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version 1.62, 2002/11/20 07:56:21
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version 1.76, 2003/05/16 10:44:42
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| hPijx is the probability to be observed in state i at age x+h |
hPijx is the probability to be observed in state i at age x+h |
| conditional to the observed state i at age x. The delay 'h' can be |
conditional to the observed state i at age x. The delay 'h' can be |
| split into an exact number (nh*stepm) of unobserved intermediate |
split into an exact number (nh*stepm) of unobserved intermediate |
| states. This elementary transition (by month or quarter trimester, |
states. This elementary transition (by month, quarter, |
| semester or year) is model as a multinomial logistic. The hPx |
semester or year) is modelled as a multinomial logistic. The hPx |
| matrix is simply the matrix product of nh*stepm elementary matrices |
matrix is simply the matrix product of nh*stepm elementary matrices |
| and the contribution of each individual to the likelihood is simply |
and the contribution of each individual to the likelihood is simply |
| hPijx. |
hPijx. |
|
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Line 48
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| It is copyrighted identically to a GNU software product, ie programme and |
It is copyrighted identically to a GNU software product, ie programme and |
| software can be distributed freely for non commercial use. Latest version |
software can be distributed freely for non commercial use. Latest version |
| can be accessed at http://euroreves.ined.fr/imach . |
can be accessed at http://euroreves.ined.fr/imach . |
| |
|
| |
Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach |
| |
or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so |
| |
|
| **********************************************************************/ |
**********************************************************************/ |
| |
/* |
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main |
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read parameterfile |
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read datafile |
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concatwav |
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if (mle >= 1) |
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mlikeli |
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print results files |
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if mle==1 |
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computes hessian |
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read end of parameter file: agemin, agemax, bage, fage, estepm |
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begin-prev-date,... |
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open gnuplot file |
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open html file |
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stable prevalence |
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for age prevalim() |
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h Pij x |
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variance of p varprob |
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forecasting if prevfcast==1 prevforecast call prevalence() |
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health expectancies |
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Variance-covariance of DFLE |
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prevalence() |
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movingaverage() |
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varevsij() |
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if popbased==1 varevsij(,popbased) |
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total life expectancies |
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Variance of stable prevalence |
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end |
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*/ |
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|
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|
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|
| #include <math.h> |
#include <math.h> |
| #include <stdio.h> |
#include <stdio.h> |
|
Line 83
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Line 119
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| #define ODIRSEPARATOR '\\' |
#define ODIRSEPARATOR '\\' |
| #endif |
#endif |
| |
|
| char version[80]="Imach version 0.9, November 2002, INED-EUROREVES "; |
char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES "; |
| int erreur; /* Error number */ |
int erreur; /* Error number */ |
| int nvar; |
int nvar; |
| int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; |
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; |
|
Line 105 double jmean; /* Mean space between 2 wa
|
Line 141 double jmean; /* Mean space between 2 wa
|
| double **oldm, **newm, **savm; /* Working pointers to matrices */ |
double **oldm, **newm, **savm; /* Working pointers to matrices */ |
| double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ |
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ |
| FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; |
FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; |
| FILE *ficlog; |
FILE *ficlog, *ficrespow; |
| FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; |
FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor; |
| FILE *ficresprobmorprev; |
FILE *ficresprobmorprev; |
| FILE *fichtm; /* Html File */ |
FILE *fichtm; /* Html File */ |
|
Line 188 static int split( char *path, char *dirc
|
Line 224 static int split( char *path, char *dirc
|
| if ( ss == NULL ) { /* no directory, so use current */ |
if ( ss == NULL ) { /* no directory, so use current */ |
| /*if(strrchr(path, ODIRSEPARATOR )==NULL) |
/*if(strrchr(path, ODIRSEPARATOR )==NULL) |
| printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ |
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ |
| #if defined(__bsd__) /* get current working directory */ |
/* get current working directory */ |
| extern char *getwd( ); |
/* extern char* getcwd ( char *buf , int len);*/ |
| |
|
| if ( getwd( dirc ) == NULL ) { |
|
| #else |
|
| extern char *getcwd( ); |
|
| |
|
| if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { |
