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version 1.281, 2018/02/27 19:25:23
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version 1.290, 2019/05/09 13:39:37
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| /* $Id$ |
/* $Id$ |
| $State$ |
$State$ |
| $Log$ |
$Log$ |
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Revision 1.290 2019/05/09 13:39:37 brouard |
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Summary: 0.99r18 unlimited number of individuals |
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The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur. |
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Revision 1.289 2018/12/13 09:16:26 brouard |
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Summary: Bug for young ages (<-30) will be in r17 |
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Revision 1.288 2018/05/02 20:58:27 brouard |
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Summary: Some bugs fixed |
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Revision 1.287 2018/05/01 17:57:25 brouard |
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Summary: Bug fixed by providing frequencies only for non missing covariates |
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Revision 1.286 2018/04/27 14:27:04 brouard |
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Summary: some minor bugs |
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Revision 1.285 2018/04/21 21:02:16 brouard |
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Summary: Some bugs fixed, valgrind tested |
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Revision 1.284 2018/04/20 05:22:13 brouard |
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Summary: Computing mean and stdeviation of fixed quantitative variables |
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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 |
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*** empty log message *** |
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| Revision 1.281 2018/02/27 19:25:23 brouard |
Revision 1.281 2018/02/27 19:25:23 brouard |
| Summary: Adding second argument for quitting |
Summary: Adding second argument for quitting |
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Line 1025 typedef struct {
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Line 1054 typedef struct {
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| #define NINTERVMAX 8 |
#define NINTERVMAX 8 |
| #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ |
#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ |
| #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ |
#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ |
| #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ |
/* #define NCOVMAX 20 */ /**< Maximum number of covariates, including generated covariates V1*V2 */ |
| #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 |
#define codtabm(h,k) (1 & (h-1) >> (k-1))+1 |
| /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/ |
/*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/ |
| #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 |
#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 |
| #define MAXN 20000 |
/*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */ |
| #define YEARM 12. /**< Number of months per year */ |
#define YEARM 12. /**< Number of months per year */ |
| /* #define AGESUP 130 */ |
/* #define AGESUP 130 */ |
| #define AGESUP 150 |
/* #define AGESUP 150 */ |
| |
#define AGESUP 200 |
| #define AGEINF 0 |
#define AGEINF 0 |
| #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */ |
#define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */ |
| #define AGEBASE 40 |
#define AGEBASE 40 |
|
Line 1052 typedef struct {
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Line 1082 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 1076 int nqfveff=0; /**< nqfveff Number of Qu
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Line 1106 int nqfveff=0; /**< nqfveff Number of Qu
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| int ntveff=0; /**< ntveff number of effective time varying variables */ |
int ntveff=0; /**< ntveff number of effective time varying variables */ |
| int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */ |
int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */ |
| int cptcov=0; /* Working variable */ |
int cptcov=0; /* Working variable */ |
| |
int nobs=10; /* Number of observations in the data lastobs-firstobs */ |
| int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */ |
int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */ |
| int npar=NPARMAX; |
int npar=NPARMAX; |
| int nlstate=2; /* Number of live states */ |
int nlstate=2; /* Number of live states */ |
|
Line 2559 void powell(double p[], double **xi, int
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Line 2590 void powell(double p[], double **xi, int
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| double **newm; |
double **newm; |
| double agefin, delaymax=200. ; /* 100 Max number of years to converge */ |
double agefin, delaymax=200. ; /* 100 Max number of years to converge */ |
| int ncvloop=0; |
int ncvloop=0; |
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int first=0; |
| |
|
| min=vector(1,nlstate); |
min=vector(1,nlstate); |
| max=vector(1,nlstate); |
max=vector(1,nlstate); |
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Line 2655 void powell(double p[], double **xi, int
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Line 2687 void powell(double p[], double **xi, int
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| free_vector(meandiff,1,nlstate); |
free_vector(meandiff,1,nlstate); |
| return prlim; |
return prlim; |
| } |
} |
| } /* age loop */ |
} /* agefin loop */ |
| /* After some age loop it doesn't converge */ |
/* After some age loop it doesn't converge */ |
| printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ |
if(!first){ |
| Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
first=1; |
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printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); |
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} |
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fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); |
| |
|
| /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ |
/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ |
| free_vector(min,1,nlstate); |
free_vector(min,1,nlstate); |
| free_vector(max,1,nlstate); |
free_vector(max,1,nlstate); |
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Line 2724 Earliest age to start was %d-%d=%d, ncvl
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Line 2760 Earliest age to start was %d-%d=%d, ncvl
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| /* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
/* Even if hstepm = 1, at least one multiplication by the unit matrix */ |
| /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */ |
/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */ |
| /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */ |
/* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */ |
| for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */ |
/* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */ |
| |
