--- imach/src/imach.c 2021/02/12 11:34:20 1.304
+++ imach/src/imach.c 2022/04/13 17:43:09 1.314
@@ -1,6 +1,51 @@
-/* $Id: imach.c,v 1.304 2021/02/12 11:34:20 brouard Exp $
+/* $Id: imach.c,v 1.314 2022/04/13 17:43:09 brouard Exp $
$State: Exp $
$Log: imach.c,v $
+ Revision 1.314 2022/04/13 17:43:09 brouard
+ * imach.c (Module): Adding link to text data files
+
+ Revision 1.313 2022/04/11 15:57:42 brouard
+ * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
+
+ Revision 1.312 2022/04/05 21:24:39 brouard
+ *** empty log message ***
+
+ Revision 1.311 2022/04/05 21:03:51 brouard
+ Summary: Fixed quantitative covariates
+
+ Fixed covariates (dummy or quantitative)
+ with missing values have never been allowed but are ERRORS and
+ program quits. Standard deviations of fixed covariates were
+ wrongly computed. Mean and standard deviations of time varying
+ covariates are still not computed.
+
+ Revision 1.310 2022/03/17 08:45:53 brouard
+ Summary: 99r25
+
+ Improving detection of errors: result lines should be compatible with
+ the model.
+
+ Revision 1.309 2021/05/20 12:39:14 brouard
+ Summary: Version 0.99r24
+
+ Revision 1.308 2021/03/31 13:11:57 brouard
+ Summary: Version 0.99r23
+
+
+ * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
+
+ Revision 1.307 2021/03/08 18:11:32 brouard
+ Summary: 0.99r22 fixed bug on result:
+
+ Revision 1.306 2021/02/20 15:44:02 brouard
+ Summary: Version 0.99r21
+
+ * imach.c (Module): Fix bug on quitting after result lines!
+ (Module): Version 0.99r21
+
+ Revision 1.305 2021/02/20 15:28:30 brouard
+ * imach.c (Module): Fix bug on quitting after result lines!
+
Revision 1.304 2021/02/12 11:34:20 brouard
* imach.c (Module): The use of a Windows BOM (huge) file is now an error
@@ -1132,12 +1177,12 @@ typedef struct {
#define ODIRSEPARATOR '\\'
#endif
-/* $Id: imach.c,v 1.304 2021/02/12 11:34:20 brouard Exp $ */
+/* $Id: imach.c,v 1.314 2022/04/13 17:43:09 brouard Exp $ */
/* $State: Exp $ */
#include "version.h"
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 fullversion[]="$Revision: 1.304 $ $Date: 2021/02/12 11:34:20 $";
+char copyright[]="March 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021, INED 2000-2021";
+char fullversion[]="$Revision: 1.314 $ $Date: 2022/04/13 17:43:09 $";
char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
@@ -1553,7 +1598,7 @@ char *cutl(char *blocc, char *alocc, cha
{
/* 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')
- 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
*/
char *s, *t;
@@ -1835,7 +1880,9 @@ char *subdirf(char fileres[])
/*************** function subdirf2 ***********/
char *subdirf2(char fileres[], char *preop)
{
-
+ /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
+ Errors in subdirf, 2, 3 while printing tmpout is
+ rewritten within the same printf. Workaround: many printfs
/* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/");
@@ -3820,7 +3867,7 @@ double funcone( double *x)
/* Fixed */
/* 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<=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[1]]=covar[Tvar[TvarFind[1]]][i]; */
/* cov[2+6]=covar[Tvar[6]][i]; */
@@ -4675,10 +4722,13 @@ Title=%s
Datafile=%s Firstpass=%d La
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.));
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 */
- idq[z1]=idq[z1]+weight[iind];
- meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
- stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
+ for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
+ if(!isnan(covar[ncovcol+z1][iind])){
+ idq[z1]=idq[z1]+weight[iind];
+ meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
+ /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
+ stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
+ }
}
/* 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); */
@@ -4741,16 +4791,19 @@ Title=%s
Datafile=%s Firstpass=%d La
Printing means of quantitative variables if any
*/
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]);
if(weightopt==1){
printf(" Weighted mean and standard deviation of");
fprintf(ficlog," 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]));
- 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]));
- fprintf(ficresphtmfr," 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}
+ var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
+ */
+ 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]));
+ 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]));
+ fprintf(ficresphtmfr," 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]));
}
/* for (z1=1; z1<= nqtveff; z1++) { */
/* for(m=1;m<=lastpass;m++){ */
@@ -5253,33 +5306,33 @@ void concatwav(int wav[], int **dh, int
for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
mi=0; /* First valid wave */
mli=0; /* Last valid wave */
- m=firstpass;
- while(s[m][i] <= nlstate){ /* a live state */
+ m=firstpass; /* Loop on waves */
+ 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 */
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 */
- 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;
} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
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 */
}
- else{ /* m >= lastpass, eventual special issue with warning */
+ else{ /* m = lastpass, eventual special issue with warning */
#ifdef UNKNOWNSTATUSNOTCONTRIBUTING
break;
#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){
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;
}
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;
}
if(s[m][i]==-2){ /* Vital status is really unknown */
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);
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);
}
@@ -5304,34 +5357,35 @@ void concatwav(int wav[], int **dh, int
#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
else if ((int) andc[i] != 9999) { /* Date of death 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++;
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;
}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 */
+ }else{ /* Month of Death occured afer last wave month, potential bias */
nberr++;
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;
}
- 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 */
/* death is known but not confirmed by death status at any wave */
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;
}
- 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 */
#endif
- wav[i]=mi; /* mi should be the last effective wave (or mli) */
- /* wav[i]=mw[mi][i]; */
+ wav[i]=mi; /* mi should be the last effective wave (or mli), */
+ /* wav[i]=mw[mi][i]; */
if(mi==0){
nbwarn++;
if(first==0){
@@ -5466,6 +5520,8 @@ void concatwav(int wav[], int **dh, int
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
switch(Fixed[k]) {
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*/
ij=(int)(covar[Tvar[k]][i]);
/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
@@ -5479,8 +5535,10 @@ void concatwav(int wav[], int **dh, int
else if (ij < modmincovj)