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { |
| #endif |
|
| return( GLOCK_ERROR_GETCWD ); |
return( GLOCK_ERROR_GETCWD ); |
| } |
} |
| strcpy( name, path ); /* we've got it */ |
strcpy( name, path ); /* we've got it */ |
|
Line 297 void free_vector(double*v, int nl, int n
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Line 327 void free_vector(double*v, int nl, int n
|
| } |
} |
| |
|
| /************************ivector *******************************/ |
/************************ivector *******************************/ |
| |
char *cvector(long nl,long nh) |
| |
{ |
| |
char *v; |
| |
v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char))); |
| |
if (!v) nrerror("allocation failure in cvector"); |
| |
return v-nl+NR_END; |
| |
} |
| |
|
| |
/******************free ivector **************************/ |
| |
void free_cvector(char *v, long nl, long nh) |
| |
{ |
| |
free((FREE_ARG)(v+nl-NR_END)); |
| |
} |
| |
|
| |
/************************ivector *******************************/ |
| int *ivector(long nl,long nh) |
int *ivector(long nl,long nh) |
| { |
{ |
| int *v; |
int *v; |
|
Line 365 double **matrix(long nrl, long nrh, long
|
Line 410 double **matrix(long nrl, long nrh, long
|
| |
|
| for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; |
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; |
| return m; |
return m; |
| |
/* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) |
| |
*/ |
| } |
} |
| |
|
| /*************************free matrix ************************/ |
/*************************free matrix ************************/ |
|
Line 404 double ***ma3x(long nrl, long nrh, long
|
Line 451 double ***ma3x(long nrl, long nrh, long
|
| for (j=ncl+1; j<=nch; j++) |
for (j=ncl+1; j<=nch; j++) |
| m[i][j]=m[i][j-1]+nlay; |
m[i][j]=m[i][j-1]+nlay; |
| } |
} |
| return m; |
return m; |
| |
/* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) |
| |
&(m[i][j][k]) <=> *((*(m+i) + j)+k) |
| |
*/ |
| } |
} |
| |
|
| /*************************free ma3x ************************/ |
/*************************free ma3x ************************/ |
|
Line 612 void powell(double p[], double **xi, int
|
Line 662 void powell(double p[], double **xi, int
|
| del=0.0; |
del=0.0; |
| printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret); |
printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret); |
| fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret); |
fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret); |
| for (i=1;i<=n;i++) |
fprintf(ficrespow,"%d %.12f",*iter,*fret); |
| |
for (i=1;i<=n;i++) { |
| printf(" %d %.12f",i, p[i]); |
printf(" %d %.12f",i, p[i]); |
| fprintf(ficlog," %d %.12f",i, p[i]); |
fprintf(ficlog," %d %.12lf",i, p[i]); |
| |
fprintf(ficrespow," %.12lf", p[i]); |
| |
} |
| printf("\n"); |
printf("\n"); |
| fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
| |
fprintf(ficrespow,"\n"); |
| for (i=1;i<=n;i++) { |
for (i=1;i<=n;i++) { |
| for (j=1;j<=n;j++) xit[j]=xi[j][i]; |
for (j=1;j<=n;j++) xit[j]=xi[j][i]; |
| fptt=(*fret); |
fptt=(*fret); |
|
Line 856 double **matprod2(double **out, double *
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Line 910 double **matprod2(double **out, double *
|
| |
|
| double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) |
double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) |
| { |
{ |
| /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month |
/* Computes the transition matrix starting at age 'age' over |
| duration (i.e. until |
'nhstepm*hstepm*stepm' months (i.e. until |
| age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. |
age (in years) age+nhstepm*hstepm*stepm/12) by multiplying |
| |
nhstepm*hstepm matrices. |
| Output is stored in matrix po[i][j][h] for h every 'hstepm' step |
Output is stored in matrix po[i][j][h] for h every 'hstepm' step |
| (typically every 2 years instead of every month which is too big). |
(typically every 2 years instead of every month which is too big |
| |
for the memory). |
| Model is determined by parameters x and covariates have to be |
Model is determined by parameters x and covariates have to be |
| included manually here. |
included manually here. |
| |
|
|
Line 917 double func( double *x)
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Line 973 double func( double *x)
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| double sw; /* Sum of weights */ |
double sw; /* Sum of weights */ |
| double lli; /* Individual log likelihood */ |
double lli; /* Individual log likelihood */ |
| int s1, s2; |
int s1, s2; |
| double bbh; |
double bbh, survp; |
| long ipmx; |
long ipmx; |
| /*extern weight */ |
/*extern weight */ |
| /* We are differentiating ll according to initial status */ |
/* We are differentiating ll according to initial status */ |
|
Line 944 double func( double *x)
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Line 1000 double func( double *x)
|
| for (kk=1; kk<=cptcovage;kk++) { |
for (kk=1; kk<=cptcovage;kk++) { |
| cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
| } |
} |
| |
|
| out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
| 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| savm=oldm; |
savm=oldm; |
| oldm=newm; |
oldm=newm; |
| |
|
| |
|
| } /* end mult */ |
} /* end mult */ |
| |
|
| /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
|
Line 968 double func( double *x)
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Line 1021 double func( double *x)
|
| */ |
*/ |
| s1=s[mw[mi][i]][i]; |
s1=s[mw[mi][i]][i]; |
| s2=s[mw[mi+1][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
| bbh=(double)bh[mi][i]/(double)stepm; |
bbh=(double)bh[mi][i]/(double)stepm; |
| lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); |
/* bias is positive if real duration |
| /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-bbh)*out[s1][s2]));*/ |
* is higher than the multiple of stepm and negative otherwise. |
| |
*/ |
| |
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ |
| |
if( s2 > nlstate){ |
| |
/* i.e. if s2 is a death state and if the date of death is known then the contribution |
| |
to the likelihood is the probability to die between last step unit time and current |
| |
step unit time, which is also the differences between probability to die before dh |
| |
and probability to die before dh-stepm . |
| |
In version up to 0.92 likelihood was computed |
| |
as if date of death was unknown. Death was treated as any other |
| |