for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */ |
| ncvloop++; |
ncvloop++; |
| newm=savm; /* oldm should be kept from previous iteration or unity at start */ |
newm=savm; /* oldm should be kept from previous iteration or unity at start */ |
| /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */ |
/* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */ |
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Line 2838 Earliest age to start was %d-%d=%d, ncvl
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Line 2875 Earliest age to start was %d-%d=%d, ncvl
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| free_vector(meandiff,1,nlstate); |
free_vector(meandiff,1,nlstate); |
| return bprlim; |
return bprlim; |
| } |
} |
| } /* age loop */ |
} /* agefin loop */ |
| /* After some age loop it doesn't converge */ |
/* After some age loop it doesn't converge */ |
| if(first){ |
if(!first){ |
| first=1; |
first=1; |
| printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\ |
printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\ |
| Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
|
Line 4365 void freqsummary(char fileres[], double
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Line 4402 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, *stdq, *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; |
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Line 4378 void freqsummary(char fileres[], double
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Line 4415 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 */ |
| |
stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ |
| |
idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ |
| meanqt=matrix(1,lastpass,1,nqtveff); |
meanqt=matrix(1,lastpass,1,nqtveff); |
| strcpy(fileresp,"P_"); |
strcpy(fileresp,"P_"); |
| strcat(fileresp,fileresu); |
strcat(fileresp,fileresu); |
|
Line 4486 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4525 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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stdq[z1]=0.; |
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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.; */ |
| /* } */ |
/* } */ |
| /* } */ |
/* } */ |
| |
|
| /* dateintsum=0; */ |
/* dateintsum=0; */ |
| /* k2cpt=0; */ |
/* k2cpt=0; */ |
| |
|
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Line 4502 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4544 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++) { */ |
|
| /* 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 */ |
| /* if(Tvaraff[z1] ==-20){ */ |
/* if(Tvaraff[z1] ==-20){ */ |
| /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */ |
/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */ |
|
Line 4525 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4564 Title=%s <br>Datafile=%s Firstpass=%d La
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| }/* end j==0 */ |
}/* end j==0 */ |
| if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */ |
if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */ |
| /* for(m=firstpass; m<=lastpass; m++){ */ |
/* for(m=firstpass; m<=lastpass; m++){ */ |
| for(mi=1; mi<wav[iind];mi++){ /* For that wave */ |
for(mi=1; mi<wav[iind];mi++){ /* For each wave */ |
| m=mw[mi][iind]; |
m=mw[mi][iind]; |
| if(j!=0){ |
if(j!=0){ |
| if(anyvaryingduminmodel==1){ /* Some are varying covariates */ |
if(anyvaryingduminmodel==1){ /* Some are varying covariates */ |
|
Line 4545 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4584 Title=%s <br>Datafile=%s Firstpass=%d La
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| }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */ |
}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */ |
| } /* end j==0 */ |
} /* end j==0 */ |
| /* bool =0 we keep that guy which corresponds to the combination of dummy values */ |
/* bool =0 we keep that guy which corresponds to the combination of dummy values */ |
| if(bool==1){ |
if(bool==1){ /*Selected */ |
| /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind] |
/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind] |
| and mw[mi+1][iind]. dh depends on stepm. */ |
and mw[mi+1][iind]. dh depends on stepm. */ |
| agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/ |
agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/ |
|
Line 4563 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4602 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 */ |
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for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */ |
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idq[z1]=idq[z1]+weight[iind]; |
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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]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */ |
| |
} |
| /* 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); */ |
| /* 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]; */ |
|
Line 4578 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4622 Title=%s <br>Datafile=%s Firstpass=%d La
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| bool=1; |
bool=1; |
| }/* end bool 2 */ |
}/* end bool 2 */ |
| } /* end m */ |
} /* end m */ |
| |
/* 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 *\/ */ |
| |
/* } */ |
| } /* end bool */ |
} /* end bool */ |
| } /* end iind = 1 to imx */ |
} /* end iind = 1 to imx */ |
| /* prop[s][age] is feeded for any initial and valid live state as well as |
/* prop[s][age] is feeded for any initial and valid live state as well as |
|
Line 4615 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4664 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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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(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]); |
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fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]); |
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if(weightopt==1){ |
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printf(" Weighted mean and standard deviation of"); |
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fprintf(ficlog," Weighted mean and standard deviation of"); |
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fprintf(ficresphtmfr," Weighted mean and standard deviation of"); |
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} |
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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])); |
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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])); |
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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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} |
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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 4849 Title=%s <br>Datafile=%s Firstpass=%d La
|
Line 4919 Title=%s <br>Datafile=%s Firstpass=%d La
|
| fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
| } |
} |
| } |
} |
| } |
} /* end of state i */ |
| printf("#Freqsummary\n"); |
printf("#Freqsummary\n"); |
| fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
| for(s1=-1; s1 <=nlstate+ndeath; s1++){ |
for(s1=-1; s1 <=nlstate+ndeath; s1++){ |