modmincovj=ij;
if (ij <0 || ij >1 ){
- printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
- fprintf(ficlog,"Information, currently 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,"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)){
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
@@ -5555,6 +5613,16 @@ void concatwav(int wav[], int **dh, int
break;
} /* end switch */
} /* 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*/
for (k=-1; k< maxncov; k++) Ndum[k]=0;
@@ -7026,8 +7094,10 @@ divided by h: hPij
if(prevfcast==1){
/* Projection of prevalence up to period (forward stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){
- fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg
\
-![](\"%s_%d-%d-%d.svg\")
", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
+ fprintf(fichtm,"",
+ subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
}
}
if(prevbcast==1){
@@ -7036,14 +7106,16 @@ divided by h: hPij
fprintf(fichtm,"
\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
-with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg
\
- ", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
+ fprintf(fichtm," ", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
}
}
for(cpt=1; cpt<=nlstate;cpt++) {
- fprintf(fichtm,"\n
- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d-%d-%d.svg
\
-",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+ fprintf(fichtm,"\n
- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d-%d-%d.svg",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
+ fprintf(fichtm,"", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
}
/* } /\* end i1 *\/ */
}/* End k1 */
@@ -7126,15 +7198,17 @@ See page 'Matrix of variance-covariance
}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n
- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
-prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d-%d.svg\n
\
-",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
+prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d-%d.svg",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
+ fprintf(fichtm," (data from text file %s)\n
",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
+ fprintf(fichtm,"",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
}
fprintf(fichtm,"\n
- Total life expectancy by age and \
-health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\
- observed and cahotic prevalences: %s_%d-%d.svg\n
\
-![](\"%s_%d-%d.svg\")
",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
+ observed and cahotic prevalences: %s_%d-%d.svg",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
+ fprintf(fichtm," (data from text file %s.txt) \n
",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
+ fprintf(fichtm,"",subdirf2(optionfilefiname,"E_"),k1,nres);
/* } /\* end i1 *\/ */
}/* End k1 */
}/* End nres */
@@ -9479,6 +9553,8 @@ int readdata(char datafile[], int firsto
cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing value */
lval=-1;
+ coqvar[iv][i]=NAN;
+ covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
}else{
errno=0;
/* what_kind_of_number(strb); */
@@ -9582,7 +9658,6 @@ int decoderesult ( char resultline[], in
char stra[80], strb[80], strc[80], strd[80],stre[80];
removefirstspace(&resultline);
- printf("decoderesult:%s\n",resultline);
if (strstr(resultline,"v") !=0){
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
@@ -9597,15 +9672,14 @@ int decoderesult ( char resultline[], in
TKresult[nres]=0; /* Combination for the nresult and the model */
return (0);
}
-
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);
- 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);
+ 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 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 */
if(nbocc(resultsav,'=') >1){
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 */
}else
cutl(strc,strd,resultsav,'=');
@@ -9630,7 +9704,9 @@ int decoderesult ( char resultline[], in
}
}
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;
}
}
}
@@ -9647,8 +9723,12 @@ int decoderesult ( char resultline[], in
}
if(match == 0){
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){
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;
}
}
@@ -12408,11 +12488,13 @@ Please run with mle=-1 to get a correct
}
/* Results */
+ endishere=0;
nresult=0;
+ parameterline=0;
do{
if(!fgets(line, MAXLINE, ficpar)){
endishere=1;
- parameterline=14;
+ parameterline=15;
}else if (line[0] == '#') {
/* If line starts with a # it is a comment */
numlinepar++;
@@ -12425,12 +12507,13 @@ Please run with mle=-1 to get a correct
parameterline=11;
else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
parameterline=12;
- else if(sscanf(line,"result:%[^\n]\n",modeltemp))
+ else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
parameterline=13;
+ }
else{
parameterline=14;
}
- switch (parameterline){
+ switch (parameterline){ /* =0 only if only comments */
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)){
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);
@@ -12443,9 +12526,9 @@ Please run with mle=-1 to get a correct
prvforecast = 1;
}
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);
- fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
- fprintf(ficres,"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=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
+ fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
prvforecast = 2;
}
else {
@@ -12466,9 +12549,9 @@ Please run with mle=-1 to get a correct
prvbackcast = 1;
}
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);
- fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
- fprintf(ficres,"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=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
+ fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
prvbackcast = 2;
}
else {
@@ -12478,41 +12561,41 @@ Please run with mle=-1 to get a correct
}
break;
case 13:
- if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
- if (num_filled == 0){
- resultline[0]='\0';
- printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
- 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);
- break;
- } 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 */
+ num_filled=sscanf(line,"result:%[^\n]\n",resultline);
+ 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\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
+ 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);
+ goto end;
+ }
+ 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);
- 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);
- }
+ } else
goto end;
- break;
- default:
- nresult=1;
- decoderesult(".",nresult ); /* No covariate */
+ break;
+ case 14:
+ printf("Error: Unknown command '%s'\n",line);
+ fprintf(ficlog,"Error: Unknown command '%s'\n",line);
+ if(line[0] == ' ' || line[0] == '\n'){
+ printf("It should not be an empty line '%s'\n",line);
+ fprintf(ficlog,"It should not be an empty line '%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 */
}while(endishere==0); /* End do */