health state: the date of the interview describes the actual state |
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and not the date of a change in health state. The former idea was |
| |
to consider that at each interview the state was recorded |
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(healthy, disable or death) and IMaCh was corrected; but when we |
| |
introduced the exact date of death then we should have modified |
| |
the contribution of an exact death to the likelihood. This new |
| |
contribution is smaller and very dependent of the step unit |
| |
stepm. It is no more the probability to die between last interview |
| |
and month of death but the probability to survive from last |
| |
interview up to one month before death multiplied by the |
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probability to die within a month. Thanks to Chris |
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Jackson for correcting this bug. Former versions increased |
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mortality artificially. The bad side is that we add another loop |
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which slows down the processing. The difference can be up to 10% |
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lower mortality. |
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*/ |
| |
lli=log(out[s1][s2] - savm[s1][s2]); |
| |
}else{ |
| |
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
| |
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */ |
| |
} |
| |
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
| |
/*if(lli ==000.0)*/ |
| |
/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ |
| |
ipmx +=1; |
| |
sw += weight[i]; |
| |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| |
} /* end of wave */ |
| |
} /* end of individual */ |
| |
} else if(mle==2){ |
| |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
| |
for(mi=1; mi<= wav[i]-1; mi++){ |
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for (ii=1;ii<=nlstate+ndeath;ii++) |
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for (j=1;j<=nlstate+ndeath;j++){ |
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oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| |
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
| |
} |
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for(d=0; d<=dh[mi][i]; d++){ |
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newm=savm; |
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cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
| |
for (kk=1; kk<=cptcovage;kk++) { |
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cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
| |
} |
| |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
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1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| |
savm=oldm; |
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oldm=newm; |
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} /* end mult */ |
| |
|
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/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
| |
/* But now since version 0.9 we anticipate for bias and large stepm. |
| |
* If stepm is larger than one month (smallest stepm) and if the exact delay |
| |
* (in months) between two waves is not a multiple of stepm, we rounded to |
| |
* the nearest (and in case of equal distance, to the lowest) interval but now |
| |
* we keep into memory the bias bh[mi][i] and also the previous matrix product |
| |
* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the |
| |
* probability in order to take into account the bias as a fraction of the way |
| |
* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies |
| |
* -stepm/2 to stepm/2 . |
| |
* For stepm=1 the results are the same as for previous versions of Imach. |
| |
* For stepm > 1 the results are less biased than in previous versions. |
| |
*/ |
| |
s1=s[mw[mi][i]][i]; |
| |
s2=s[mw[mi+1][i]][i]; |
| |
bbh=(double)bh[mi][i]/(double)stepm; |
| |
/* bias is positive if real duration |
| |
* is higher than the multiple of stepm and negative otherwise. |
| |
*/ |
| |
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ |
| |
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ |
| |
/*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */ |
| /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
| /*if(lli ==000.0)*/ |
/*if(lli ==000.0)*/ |
| /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ |
/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ |
|
Line 979 double func( double *x)
|
Line 1113 double func( double *x)
|
| ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| } /* end of wave */ |
} /* end of wave */ |
| } /* end of individual */ |
} /* end of individual */ |
| } else{ |
} else if(mle==3){ /* exponential inter-extrapolation */ |
| |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
| |
for(mi=1; mi<= wav[i]-1; mi++){ |
| |
for (ii=1;ii<=nlstate+ndeath;ii++) |
| |
for (j=1;j<=nlstate+ndeath;j++){ |
| |
oldm[ii][j]=(ii==j ? 1.0 : 0.0); |
| |
savm[ii][j]=(ii==j ? 1.0 : 0.0); |
| |
} |
| |
for(d=0; d<dh[mi][i]; d++){ |
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newm=savm; |
| |
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; |
| |
for (kk=1; kk<=cptcovage;kk++) { |
| |
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; |
| |
} |
| |
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, |
| |
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); |
| |
savm=oldm; |
| |
oldm=newm; |
| |
} /* end mult */ |
| |
|
| |
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
| |
/* But now since version 0.9 we anticipate for bias and large stepm. |
| |
* If stepm is larger than one month (smallest stepm) and if the exact delay |
| |
* (in months) between two waves is not a multiple of stepm, we rounded to |
| |
* the nearest (and in case of equal distance, to the lowest) interval but now |
| |
* we keep into memory the bias bh[mi][i] and also the previous matrix product |
| |
* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the |
| |
* probability in order to take into account the bias as a fraction of the way |
| |
* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies |
| |
* -stepm/2 to stepm/2 . |
| |
* For stepm=1 the results are the same as for previous versions of Imach. |
| |
* For stepm > 1 the results are less biased than in previous versions. |
| |
*/ |
| |