|
Line 4895 Title=%s <br>Datafile=%s Firstpass=%d La
|
Line 4965 Title=%s <br>Datafile=%s Firstpass=%d La
|
| fclose(ficresp); |
fclose(ficresp); |
| fclose(ficresphtm); |
fclose(ficresphtm); |
| fclose(ficresphtmfr); |
fclose(ficresphtmfr); |
| |
free_vector(idq,1,nqfveff); |
| free_vector(meanq,1,nqfveff); |
free_vector(meanq,1,nqfveff); |
| |
free_vector(stdq,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); |
| free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE); |
free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE); |
|
Line 5002 void prevalence(double ***probs, double
|
Line 5074 void prevalence(double ***probs, double
|
| /*j=cptcoveff;*/ |
/*j=cptcoveff;*/ |
| if (cptcovn<1) {j=1;ncodemax[1]=1;} |
if (cptcovn<1) {j=1;ncodemax[1]=1;} |
| |
|
| first=1; |
first=0; |
| for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */ |
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */ |
| for (i=1; i<=nlstate; i++) |
for (i=1; i<=nlstate; i++) |
| for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++) |
for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++) |
|
Line 5060 void prevalence(double ***probs, double
|
Line 5132 void prevalence(double ***probs, double
|
| if(posprop>=1.e-5){ |
if(posprop>=1.e-5){ |
| probs[i][jk][j1]= prop[jk][i]/posprop; |
probs[i][jk][j1]= prop[jk][i]/posprop; |
| } else{ |
} else{ |
| if(first==1){ |
if(!first){ |
| first=0; |
first=1; |
| printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); |
printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); |
| fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); |
|
| }else{ |
}else{ |
| fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); |
fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]); |
| } |
} |
| } |
} |
| } |
} |
|
Line 5311 void concatwav(int wav[], int **dh, int
|
Line 5382 void concatwav(int wav[], int **dh, int
|
| /* *cptcov=0; */ |
/* *cptcov=0; */ |
| |
|
| for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ |
for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ |
| |
for (k=1; k <= maxncov; k++) |
| |
for(j=1; j<=2; j++) |
| |
nbcode[k][j]=0; /* Valgrind */ |
| |
|
| /* Loop on covariates without age and products and no quantitative variable */ |
/* Loop on covariates without age and products and no quantitative variable */ |
| /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */ |
|
| for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */ |
for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */ |
| for (j=-1; (j < maxncov); j++) Ndum[j]=0; |
for (j=-1; (j < maxncov); j++) Ndum[j]=0; |
| 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 */ |
|
Line 5331 void concatwav(int wav[], int **dh, int
|
Line 5404 void concatwav(int wav[], int **dh, int
|
| modmaxcovj=ij; |
modmaxcovj=ij; |
| else if (ij < modmincovj) |
else if (ij < modmincovj) |
| modmincovj=ij; |
modmincovj=ij; |
| if ((ij < -1) && (ij > NCOVMAX)){ |
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); |
| |
} |
| |
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 ); |
| exit(1); |
exit(1); |
| }else |
}else |
|
Line 5377 void concatwav(int wav[], int **dh, int
|
Line 5454 void concatwav(int wav[], int **dh, int
|
| /* nbcode[Tvar[j]][3]=2; */ |
/* nbcode[Tvar[j]][3]=2; */ |
| /* To be continued (not working yet). */ |
/* To be continued (not working yet). */ |
| ij=0; /* ij is similar to i but can jump over null modalities */ |
ij=0; /* ij is similar to i but can jump over null modalities */ |
| for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ |
|
| |
/* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ |
| |
/* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */ |
| |
/* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of |
| |
* nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */ |
| |
/*, could be restored in the future */ |
| |
for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ |
| if (Ndum[i] == 0) { /* If nobody responded to this modality k */ |
if (Ndum[i] == 0) { /* If nobody responded to this modality k */ |
| break; |
break; |
| } |
} |
| ij++; |
ij++; |
| nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/ |
nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/ |
| cptcode = ij; /* New max modality for covar j */ |
cptcode = ij; /* New max modality for covar j */ |
| } /* end of loop on modality i=-1 to 1 or more */ |
} /* end of loop on modality i=-1 to 1 or more */ |
| break; |
break; |
|
Line 5398 void concatwav(int wav[], int **dh, int
|
Line 5481 void concatwav(int wav[], int **dh, int
|
| break; |
break; |
| } /* end switch */ |
} /* end switch */ |
| } /* end dummy test */ |
} /* end dummy test */ |
| |
} /* 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=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ |
|
| /* /\*recode from 0 *\/ */ |
|
| /* k is a modality. If we have model=V1+V1*sex */ |
|
| /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ |
|
| /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ |
|
| /* } */ |
|
| /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ |
|
| /* if (ij > ncodemax[j]) { */ |
|
| /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ |
|
| /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ |
|
| /* break; */ |
|
| /* } */ |
|
| /* } /\* end of loop on modality k *\/ */ |
|
| } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ |
|
| |
|
| for (k=-1; k< maxncov; k++) Ndum[k]=0; |
for (k=-1; k< maxncov; k++) Ndum[k]=0; |
| /* Look at fixed dummy (single or product) covariates to check empty modalities */ |
/* Look at fixed dummy (single or product) covariates to check empty modalities */ |
|
Line 5796 void concatwav(int wav[], int **dh, int
|
Line 5865 void concatwav(int wav[], int **dh, int
|
| double **dnewm,**doldm; |
double **dnewm,**doldm; |
| double **dnewmp,**doldmp; |
double **dnewmp,**doldmp; |
| int i, j, nhstepm, hstepm, h, nstepm ; |
int i, j, nhstepm, hstepm, h, nstepm ; |
| |
int first=0; |
| int k; |
int k; |
| double *xp; |
double *xp; |
| double **gp, **gm; /**< for var eij */ |
double **gp, **gm; /**< for var eij */ |
|
Line 5920 void concatwav(int wav[], int **dh, int
|
Line 5990 void concatwav(int wav[], int **dh, int
|
| } |
} |
| /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and |
/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and |
| * returns into prlim . |
* returns into prlim . |
| */ |
*/ |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres); |
| |
|
| /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */ |
/* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */ |
|
Line 5958 void concatwav(int wav[], int **dh, int
|
Line 6028 void concatwav(int wav[], int **dh, int
|
| |
|
| for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
for(i=1; i<=npar; i++) /* Computes gradient x - delta */ |
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
| |
|
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres); |
| |
|
| if (popbased==1) { |
if (popbased==1) { |
|
Line 6144 void concatwav(int wav[], int **dh, int
|
Line 6214 void concatwav(int wav[], int **dh, int
|
| int theta; |
int theta; |
| |
|
| pstamp(ficresvpl); |
pstamp(ficresvpl); |
| fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); |
fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n"); |
| fprintf(ficresvpl,"# Age "); |
fprintf(ficresvpl,"# Age "); |
