; |
}else if (line[0] == '#') { |
}else if (line[0] == '#') { |
/* If line starts with a # it is a comment */ |
/* If line starts with a # it is a comment */ |
numlinepar++; |
numlinepar++; |
Line 12422 Please run with mle=-1 to get a correct
|
Line 12496 Please run with mle=-1 to get a correct
|
parameterline=11; |
parameterline=11; |
else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp)) |
else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp)) |
parameterline=12; |
parameterline=12; |
else if(sscanf(line,"result:%[^\n]\n",modeltemp)) |
else if(sscanf(line,"result:%[^\n]\n",modeltemp)){ |
parameterline=13; |
parameterline=13; |
|
} |
else{ |
else{ |
parameterline=14; |
parameterline=14; |
} |
} |
switch (parameterline){ |
switch (parameterline){ /* =0 only if only comments */ |
case 11: |
case 11: |
if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){ |
if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){ |
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
Line 12440 Please run with mle=-1 to get a correct
|
Line 12515 Please run with mle=-1 to get a correct
|
prvforecast = 1; |
prvforecast = 1; |
} |
} |
else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/ |
else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/ |
printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); |
printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); |
fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); |
fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); |
fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); |
fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj); |
prvforecast = 2; |
prvforecast = 2; |
} |
} |
else { |
else { |
Line 12463 Please run with mle=-1 to get a correct
|
Line 12538 Please run with mle=-1 to get a correct
|
prvbackcast = 1; |
prvbackcast = 1; |
} |
} |
else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/ |
else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/ |
printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); |
printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); |
fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); |
fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); |
fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); |
fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj); |
prvbackcast = 2; |
prvbackcast = 2; |
} |
} |
else { |
else { |
Line 12475 Please run with mle=-1 to get a correct
|
Line 12550 Please run with mle=-1 to get a correct
|
} |
} |
break; |
break; |
case 13: |
case 13: |
if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){ |
num_filled=sscanf(line,"result:%[^\n]\n",resultline); |
if (num_filled == 0){ |
nresult++; /* Sum of resultlines */ |
resultline[0]='\0'; |
printf("Result %d: result:%s\n",nresult, resultline); |
printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line); |
if(nresult > MAXRESULTLINES){ |
fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line); |
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres); |
break; |
fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres); |
} else if (num_filled != 1){ |
|
printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line); |
|
fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line); |
|
} |
|
nresult++; /* Sum of resultlines */ |
|
printf("Result %d: result=%s\n",nresult, resultline); |
|
if(nresult > MAXRESULTLINES){ |
|
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); |
|
fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); |
|
goto end; |
|
} |
|
decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ |
|
fprintf(ficparo,"result: %s\n",resultline); |
|
fprintf(ficres,"result: %s\n",resultline); |
|
fprintf(ficlog,"result: %s\n",resultline); |
|
break; |
|
case 14: |
|
printf("Error: Unknown command '%s'\n",line); |
|
fprintf(ficlog,"Error: Unknown command '%s'\n",line); |
|
if(ncovmodel >=2 && nresult==0 ){ |
|
printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); |
|
fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); |
|
} |
|
goto end; |
goto end; |
break; |
|
default: |
|
nresult=1; |
|
decoderesult(".",nresult ); /* No covariate */ |
|
} |
} |
|
if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ |
|
fprintf(ficparo,"result: %s\n",resultline); |
|
fprintf(ficres,"result: %s\n",resultline); |
|
fprintf(ficlog,"result: %s\n",resultline); |
|
} else |
|
goto end; |
|
break; |
|
case 14: |
|
printf("Error: Unknown command '%s'\n",line); |
|
fprintf(ficlog,"Error: Unknown command '%s'\n",line); |
|
if(ncovmodel >=2 && nresult==0 ){ |
|
printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); |
|
fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); |
|
} |
|
/* goto end; */ |
|
break; |
|
case 15: |
|
printf("End of resultlines.\n"); |
|
fprintf(ficlog,"End of resultlines.\n"); |
|
break; |
|
default: /* parameterline =0 */ |
|
nresult=1; |
|
decoderesult(".",nresult ); /* No covariate */ |
} /* End switch parameterline */ |
} /* End switch parameterline */ |
}while(endishere==0); /* End do */ |
}while(endishere==0); /* End do */ |
|
|