s1=s[mw[mi][i]][i]; |
| |
s2=s[mw[mi+1][i]][i]; |
| |
bbh=(double)bh[mi][i]/(double)stepm; |
| |
/* bias is positive if real duration |
| |
* is higher than the multiple of stepm and negative otherwise. |
| |
*/ |
| |
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */ |
| |
lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ |
| |
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
| |
/*if(lli ==000.0)*/ |
| |
/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ |
| |
ipmx +=1; |
| |
sw += weight[i]; |
| |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
| |
} /* end of wave */ |
| |
} /* end of individual */ |
| |
}else{ /* ml=4 no inter-extrapolation */ |
| for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
for (i=1,ipmx=0, sw=0.; i<=imx; i++){ |
| for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; |
| for(mi=1; mi<= wav[i]-1; mi++){ |
for(mi=1; mi<= wav[i]-1; mi++){ |
|
Line 1020 double func( double *x)
|
Line 1204 double func( double *x)
|
| void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) |
void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) |
| { |
{ |
| int i,j, iter; |
int i,j, iter; |
| double **xi,*delti; |
double **xi; |
| double fret; |
double fret; |
| |
char filerespow[FILENAMELENGTH]; |
| xi=matrix(1,npar,1,npar); |
xi=matrix(1,npar,1,npar); |
| for (i=1;i<=npar;i++) |
for (i=1;i<=npar;i++) |
| for (j=1;j<=npar;j++) |
for (j=1;j<=npar;j++) |
| xi[i][j]=(i==j ? 1.0 : 0.0); |
xi[i][j]=(i==j ? 1.0 : 0.0); |
| printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
| |
strcpy(filerespow,"pow"); |
| |
strcat(filerespow,fileres); |
| |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
| |
printf("Problem with resultfile: %s\n", filerespow); |
| |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
| |
} |
| |
fprintf(ficrespow,"# Powell\n# iter -2*LL"); |
| |
for (i=1;i<=nlstate;i++) |
| |
for(j=1;j<=nlstate+ndeath;j++) |
| |
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); |
| |
fprintf(ficrespow,"\n"); |
| powell(p,xi,npar,ftol,&iter,&fret,func); |
powell(p,xi,npar,ftol,&iter,&fret,func); |
| |
|
| printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); |
fclose(ficrespow); |
| fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); |
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); |
| |
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); |
| fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); |
fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); |
| |
|
| } |
} |
|
Line 1293 void lubksb(double **a, int n, int *indx
|
Line 1490 void lubksb(double **a, int n, int *indx
|
| } |
} |
| |
|
| /************ Frequencies ********************/ |
/************ Frequencies ********************/ |
| void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) |
void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) |
| { /* Some frequencies */ |
{ /* Some frequencies */ |
| |
|
| int i, m, jk, k1,i1, j1, bool, z1,z2,j; |
int i, m, jk, k1,i1, j1, bool, z1,z2,j; |
| int first; |
int first; |
| double ***freq; /* Frequencies */ |
double ***freq; /* Frequencies */ |
| double *pp; |
double *pp, **prop; |
| double pos, k2, dateintsum=0,k2cpt=0; |
double pos,posprop, k2, dateintsum=0,k2cpt=0; |
| FILE *ficresp; |
FILE *ficresp; |
| char fileresp[FILENAMELENGTH]; |
char fileresp[FILENAMELENGTH]; |
| |
|
| pp=vector(1,nlstate); |
pp=vector(1,nlstate); |
| probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); |
prop=matrix(1,nlstate,iagemin,iagemax+3); |
| strcpy(fileresp,"p"); |
strcpy(fileresp,"p"); |
| strcat(fileresp,fileres); |
strcat(fileresp,fileres); |
| if((ficresp=fopen(fileresp,"w"))==NULL) { |
if((ficresp=fopen(fileresp,"w"))==NULL) { |
|
Line 1313 void freqsummary(char fileres[], int ag
|
Line 1510 void freqsummary(char fileres[], int ag
|
| fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); |
| exit(0); |
exit(0); |
| } |
} |
| freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); |
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3); |
| j1=0; |
j1=0; |
| |
|
| j=cptcoveff; |
j=cptcoveff; |
|
Line 1328 void freqsummary(char fileres[], int ag
|
Line 1525 void freqsummary(char fileres[], int ag
|
| scanf("%d", i);*/ |
scanf("%d", i);*/ |
| for (i=-1; i<=nlstate+ndeath; i++) |
for (i=-1; i<=nlstate+ndeath; i++) |
| for (jk=-1; jk<=nlstate+ndeath; jk++) |
for (jk=-1; jk<=nlstate+ndeath; jk++) |
| for(m=agemin; m <= agemax+3; m++) |
for(m=iagemin; m <= iagemax+3; m++) |
| freq[i][jk][m]=0; |
freq[i][jk][m]=0; |
| |
|
| |
for (i=1; i<=nlstate; i++) |
| |
for(m=iagemin; m <= iagemax+3; m++) |
| |
prop[i][m]=0; |
| |
|
| dateintsum=0; |
dateintsum=0; |
| k2cpt=0; |
k2cpt=0; |
|
Line 1344 void freqsummary(char fileres[], int ag
|
Line 1545 void freqsummary(char fileres[], int ag
|
| for(m=firstpass; m<=lastpass; m++){ |
for(m=firstpass; m<=lastpass; m++){ |
| k2=anint[m][i]+(mint[m][i]/12.); |
k2=anint[m][i]+(mint[m][i]/12.); |
| if ((k2>=dateprev1) && (k2<=dateprev2)) { |
if ((k2>=dateprev1) && (k2<=dateprev2)) { |
| if(agev[m][i]==0) agev[m][i]=agemax+1; |
if(agev[m][i]==0) agev[m][i]=iagemax+1; |
| if(agev[m][i]==1) agev[m][i]=agemax+2; |
if(agev[m][i]==1) agev[m][i]=iagemax+2; |
| |
if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
| if (m<lastpass) { |
if (m<lastpass) { |
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
| freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i]; |
freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; |
| } |
} |
| |
|
| if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) { |
if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { |
| dateintsum=dateintsum+k2; |
dateintsum=dateintsum+k2; |
| k2cpt++; |
k2cpt++; |
| } |
} |
|
Line 1371 void freqsummary(char fileres[], int ag
|
Line 1573 void freqsummary(char fileres[], int ag
|
| fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); |
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); |
| fprintf(ficresp, "\n"); |
fprintf(ficresp, "\n"); |
| |
|
| for(i=(int)agemin; i <= (int)agemax+3; i++){ |
for(i=iagemin; i <= iagemax+3; i++){ |
| if(i==(int)agemax+3){ |
if(i==iagemax+3){ |
| fprintf(ficlog,"Total"); |
fprintf(ficlog,"Total"); |
| }else{ |
}else{ |
| if(first==1){ |
if(first==1){ |
|
Line 1403 void freqsummary(char fileres[], int ag
|
Line 1605 void freqsummary(char fileres[], int ag
|
| for(jk=1; jk <=nlstate ; jk++){ |
for(jk=1; jk <=nlstate ; jk++){ |
| for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) |
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) |