| if(nresult >=1) |
if(nresult >=1) |
| fprintf(ficresvpl," Result# "); |
fprintf(ficresvpl," Result# "); |
|
Line 6173 void concatwav(int wav[], int **dh, int
|
Line 6243 void concatwav(int wav[], int **dh, int
|
| for(i=1; i<=npar; i++){ /* Computes gradient */ |
for(i=1; i<=npar; i++){ /* Computes gradient */ |
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:0); |
| } |
} |
| if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) |
/* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */ |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); |
/* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */ |
| else |
/* else */ |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); |
| for(i=1;i<=nlstate;i++){ |
for(i=1;i<=nlstate;i++){ |
| gp[i] = prlim[i][i]; |
gp[i] = prlim[i][i]; |
| mgp[theta][i] = prlim[i][i]; |
mgp[theta][i] = prlim[i][i]; |
| } |
} |
| for(i=1; i<=npar; i++) /* Computes gradient */ |
for(i=1; i<=npar; i++) /* Computes gradient */ |
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:0); |
| if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) |
/* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */ |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); |
/* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */ |
| else |
/* else */ |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); |
| for(i=1;i<=nlstate;i++){ |
for(i=1;i<=nlstate;i++){ |
| gm[i] = prlim[i][i]; |
gm[i] = prlim[i][i]; |
| mgm[theta][i] = prlim[i][i]; |
mgm[theta][i] = prlim[i][i]; |
|
Line 6235 void concatwav(int wav[], int **dh, int
|
Line 6305 void concatwav(int wav[], int **dh, int
|
| fprintf(ficresvpl,"%.0f ",age ); |
fprintf(ficresvpl,"%.0f ",age ); |
| if(nresult >=1) |
if(nresult >=1) |
| fprintf(ficresvpl,"%d ",nres ); |
fprintf(ficresvpl,"%d ",nres ); |
| for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++){ |
| fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); |
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); |
| |
/* for(j=1;j<=nlstate;j++) */ |
| |
/* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */ |
| |
} |
| fprintf(ficresvpl,"\n"); |
fprintf(ficresvpl,"\n"); |
| free_vector(gp,1,nlstate); |
free_vector(gp,1,nlstate); |
| free_vector(gm,1,nlstate); |
free_vector(gm,1,nlstate); |
|
Line 6453 void varprob(char optionfilefiname[], do
|
Line 6526 void varprob(char optionfilefiname[], do
|
| fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
| fprintf(fichtm,"\n"); |
fprintf(fichtm,"\n"); |
| |
|
| fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s</li>\n",optionfilehtmcov,optionfilehtmcov); |
fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov); |
| fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov); |
fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov); |
| fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \ |
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \ |
| and drawn. It helps understanding how is the covariance between two incidences.\ |
and drawn. It helps understanding how is the covariance between two incidences.\ |
|
Line 6746 void printinghtml(char fileresu[], char
|
Line 6819 void printinghtml(char fileresu[], char
|
| - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ", |
- Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ", |
| stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_")); |
stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_")); |
| fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
| - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
- Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
| subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); |
subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_")); |
| fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
| - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
- Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n", |
| subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_")); |
subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_")); |
| fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
| - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ |
- (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ |
|
Line 6862 divided by h: <sub>h</sub>P<sub>ij</sub>
|
Line 6935 divided by h: <sub>h</sub>P<sub>ij</sub>
|
| 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 (forward stable) prevalence in each health state */ |
| for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
| fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \ |
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <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,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); |
<img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); |
| } |
} |
| if(backcast==1){ |
if(backcast==1){ |
| /* Period (stable) back prevalence in each health state */ |
/* Backward prevalence in each health state */ |
| for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
| fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \ |
fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \ |
| <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres); |
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres); |
| } |
} |
| } |
} |
| if(prevfcast==1){ |
if(prevfcast==1){ |
| /* Projection of prevalence up to period (stable) prevalence in each health state */ |
/* Projection of prevalence up to period (forward stable) prevalence in each health state */ |
| for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
| fprintf(fichtm,"<br>\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) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \ |
fprintf(fichtm,"<br>\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). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \ |
| <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); |
<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); |
| } |
} |
| } |
} |
|
Line 6932 See page 'Matrix of variance-covariance
|
Line 7005 See page 'Matrix of variance-covariance
|
| <a href=\"%s\">%s</a> <br>\n</li>", |
<a href=\"%s\">%s</a> <br>\n</li>", |
| estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_")); |
estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_")); |
| fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
| - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n", |
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n", |
| estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_")); |
estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_")); |
| fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
| - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n", |
- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n", |
| estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_")); |
estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_")); |
| fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
| - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\ |
- Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\ |
| subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); |
subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_")); |
| |
|
| /* if(popforecast==1) fprintf(fichtm,"\n */ |
/* if(popforecast==1) fprintf(fichtm,"\n */ |
|
Line 7074 void printinggnuplot(char fileresu[], ch
|
Line 7147 void printinggnuplot(char fileresu[], ch