| pp[jk] += freq[jk][m][i]; |
pp[jk] += freq[jk][m][i]; |
| } |
} |
| |
for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ |
| for(jk=1,pos=0; jk <=nlstate ; jk++) |
|
| pos += pp[jk]; |
pos += pp[jk]; |
| |
posprop += prop[jk][i]; |
| |
} |
| for(jk=1; jk <=nlstate ; jk++){ |
for(jk=1; jk <=nlstate ; jk++){ |
| if(pos>=1.e-5){ |
if(pos>=1.e-5){ |
| if(first==1) |
if(first==1) |
|
Line 1417 void freqsummary(char fileres[], int ag
|
Line 1620 void freqsummary(char fileres[], int ag
|
| printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
| fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); |
| } |
} |
| if( i <= (int) agemax){ |
if( i <= iagemax){ |
| if(pos>=1.e-5){ |
if(pos>=1.e-5){ |
| fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); |
fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); |
| probs[i][jk][j1]= pp[jk]/pos; |
probs[i][jk][j1]= pp[jk]/pos; |
| /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ |
/*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ |
| } |
} |
| else |
else |
| fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); |
fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); |
| } |
} |
| } |
} |
| |
|
|
Line 1435 void freqsummary(char fileres[], int ag
|
Line 1638 void freqsummary(char fileres[], int ag
|
| printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); |
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); |
| fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); |
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); |
| } |
} |
| if(i <= (int) agemax) |
if(i <= iagemax) |
| fprintf(ficresp,"\n"); |
fprintf(ficresp,"\n"); |
| if(first==1) |
if(first==1) |
| printf("Others in log...\n"); |
printf("Others in log...\n"); |
|
Line 1446 void freqsummary(char fileres[], int ag
|
Line 1649 void freqsummary(char fileres[], int ag
|
| dateintmean=dateintsum/k2cpt; |
dateintmean=dateintsum/k2cpt; |
| |
|
| fclose(ficresp); |
fclose(ficresp); |
| free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); |
free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3); |
| free_vector(pp,1,nlstate); |
free_vector(pp,1,nlstate); |
| |
free_matrix(prop,1,nlstate,iagemin, iagemax+3); |
| /* End of Freq */ |
/* End of Freq */ |
| } |
} |
| |
|
| /************ Prevalence ********************/ |
/************ Prevalence ********************/ |
| void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate) |
void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) |
| { /* Some frequencies */ |
{ |
| |
/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people |
| |
in each health status at the date of interview (if between dateprev1 and dateprev2). |
| |
We still use firstpass and lastpass as another selection. |
| |
*/ |
| |
|
| int i, m, jk, k1, i1, j1, bool, z1,z2,j; |
int i, m, jk, k1, i1, j1, bool, z1,z2,j; |
| double ***freq; /* Frequencies */ |
double ***freq; /* Frequencies */ |
| double *pp; |
double *pp, **prop; |
| double pos, k2; |
double pos,posprop; |
| |
double y2; /* in fractional years */ |
| pp=vector(1,nlstate); |
int iagemin, iagemax; |
| |
|
| freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); |
iagemin= (int) agemin; |
| |
iagemax= (int) agemax; |
| |
/*pp=vector(1,nlstate);*/ |
| |
prop=matrix(1,nlstate,iagemin,iagemax+3); |
| |
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ |
| j1=0; |
j1=0; |
| |
|
| j=cptcoveff; |
j=cptcoveff; |
|
Line 1473 void prevalence(int agemin, float agemax
|
Line 1684 void prevalence(int agemin, float agemax
|
| for(i1=1; i1<=ncodemax[k1];i1++){ |
for(i1=1; i1<=ncodemax[k1];i1++){ |
| j1++; |
j1++; |
| |
|
| for (i=-1; i<=nlstate+ndeath; i++) |
for (i=1; i<=nlstate; i++) |
| for (jk=-1; jk<=nlstate+ndeath; jk++) |
for(m=iagemin; m <= iagemax+3; m++) |
| for(m=agemin; m <= agemax+3; m++) |
prop[i][m]=0.0; |
| freq[i][jk][m]=0; |
|
| |
|
| for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { /* Each individual */ |
| bool=1; |
bool=1; |
| if (cptcovn>0) { |
if (cptcovn>0) { |
| for (z1=1; z1<=cptcoveff; z1++) |
for (z1=1; z1<=cptcoveff; z1++) |
|
Line 1486 void prevalence(int agemin, float agemax
|
Line 1696 void prevalence(int agemin, float agemax
|
| bool=0; |
bool=0; |
| } |
} |
| if (bool==1) { |
if (bool==1) { |
| for(m=firstpass; m<=lastpass; m++){ |
for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ |
| k2=anint[m][i]+(mint[m][i]/12.); |
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ |
| if ((k2>=dateprev1) && (k2<=dateprev2)) { |
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ |
| if(agev[m][i]==0) agev[m][i]=agemax+1; |
if(agev[m][i]==0) agev[m][i]=iagemax+1; |
| if(agev[m][i]==1) agev[m][i]=agemax+2; |
if(agev[m][i]==1) agev[m][i]=iagemax+2; |
| if (m<lastpass) { |
if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); |
| if (calagedate>0) |
if (s[m][i]>0 && s[m][i]<=nlstate) { |
| freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; |
/*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/ |
| else |
prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
prop[s[m][i]][iagemax+3] += weight[i]; |
| freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; |
} |
| } |
|
| } |
} |
| } |
} /* end selection of waves */ |
| } |
} |
| } |
} |
| for(i=(int)agemin; i <= (int)agemax+3; i++){ |
for(i=iagemin; i <= iagemax+3; i++){ |
| for(jk=1; jk <=nlstate ; jk++){ |
|
| for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) |
|
| pp[jk] += freq[jk][m][i]; |
|
| } |
|
| for(jk=1; jk <=nlstate ; jk++){ |
|
| for(m=-1, pos=0; m <=0 ; m++) |
|
| pos += freq[jk][m][i]; |
|
| } |
|
| |
|
| for(jk=1; jk <=nlstate ; jk++){ |
for(jk=1,posprop=0; jk <=nlstate ; jk++) { |
| for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) |
posprop += prop[jk][i]; |
| pp[jk] += freq[jk][m][i]; |
} |
| } |
|
| |
for(jk=1; jk <=nlstate ; jk++){ |
| for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; |
if( i <= iagemax){ |
| |
if(posprop>=1.e-5){ |
| for(jk=1; jk <=nlstate ; jk++){ |
probs[i][jk][j1]= prop[jk][i]/posprop; |
| if( i <= (int) agemax){ |
} |
| if(pos>=1.e-5){ |
} |
| probs[i][jk][j1]= pp[jk]/pos; |
}/* end jk */ |
| } |
}/* end i */ |
| } |
|
| }/* end jk */ |
|
| }/* end i */ |
|
| } /* end i1 */ |
} /* end i1 */ |
| } /* end k1 */ |
} /* end k1 */ |
| |
|
| |
|
| free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); |
|
| free_vector(pp,1,nlstate); |
|
| |
|
| } /* End of Freq */ |
/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ |
| |
/*free_vector(pp,1,nlstate);*/ |
| |
free_matrix(prop,1,nlstate, iagemin,iagemax+3); |
| |
} /* End of prevalence */ |
| |
|
| /************* Waves Concatenation ***************/ |
/************* Waves Concatenation ***************/ |
| |
|
|
Line 1601 void concatwav(int wav[], int **dh, int
|
Line 1798 void concatwav(int wav[], int **dh, int
|
| if (j <= jmin) jmin=j; |
if (j <= jmin) jmin=j; |
| sum=sum+j; |
sum=sum+j; |
| /*if (j<0) printf("j=%d num=%d \n",j,i); */ |
/*if (j<0) printf("j=%d num=%d \n",j,i); */ |
| |
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ |
| |
/*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ |
| } |
} |
| } |
} |
| else{ |
else{ |
| j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); |
j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); |
| |
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ |
| k=k+1; |
k=k+1; |
| if (j >= jmax) jmax=j; |
if (j >= jmax) jmax=j; |
| else if (j <= jmin)jmin=j; |
else if (j <= jmin)jmin=j; |
| /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ |
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ |
| |
/*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ |
| sum=sum+j; |
sum=sum+j; |
| } |
} |
| jk= j/stepm; |
jk= j/stepm; |
| jl= j -jk*stepm; |
jl= j -jk*stepm; |
| ju= j -(jk+1)*stepm; |
ju= j -(jk+1)*stepm; |
| if(jl <= -ju){ |
if(mle <=1){ |
| dh[mi][i]=jk; |
if(jl==0){ |
| bh[mi][i]=jl; |
dh[mi][i]=jk; |
| } |
bh[mi][i]=0; |
| else{ |
}else{ /* We want a negative bias in order to only have interpolation ie |
| dh[mi][i]=jk+1; |
* at the price of an extra matrix product in likelihood */ |
| bh[mi][i]=ju; |
dh[mi][i]=jk+1; |
| } |
bh[mi][i]=ju; |
| if(dh[mi][i]==0){ |
} |
| dh[mi][i]=1; /* At least one step */ |
}else{ |
| bh[mi][i]=ju; /* At least one step */ |
if(jl <= -ju){ |
| printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i); |
dh[mi][i]=jk; |
| |
bh[mi][i]=jl; /* bias is positive if real duration |
| |
* is higher than the multiple of stepm and negative otherwise. |
| |
*/ |
| |
} |
| |
else{ |
| |
dh[mi][i]=jk+1; |
| |
bh[mi][i]=ju; |
| |
} |
| |
if(dh[mi][i]==0){ |
| |
dh[mi][i]=1; /* At least one step */ |
| |
bh[mi][i]=ju; /* At least one step */ |
| |
/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/ |
| |
} |
| } |
} |
| if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm); |
} /* end if mle */ |
| } |
} /* end wave */ |
| } |
|
| } |
} |
| jmean=sum/k; |
jmean=sum/k; |
| printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); |
printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); |
|
Line 1710 void evsij(char fileres[], double ***eij
|
Line 1923 void evsij(char fileres[], double ***eij
|
| double ***gradg, ***trgradg; |
double ***gradg, ***trgradg; |
| int theta; |
int theta; |
| |
|
| varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage); |
varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); |
| xp=vector(1,npar); |
xp=vector(1,npar); |
| dnewm=matrix(1,nlstate*2,1,npar); |
dnewm=matrix(1,nlstate*nlstate,1,npar); |
| doldm=matrix(1,nlstate*2,1,nlstate*2); |
doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); |
| |
|
| fprintf(ficreseij,"# Health expectancies\n"); |
fprintf(ficreseij,"# Health expectancies\n"); |
| fprintf(ficreseij,"# Age"); |
fprintf(ficreseij,"# Age"); |
|
Line 1730 void evsij(char fileres[], double ***eij
|
Line 1943 void evsij(char fileres[], double ***eij
|
| * This is mainly to measure the difference between two models: for example |
* This is mainly to measure the difference between two models: for example |
| * if stepm=24 months pijx are given only every 2 years and by summing them |
* if stepm=24 months pijx are given only every 2 years and by summing them |
| * we are calculating an estimate of the Life Expectancy assuming a linear |
* we are calculating an estimate of the Life Expectancy assuming a linear |
| * progression inbetween and thus overestimating or underestimating according |
* progression in between and thus overestimating or underestimating according |
| * to the curvature of the survival function. If, for the same date, we |
* to the curvature of the survival function. If, for the same date, we |
| * estimate the model with stepm=1 month, we can keep estepm to 24 months |
* estimate the model with stepm=1 month, we can keep estepm to 24 months |
| * to compare the new estimate of Life expectancy with the same linear |
* to compare the new estimate of Life expectancy with the same linear |
|
Line 1759 void evsij(char fileres[], double ***eij
|
Line 1972 void evsij(char fileres[], double ***eij
|
| /* if (stepm >= YEARM) hstepm=1;*/ |
/* if (stepm >= YEARM) hstepm=1;*/ |
| nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ |
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ |
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2); |
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); |
| gp=matrix(0,nhstepm,1,nlstate*2); |
gp=matrix(0,nhstepm,1,nlstate*nlstate); |
| gm=matrix(0,nhstepm,1,nlstate*2); |
gm=matrix(0,nhstepm,1,nlstate*nlstate); |
| |
|
| /* Computed by stepm unit matrices, product of hstepm matrices, stored |
/* Computed by stepm unit matrices, product of hstepm matrices, stored |
| in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ |
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ |
|
Line 1802 void evsij(char fileres[], double ***eij
|
Line 2015 void evsij(char fileres[], double ***eij
|
| } |
} |
| } |
} |
| } |
} |
| for(j=1; j<= nlstate*2; j++) |
for(j=1; j<= nlstate*nlstate; j++) |
| for(h=0; h<=nhstepm-1; h++){ |
for(h=0; h<=nhstepm-1; h++){ |
| gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
| } |
} |
|
Line 1810 void evsij(char fileres[], double ***eij
|
Line 2023 void evsij(char fileres[], double ***eij
|
| |
|
| /* End theta */ |
/* End theta */ |
| |
|
| trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar); |
trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); |
| |
|
| for(h=0; h<=nhstepm-1; h++) |
for(h=0; h<=nhstepm-1; h++) |
| for(j=1; j<=nlstate*2;j++) |
for(j=1; j<=nlstate*nlstate;j++) |
| for(theta=1; theta <=npar; theta++) |
for(theta=1; theta <=npar; theta++) |
| trgradg[h][j][theta]=gradg[h][theta][j]; |
trgradg[h][j][theta]=gradg[h][theta][j]; |
| |
|
| |
|
| for(i=1;i<=nlstate*2;i++) |
for(i=1;i<=nlstate*nlstate;i++) |
| for(j=1;j<=nlstate*2;j++) |
for(j=1;j<=nlstate*nlstate;j++) |
| varhe[i][j][(int)age] =0.; |
varhe[i][j][(int)age] =0.; |
| |
|
| printf("%d|",(int)age);fflush(stdout); |