|
| continue; |
continue; |
| /* We are interested in selected combination by the resultline */ |
/* We are interested in selected combination by the resultline */ |
| /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */ |
/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */ |
| fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); |
fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt); |
| strcpy(gplotlabel,"("); |
strcpy(gplotlabel,"("); |
| for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */ |
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */ |
| lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ |
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ |
|
Line 7112 void printinggnuplot(char fileresu[], ch
|
Line 7185 void printinggnuplot(char fileresu[], ch
|
| if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
| else fprintf(ficgp," %%*lf (%%*lf)"); |
else fprintf(ficgp," %%*lf (%%*lf)"); |
| } |
} |
| fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); |
fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); |
| for (i=1; i<= nlstate ; i ++) { |
for (i=1; i<= nlstate ; i ++) { |
| if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); |
| else fprintf(ficgp," %%*lf (%%*lf)"); |
else fprintf(ficgp," %%*lf (%%*lf)"); |
|
Line 7441 set ter svg size 640, 480\nunset log y\n
|
Line 7514 set ter svg size 640, 480\nunset log y\n
|
| continue; |
continue; |
| for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */ |
| strcpy(gplotlabel,"("); |
strcpy(gplotlabel,"("); |
| fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); |
fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); |
| for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
| lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
| /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
Line 7485 set ter svg size 640, 480\nunset log y\n
|
Line 7558 set ter svg size 640, 480\nunset log y\n
|
| |
|
| /* 7eme */ |
/* 7eme */ |
| if(backcast == 1){ |
if(backcast == 1){ |
| /* CV back preval stable (period) for each covariate */ |
/* CV backward prevalence for each covariate */ |
| for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ |
for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ |
| for(nres=1; nres <= nresult; nres++){ /* For each resultline */ |
for(nres=1; nres <= nresult; nres++){ /* For each resultline */ |
| if(m != 1 && TKresult[nres]!= k1) |
if(m != 1 && TKresult[nres]!= k1) |
| continue; |
continue; |
| for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */ |
| strcpy(gplotlabel,"("); |
strcpy(gplotlabel,"("); |
| fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt); |
fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt); |
| for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ |
| lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ |
| /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
Line 7540 set ter svg size 640, 480\nunset log y\n
|
Line 7613 set ter svg size 640, 480\nunset log y\n
|
| |
|
| /* 8eme */ |
/* 8eme */ |
| if(prevfcast==1){ |
if(prevfcast==1){ |
| /* Projection from cross-sectional to stable (period) for each covariate */ |
/* Projection from cross-sectional to forward stable (period) prevalence for each covariate */ |
| |
|
| for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ |
for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ |
| for(nres=1; nres <= nresult; nres++){ /* For each resultline */ |
for(nres=1; nres <= nresult; nres++){ /* For each resultline */ |
|
Line 7548 set ter svg size 640, 480\nunset log y\n
|
Line 7621 set ter svg size 640, 480\nunset log y\n
|
| continue; |
continue; |
| for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ |
| strcpy(gplotlabel,"("); |
strcpy(gplotlabel,"("); |
| fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); |
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); |
| for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ |
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ |
| lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ |
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ |
| /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ |
|
Line 7982 set ter svg size 640, 480\nunset log y\n
|
Line 8055 set ter svg size 640, 480\nunset log y\n
|
| int modcovmax =1; |
int modcovmax =1; |
| int mobilavrange, mob; |
int mobilavrange, mob; |
| int iage=0; |
int iage=0; |
| |
int firstA1=0, firstA2=0; |
| |
|
| double sum=0., sumr=0.; |
double sum=0., sumr=0.; |
| double age; |
double age; |
|
Line 8079 set ter svg size 640, 480\nunset log y\n
|
Line 8153 set ter svg size 640, 480\nunset log y\n
|
| } /* age */ |
} /* age */ |
| /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */ |
/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */ |
| /* but they will change */ |
/* but they will change */ |
| |
firstA1=0;firstA2=0; |
| for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */ |
for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */ |
| sumnewm[cptcod]=0.; |
sumnewm[cptcod]=0.; |
| sumnewmr[cptcod]=0.; |
sumnewmr[cptcod]=0.; |
|
Line 8111 set ter svg size 640, 480\nunset log y\n
|
Line 8186 set ter svg size 640, 480\nunset log y\n
|
| sumr+=probs[(int)age][i][cptcod]; |
sumr+=probs[(int)age][i][cptcod]; |
| } |
} |
| if(fabs(sum - 1.) > 1.e-3) { /* bad */ |
if(fabs(sum - 1.) > 1.e-3) { /* bad */ |
| printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); |
if(!firstA1){ |
| |
firstA1=1; |
| |
printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage); |
| |
} |
| |
fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); |
| } /* end bad */ |
} /* end bad */ |
| /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */ |
/* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */ |
| if(fabs(sumr - 1.) > 1.e-3) { /* bad */ |
if(fabs(sumr - 1.) > 1.e-3) { /* bad */ |
| printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); |
if(!firstA2){ |
| |
firstA2=1; |
| |
printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage); |
| |
} |
| |
fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); |
| } /* end bad */ |
} /* end bad */ |
| }/* age */ |
}/* age */ |
| |
|
|
Line 8490 set ter svg size 640, 480\nunset log y\n
|
Line 8573 set ter svg size 640, 480\nunset log y\n
|
| |
|
| /* Variance of prevalence limit: varprlim */ |
/* Variance of prevalence limit: varprlim */ |
| void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){ |
void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){ |
| /*------- Variance of period (stable) prevalence------*/ |
/*------- Variance of forward period (stable) prevalence------*/ |
| |
|
| char fileresvpl[FILENAMELENGTH]; |
char fileresvpl[FILENAMELENGTH]; |
| FILE *ficresvpl; |
FILE *ficresvpl; |
|
Line 8501 set ter svg size 640, 480\nunset log y\n
|
Line 8584 set ter svg size 640, 480\nunset log y\n
|
| strcpy(fileresvpl,"VPL_"); |
strcpy(fileresvpl,"VPL_"); |
| strcat(fileresvpl,fileresu); |
strcat(fileresvpl,fileresu); |
| if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { |
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { |
| printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); |
printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl); |
| exit(0); |
exit(0); |
| } |
} |
| printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); |
printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); |
| fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); |
fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); |
| |
|
| /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ |
| for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ |
|
Line 8542 set ter svg size 640, 480\nunset log y\n
|
Line 8625 set ter svg size 640, 480\nunset log y\n
|
| } |
} |
| |
|
| fclose(ficresvpl); |
fclose(ficresvpl); |
| printf("done variance-covariance of period prevalence\n");fflush(stdout); |
printf("done variance-covariance of forward period prevalence\n");fflush(stdout); |
| fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); |
fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog); |
| |
|
| } |
} |
| /* Variance of back prevalence: varbprlim */ |
/* Variance of back prevalence: varbprlim */ |
|
Line 9686 Dummy[k] 0=dummy (0 1), 1 quantitative (
|
Line 9769 Dummy[k] 0=dummy (0 1), 1 quantitative (
|
| Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ |
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ |
| Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ |
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ |
| Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); |
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); |
| for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;} |
for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;} |
| for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */ |
for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */ |
| if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */ |
if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */ |
| Fixed[k]= 0; |
Fixed[k]= 0; |
|
Line 9936 Dummy[k] 0=dummy (0 1), 1 quantitative (
|
Line 10019 Dummy[k] 0=dummy (0 1), 1 quantitative (
|
| /* Searching for doublons in the model */ |
/* Searching for doublons in the model */ |
| for(k1=1; k1<= cptcovt;k1++){ |
for(k1=1; k1<= cptcovt;k1++){ |
| for(k2=1; k2 <k1;k2++){ |
for(k2=1; k2 <k1;k2++){ |
| if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ |
/* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */ |
| |
if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){ |
| if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */ |
if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */ |
| if(Tvar[k1]==Tvar[k2]){ |
if(Tvar[k1]==Tvar[k2]){ |
| printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); |
printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); |
| fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog); |
fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog); |
| return(1); |
return(1); |
| } |
} |
| }else if (Typevar[k1] ==2){ |
}else if (Typevar[k1] ==2){ |
|
Line 10251 void syscompilerinfo(int logged)
|
Line 10335 void syscompilerinfo(int logged)
|
| #endif |
#endif |
| #endif |
#endif |
| |
|
| // void main() |
// void main () |
| // { |
// { |
| #if defined(_MSC_VER) |
#if defined(_MSC_VER) |
| if (IsWow64()){ |
if (IsWow64()){ |
|
Line 10272 void syscompilerinfo(int logged)
|
Line 10356 void syscompilerinfo(int logged)
|
| } |
} |
| |
|
| int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){ |
int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){ |
| /*--------------- Prevalence limit (period or stable prevalence) --------------*/ |
/*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/ |
| int i, j, k, i1, k4=0, nres=0 ; |
int i, j, k, i1, k4=0, nres=0 ; |
| /* double ftolpl = 1.e-10; */ |
/* double ftolpl = 1.e-10; */ |
| double age, agebase, agelim; |
double age, agebase, agelim; |
|
Line 10281 int prevalence_limit(double *p, double *
|
Line 10365 int prevalence_limit(double *p, double *
|
| strcpy(filerespl,"PL_"); |
strcpy(filerespl,"PL_"); |
| strcat(filerespl,fileresu); |
strcat(filerespl,fileresu); |
| if((ficrespl=fopen(filerespl,"w"))==NULL) { |
if((ficrespl=fopen(filerespl,"w"))==NULL) { |
| printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
| fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1; |
| } |
} |
| printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); |
printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl); |
| fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl); |
fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl); |
| pstamp(ficrespl); |
pstamp(ficrespl); |
| fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); |
fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl); |
| fprintf(ficrespl,"#Age "); |
fprintf(ficrespl,"#Age "); |
| for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); |
| fprintf(ficrespl,"\n"); |
fprintf(ficrespl,"\n"); |
|
Line 10362 int prevalence_limit(double *p, double *
|
Line 10446 int prevalence_limit(double *p, double *
|
| } |
} |
| |
|
| int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){ |
int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){ |
| /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/ |
/*--------------- Back Prevalence limit (backward stable prevalence) --------------*/ |
| |
|
| /* Computes the back prevalence limit for any combination of covariate values |
/* Computes the back prevalence limit for any combination of covariate values |
| * at any age between ageminpar and agemaxpar |
* at any age between ageminpar and agemaxpar |
|
Line 10377 int back_prevalence_limit(double *p, dou
|
Line 10461 int back_prevalence_limit(double *p, dou
|
| strcpy(fileresplb,"PLB_"); |
strcpy(fileresplb,"PLB_"); |
| strcat(fileresplb,fileresu); |
strcat(fileresplb,fileresu); |
| if((ficresplb=fopen(fileresplb,"w"))==NULL) { |
if((ficresplb=fopen(fileresplb,"w"))==NULL) { |
| printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; |
printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1; |
| fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1; |
fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1; |
| } |
} |
| printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); |
printf("Computing backward prevalence: result on file '%s' \n", fileresplb); |
| fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb); |
fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb); |
| pstamp(ficresplb); |
pstamp(ficresplb); |
| fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl); |
fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl); |
| fprintf(ficresplb,"#Age "); |
fprintf(ficresplb,"#Age "); |
| for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i); |
for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i); |
| fprintf(ficresplb,"\n"); |
fprintf(ficresplb,"\n"); |
|
Line 10572 int hPijx(double *p, int bage, int fage)
|
Line 10656 int hPijx(double *p, int bage, int fage)
|
| /*if (stepm<=24) stepsize=2;*/ |
/*if (stepm<=24) stepsize=2;*/ |
| |
|
| /* agelim=AGESUP; */ |
/* agelim=AGESUP; */ |
| ageminl=30; |
ageminl=AGEINF; /* was 30 */ |
| hstepm=stepsize*YEARM; /* Every year of age */ |
hstepm=stepsize*YEARM; /* Every year of age */ |
| hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ |
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ |
| |
|
|
Line 10651 int main(int argc, char *argv[])
|
Line 10735 int main(int argc, char *argv[])
|
| double ssval; |
double ssval; |
| #endif |
#endif |
| int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
| int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; |
int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */ |
| |
/* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */ |
| int ncvyear=0; /* Number of years needed for the period prevalence to converge */ |
int ncvyear=0; /* Number of years needed for the period prevalence to converge */ |
| int jj, ll, li, lj, lk; |
int jj, ll, li, lj, lk; |
| int numlinepar=0; /* Current linenumber of parameter file */ |
int numlinepar=0; /* Current linenumber of parameter file */ |
|
Line 10686 int main(int argc, char *argv[])
|
Line 10771 int main(int argc, char *argv[])
|
| |
|
| char pathr[MAXLINE], pathimach[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
| char *tok, *val; /* pathtot */ |
char *tok, *val; /* pathtot */ |
| int firstobs=1, lastobs=10; |
int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/ |
| int c, h , cpt, c2; |
int c, h , cpt, c2; |
| int jl=0; |
int jl=0; |
| int i1, j1, jk, stepsize=0; |
int i1, j1, jk, stepsize=0; |
|
Line 10945 int main(int argc, char *argv[])
|
Line 11030 int main(int argc, char *argv[])
|
| 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"); |
| |
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); |
| |
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
| |
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
| |
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
| } |
} |
| /* Second parameter line */ |
/* 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)) { */ |
| |
/* 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 10967 int main(int argc, char *argv[])
|
Line 11057 int main(int argc, char *argv[])
|
| 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); |
| |
fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); |
| |
fprintf(ficlog,"but line=%s\n",line); |
| } |
} |
| printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); |
if( lastpass > maxwav){ |
| |
printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav); |
| |
fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav); |
| |
fflush(ficlog); |
| |
goto end; |
| |
} |
| |
printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); |
| |
fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); |
| |
fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt); |
| |
fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); |
| } |
} |
| /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ |
/* ftolpl=6*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 10977 int main(int argc, char *argv[])
|
Line 11078 int main(int argc, char *argv[])
|
| /* 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 11001 int main(int argc, char *argv[])
|
Line 11102 int main(int argc, char *argv[])
|
| } |
} |
| /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ |
/* printf(" model=1+age%s 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); |
| |
fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout); |
| |
fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout); |
| |
fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout); |
| } |
} |
| /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ |
/* 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 11034 int main(int argc, char *argv[])
|
Line 11138 int main(int argc, char *argv[])
|
| ungetc(c,ficpar); |
ungetc(c,ficpar); |
| |
|
| |
|
| covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ |
covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */ |
| if(nqv>=1)coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */ |
if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */ |
| if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */ |
if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */ |
| if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/ |
if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/ |
| cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ |
cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ |
| /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 |
/* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 |
| v1+v2*age+v2*v3 makes cptcovn = 3 |
v1+v2*age+v2*v3 makes cptcovn = 3 |
|
Line 11240 Please run with mle=-1 to get a correct
|
Line 11344 Please run with mle=-1 to get a correct
|
| |
|
| /* Main data |
/* Main data |
| */ |
*/ |
| n= lastobs; |
nobs=lastobs-firstobs+1; /* was = lastobs;*/ |
| num=lvector(1,n); |
/* num=lvector(1,n); */ |
| moisnais=vector(1,n); |
/* moisnais=vector(1,n); */ |
| annais=vector(1,n); |
/* annais=vector(1,n); */ |
| moisdc=vector(1,n); |
/* moisdc=vector(1,n); */ |
| andc=vector(1,n); |
/* andc=vector(1,n); */ |
| weight=vector(1,n); |
/* weight=vector(1,n); */ |
| agedc=vector(1,n); |
/* agedc=vector(1,n); */ |
| cod=ivector(1,n); |
/* cod=ivector(1,n); */ |
| for(i=1;i<=n;i++){ |
/* for(i=1;i<=n;i++){ */ |
| |
num=lvector(firstobs,lastobs); |
| |
moisnais=vector(firstobs,lastobs); |
| |
annais=vector(firstobs,lastobs); |
| |
moisdc=vector(firstobs,lastobs); |
| |
andc=vector(firstobs,lastobs); |
| |
weight=vector(firstobs,lastobs); |
| |
agedc=vector(firstobs,lastobs); |
| |
cod=ivector(firstobs,lastobs); |
| |
for(i=firstobs;i<=lastobs;i++){ |
| num[i]=0; |
num[i]=0; |
| moisnais[i]=0; |
moisnais[i]=0; |
| annais[i]=0; |
annais[i]=0; |
|
Line 11259 Please run with mle=-1 to get a correct
|
Line 11372 Please run with mle=-1 to get a correct
|
| cod[i]=0; |
cod[i]=0; |
| weight[i]=1.0; /* Equal weights, 1 by default */ |
weight[i]=1.0; /* Equal weights, 1 by default */ |
| } |
} |
| mint=matrix(1,maxwav,1,n); |
mint=matrix(1,maxwav,firstobs,lastobs); |
| anint=matrix(1,maxwav,1,n); |
anint=matrix(1,maxwav,firstobs,lastobs); |
| s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ |
s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */ |
| tab=ivector(1,NCOVMAX); |
tab=ivector(1,NCOVMAX); |
| ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
| ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ |
|
Line 11363 Please run with mle=-1 to get a correct
|
Line 11476 Please run with mle=-1 to get a correct
|
| |
|
| |
|
| agegomp=(int)agemin; |
agegomp=(int)agemin; |
| free_vector(moisnais,1,n); |
free_vector(moisnais,firstobs,lastobs); |
| free_vector(annais,1,n); |
free_vector(annais,firstobs,lastobs); |
| /* free_matrix(mint,1,maxwav,1,n); |
/* free_matrix(mint,1,maxwav,1,n); |
| free_matrix(anint,1,maxwav,1,n);*/ |
free_matrix(anint,1,maxwav,1,n);*/ |
| /* free_vector(moisdc,1,n); */ |
/* free_vector(moisdc,1,n); */ |
|
Line 11390 Please run with mle=-1 to get a correct
|
Line 11503 Please run with mle=-1 to get a correct
|
| concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
| /* Concatenates waves */ |
/* Concatenates waves */ |
| |
|
| free_vector(moisdc,1,n); |
free_vector(moisdc,firstobs,lastobs); |
| free_vector(andc,1,n); |
free_vector(andc,firstobs,lastobs); |
| |
|
| /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ |
/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ |
| nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); |
|
Line 11573 Title=%s <br>Datafile=%s Firstpass=%d La
|
Line 11686 Title=%s <br>Datafile=%s Firstpass=%d La
|
| firstpass, lastpass, stepm, weightopt, model); |
firstpass, lastpass, stepm, weightopt, model); |
| |
|
| fprintf(fichtm,"\n"); |
fprintf(fichtm,"\n"); |
| fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\ |
fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\ |
| ftol, stepm); |
ftol, stepm); |
| fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol); |
fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol); |
| ncurrv=1; |
ncurrv=1; |
|
Line 11581 Title=%s <br>Datafile=%s Firstpass=%d La
|
Line 11694 Title=%s <br>Datafile=%s Firstpass=%d La
|
| fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); |
fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); |
| ncurrv=i; |
ncurrv=i; |
| for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i); |
for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i); |
| fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv); |
fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv); |
| ncurrv=i; |
ncurrv=i; |
| for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i); |
for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i); |
| fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv); |
fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv); |
| ncurrv=i; |
ncurrv=i; |
| for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i); |
for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i); |
| fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \ |
fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \ |
|
Line 11616 Interval (in months) between two waves:
|
Line 11729 Interval (in months) between two waves:
|
| for(j=1;j<=NDIM;j++) |
for(j=1;j<=NDIM;j++) |
| ximort[i][j]=0.; |
ximort[i][j]=0.; |
| /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ |
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ |
| cens=ivector(1,n); |
cens=ivector(firstobs,lastobs); |
| ageexmed=vector(1,n); |
ageexmed=vector(firstobs,lastobs); |
| agecens=vector(1,n); |
agecens=vector(firstobs,lastobs); |
| dcwave=ivector(1,n); |
dcwave=ivector(firstobs,lastobs); |
| |
|
| for (i=1; i<=imx; i++){ |
for (i=1; i<=imx; i++){ |
| dcwave[i]=-1; |
dcwave[i]=-1; |
|
Line 11833 Please run with mle=-1 to get a correct
|
Line 11946 Please run with mle=-1 to get a correct
|
| free_vector(lpop,1,AGESUP); |
free_vector(lpop,1,AGESUP); |
| free_vector(tpop,1,AGESUP); |
free_vector(tpop,1,AGESUP); |
| free_matrix(ximort,1,NDIM,1,NDIM); |
free_matrix(ximort,1,NDIM,1,NDIM); |
| free_ivector(cens,1,n); |
free_ivector(dcwave,firstobs,lastobs); |
| free_vector(agecens,1,n); |
free_vector(agecens,firstobs,lastobs); |
| free_ivector(dcwave,1,n); |
free_vector(ageexmed,firstobs,lastobs); |
| |
free_ivector(cens,firstobs,lastobs); |
| #ifdef GSL |
#ifdef GSL |
| #endif |
#endif |
| } /* Endof if mle==-3 mortality only */ |
} /* Endof if mle==-3 mortality only */ |
|
Line 11869 Please run with mle=-1 to get a correct
|
Line 11983 Please run with mle=-1 to get a correct
|
| printf("\n"); |
printf("\n"); |
| |
|
| /*--------- 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); */ |
| |
|
| |
|
| fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); |
|
Line 12241 Please run with mle=-1 to get a correct
|
Line 12355 Please run with mle=-1 to get a correct
|
| /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */ |
/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */ |
| /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */ |
/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */ |
| /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */ |
/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */ |
| free_lvector(num,1,n); |
free_lvector(num,firstobs,lastobs); |
| free_vector(agedc,1,n); |
free_vector(agedc,firstobs,lastobs); |
| /*free_matrix(covar,0,NCOVMAX,1,n);*/ |
/*free_matrix(covar,0,NCOVMAX,1,n);*/ |
| /*free_matrix(covar,1,NCOVMAX,1,n);*/ |
/*free_matrix(covar,1,NCOVMAX,1,n);*/ |
| fclose(ficparo); |
fclose(ficparo); |
|
Line 12499 Please run with mle=-1 to get a correct
|
Line 12613 Please run with mle=-1 to get a correct
|
| if(vpopbased==1) |
if(vpopbased==1) |
| fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); |
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); |
| else |
else |
| fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n"); |
fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n"); |
| fprintf(ficrest,"# Age popbased mobilav e.. (std) "); |
fprintf(ficrest,"# Age popbased mobilav e.. (std) "); |
| for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); |
| fprintf(ficrest,"\n"); |
fprintf(ficrest,"\n"); |
| /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ |
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ |
| printf("Computing age specific period (stable) prevalences in each health state \n"); |
printf("Computing age specific forward period (stable) prevalences in each health state \n"); |
| fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n"); |
fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n"); |
| for(age=bage; age <=fage ;age++){ |
for(age=bage; age <=fage ;age++){ |
| prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */ |
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */ |
| if (vpopbased==1) { |
if (vpopbased==1) { |
|
Line 12552 Please run with mle=-1 to get a correct
|
Line 12666 Please run with mle=-1 to get a correct
|
| printf("done State-specific expectancies\n");fflush(stdout); |
printf("done State-specific expectancies\n");fflush(stdout); |
| fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog); |
fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog); |
| |
|
| /* variance-covariance of period prevalence*/ |
/* variance-covariance of forward period prevalence*/ |
| varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff); |
varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff); |
| |
|
| |
|
| free_vector(weight,1,n); |
free_vector(weight,firstobs,lastobs); |
| free_imatrix(Tvard,1,NCOVMAX,1,2); |
free_imatrix(Tvard,1,NCOVMAX,1,2); |
| free_imatrix(s,1,maxwav+1,1,n); |
free_imatrix(s,1,maxwav+1,firstobs,lastobs); |
| free_matrix(anint,1,maxwav,1,n); |
free_matrix(anint,1,maxwav,firstobs,lastobs); |
| free_matrix(mint,1,maxwav,1,n); |
free_matrix(mint,1,maxwav,firstobs,lastobs); |
| free_ivector(cod,1,n); |
free_ivector(cod,firstobs,lastobs); |
| free_ivector(tab,1,NCOVMAX); |
free_ivector(tab,1,NCOVMAX); |
| fclose(ficresstdeij); |
fclose(ficresstdeij); |
| fclose(ficrescveij); |
fclose(ficrescveij); |
|
Line 12581 Please run with mle=-1 to get a correct
|
Line 12695 Please run with mle=-1 to get a correct
|
| free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); |
| free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); |
| free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
| if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n); |
if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs); |
| if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n); |
if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs); |
| if(nqv>=1)free_matrix(coqvar,1,nqv,1,n); |
if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs); |
| free_matrix(covar,0,NCOVMAX,1,n); |
free_matrix(covar,0,NCOVMAX,firstobs,lastobs); |
| free_matrix(matcov,1,npar,1,npar); |
free_matrix(matcov,1,npar,1,npar); |
| free_matrix(hess,1,npar,1,npar); |
free_matrix(hess,1,npar,1,npar); |
| /*free_vector(delti,1,npar);*/ |
/*free_vector(delti,1,npar);*/ |
|
Line 12737 end:
|
Line 12851 end:
|
| printf("\nType q for exiting: "); fflush(stdout); |
printf("\nType q for exiting: "); fflush(stdout); |
| scanf("%s",z); |
scanf("%s",z); |
| } |
} |
| |
printf("End\n"); |
| |
exit(0); |
| } |
} |
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