printf("%d|",(int)age);fflush(stdout); |
| fprintf(ficlog,"%d|",(int)age);fflush(ficlog); |
fprintf(ficlog,"%d|",(int)age);fflush(ficlog); |
| for(h=0;h<=nhstepm-1;h++){ |
for(h=0;h<=nhstepm-1;h++){ |
| for(k=0;k<=nhstepm-1;k++){ |
for(k=0;k<=nhstepm-1;k++){ |
| matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov); |
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); |
| matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]); |
matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); |
| for(i=1;i<=nlstate*2;i++) |
for(i=1;i<=nlstate*nlstate;i++) |
| for(j=1;j<=nlstate*2;j++) |
for(j=1;j<=nlstate*nlstate;j++) |
| varhe[i][j][(int)age] += doldm[i][j]*hf*hf; |
varhe[i][j][(int)age] += doldm[i][j]*hf*hf; |
| } |
} |
| } |
} |
|
Line 1852 void evsij(char fileres[], double ***eij
|
Line 2065 void evsij(char fileres[], double ***eij
|
| } |
} |
| fprintf(ficreseij,"\n"); |
fprintf(ficreseij,"\n"); |
| |
|
| free_matrix(gm,0,nhstepm,1,nlstate*2); |
free_matrix(gm,0,nhstepm,1,nlstate*nlstate); |
| free_matrix(gp,0,nhstepm,1,nlstate*2); |
free_matrix(gp,0,nhstepm,1,nlstate*nlstate); |
| free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2); |
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); |
| free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar); |
free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| } |
} |
| printf("\n"); |
printf("\n"); |
| fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
| |
|
| free_vector(xp,1,npar); |
free_vector(xp,1,npar); |
| free_matrix(dnewm,1,nlstate*2,1,npar); |
free_matrix(dnewm,1,nlstate*nlstate,1,npar); |
| free_matrix(doldm,1,nlstate*2,1,nlstate*2); |
free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); |
| free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage); |
free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); |
| } |
} |
| |
|
| /************ Variance ******************/ |
/************ Variance ******************/ |
|
Line 1920 void varevsij(char optionfilefiname[], d
|
Line 2133 void varevsij(char optionfilefiname[], d
|
| } |
} |
| printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
| fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); |
| fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); |
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); |
| fprintf(ficresprobmorprev,"# Age cov=%-d",ij); |
fprintf(ficresprobmorprev,"# Age cov=%-d",ij); |
| for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
| fprintf(ficresprobmorprev," p.%-d SE",j); |
fprintf(ficresprobmorprev," p.%-d SE",j); |
|
Line 1942 void varevsij(char optionfilefiname[], d
|
Line 2155 void varevsij(char optionfilefiname[], d
|
| exit(0); |
exit(0); |
| } |
} |
| else{ |
else{ |
| fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n"); |
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n"); |
| fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp); |
fprintf(fichtm,"\n<br>%s <br>\n",digitp); |
| } |
} |
| varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); |
| |
|
|
Line 1977 void varevsij(char optionfilefiname[], d
|
Line 2190 void varevsij(char optionfilefiname[], d
|
| and note for a fixed period like k years */ |
and note for a fixed period like k years */ |
| /* We decided (b) to get a life expectancy respecting the most precise curvature of the |
/* We decided (b) to get a life expectancy respecting the most precise curvature of the |
| survival function given by stepm (the optimization length). Unfortunately it |
survival function given by stepm (the optimization length). Unfortunately it |
| means that if the survival funtion is printed only each two years of age and if |
means that if the survival funtion is printed every two years of age and if |
| you sum them up and add 1 year (area under the trapezoids) you won't get the same |
you sum them up and add 1 year (area under the trapezoids) you won't get the same |
| results. So we changed our mind and took the option of the best precision. |
results. So we changed our mind and took the option of the best precision. |
| */ |
*/ |
|
Line 1993 void varevsij(char optionfilefiname[], d
|
Line 2206 void varevsij(char optionfilefiname[], d
|
| |
|
| |
|
| for(theta=1; theta <=npar; theta++){ |
for(theta=1; theta <=npar; theta++){ |
| for(i=1; i<=npar; i++){ /* Computes gradient */ |
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); |
| } |
} |
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
|
Line 2015 void varevsij(char optionfilefiname[], d
|
Line 2228 void varevsij(char optionfilefiname[], d
|
| gp[h][j] += prlim[i][i]*p3mat[i][j][h]; |
gp[h][j] += prlim[i][i]*p3mat[i][j][h]; |
| } |
} |
| } |
} |
| /* This for computing forces of mortality (h=1)as a weighted average */ |
/* This for computing probability of death (h=1 means |
| for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ |
computed over hstepm matrices product = hstepm*stepm months) |
| for(i=1; i<= nlstate; i++) |
as a weighted average of prlim. |
| |
*/ |
| |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
| |
for(i=1,gpp[j]=0.; i<= nlstate; i++) |
| gpp[j] += prlim[i][i]*p3mat[i][j][1]; |
gpp[j] += prlim[i][i]*p3mat[i][j][1]; |
| } |
} |
| /* end force of mortality */ |
/* end probability of death */ |
| |
|
| for(i=1; i<=npar; i++) /* Computes gradient */ |
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); |
| hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); |
| prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); |
|
Line 2043 void varevsij(char optionfilefiname[], d
|
Line 2259 void varevsij(char optionfilefiname[], d
|
| gm[h][j] += prlim[i][i]*p3mat[i][j][h]; |
gm[h][j] += prlim[i][i]*p3mat[i][j][h]; |
| } |
} |
| } |
} |
| /* This for computing force of mortality (h=1)as a weighted average */ |
/* This for computing probability of death (h=1 means |
| for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ |
computed over hstepm matrices product = hstepm*stepm months) |
| for(i=1; i<= nlstate; i++) |
as a weighted average of prlim. |
| gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
*/ |
| |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
| |
for(i=1,gmp[j]=0.; i<= nlstate; i++) |
| |
gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
| } |
} |
| /* end force of mortality */ |
/* end probability of death */ |
| |
|
| for(j=1; j<= nlstate; j++) /* vareij */ |
for(j=1; j<= nlstate; j++) /* vareij */ |
| for(h=0; h<=nhstepm; h++){ |
for(h=0; h<=nhstepm; h++){ |
| gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; |
| } |
} |
| |
|
| for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ |
for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ |
| gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; |
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; |
| } |
} |
|
Line 2070 void varevsij(char optionfilefiname[], d
|
Line 2290 void varevsij(char optionfilefiname[], d
|
| for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ |
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ |
| for(theta=1; theta <=npar; theta++) |
for(theta=1; theta <=npar; theta++) |
| trgradgp[j][theta]=gradgp[theta][j]; |
trgradgp[j][theta]=gradgp[theta][j]; |
| |
|
| |
|
| hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ |
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ |
| for(i=1;i<=nlstate;i++) |
for(i=1;i<=nlstate;i++) |
|
Line 2085 void varevsij(char optionfilefiname[], d
|
Line 2306 void varevsij(char optionfilefiname[], d
|
| vareij[i][j][(int)age] += doldm[i][j]*hf*hf; |
vareij[i][j][(int)age] += doldm[i][j]*hf*hf; |
| } |
} |
| } |
} |
| |
|
| /* pptj */ |
/* pptj */ |
| matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); |
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); |
| matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); |
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); |
|
Line 2093 void varevsij(char optionfilefiname[], d
|
Line 2314 void varevsij(char optionfilefiname[], d
|
| for(i=nlstate+1;i<=nlstate+ndeath;i++) |
for(i=nlstate+1;i<=nlstate+ndeath;i++) |
| varppt[j][i]=doldmp[j][i]; |
varppt[j][i]=doldmp[j][i]; |
| /* end ppptj */ |
/* end ppptj */ |
| |
/* x centered again */ |
| hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); |
| prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); |
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); |
| |
|
|
Line 2105 void varevsij(char optionfilefiname[], d
|
Line 2327 void varevsij(char optionfilefiname[], d
|
| prlim[i][i]=mobaverage[(int)age][i][ij]; |
prlim[i][i]=mobaverage[(int)age][i][ij]; |
| } |
} |
| } |
} |
| |
|
| /* This for computing force of mortality (h=1)as a weighted average */ |
/* This for computing probability of death (h=1 means |
| for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ |
computed over hstepm (estepm) matrices product = hstepm*stepm months) |
| for(i=1; i<= nlstate; i++) |
as a weighted average of prlim. |
| |
*/ |
| |
for(j=nlstate+1;j<=nlstate+ndeath;j++){ |
| |
for(i=1,gmp[j]=0.;i<= nlstate; i++) |
| gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
gmp[j] += prlim[i][i]*p3mat[i][j][1]; |
| } |
} |
| /* end force of mortality */ |
/* end probability of death */ |
| |
|
| fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); |
fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); |
| for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
for(j=nlstate+1; j<=(nlstate+ndeath);j++){ |
|
Line 2141 void varevsij(char optionfilefiname[], d
|
Line 2366 void varevsij(char optionfilefiname[], d
|
| fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); |
fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); |
| /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ |
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ |
| fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); |
fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); |
| fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); |
/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ |
| fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); |
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ |
| fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); |
/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ |
| |
fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev); |
| |
fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev); |
| |
fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev); |
| fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev); |
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev); |
| fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit); |
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit); |
| /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit); |
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit); |
| */ |
*/ |
| fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit); |
fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); |
| |
|
| free_vector(xp,1,npar); |
free_vector(xp,1,npar); |
| free_matrix(doldm,1,nlstate,1,nlstate); |
free_matrix(doldm,1,nlstate,1,nlstate); |
|
Line 2160 void varevsij(char optionfilefiname[], d
|
Line 2388 void varevsij(char optionfilefiname[], d
|
| fclose(ficresprobmorprev); |
fclose(ficresprobmorprev); |
| fclose(ficgp); |
fclose(ficgp); |
| fclose(fichtm); |
fclose(fichtm); |
| } |
} |
| |
|
| /************ Variance of prevlim ******************/ |
/************ Variance of prevlim ******************/ |
| void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) |
void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) |
|
Line 2306 void varprob(char optionfilefiname[], do
|
Line 2534 void varprob(char optionfilefiname[], do
|
| fprintf(ficresprobcov," p%1d-%1d ",i,j); |
fprintf(ficresprobcov," p%1d-%1d ",i,j); |
| fprintf(ficresprobcor," p%1d-%1d ",i,j); |
fprintf(ficresprobcor," p%1d-%1d ",i,j); |
| } |
} |
| fprintf(ficresprob,"\n"); |
/* fprintf(ficresprob,"\n"); |
| fprintf(ficresprobcov,"\n"); |
fprintf(ficresprobcov,"\n"); |
| fprintf(ficresprobcor,"\n"); |
fprintf(ficresprobcor,"\n"); |
| xp=vector(1,npar); |
*/ |
| |
xp=vector(1,npar); |
| dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); |
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); |
| doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); |
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); |
| mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); |
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); |
|
Line 2348 void varprob(char optionfilefiname[], do
|
Line 2577 void varprob(char optionfilefiname[], do
|
| if (cptcovn>0) { |
if (cptcovn>0) { |
| fprintf(ficresprob, "\n#********** Variable "); |
fprintf(ficresprob, "\n#********** Variable "); |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| fprintf(ficresprob, "**********\n#"); |
fprintf(ficresprob, "**********\n#\n"); |
| fprintf(ficresprobcov, "\n#********** Variable "); |
fprintf(ficresprobcov, "\n#********** Variable "); |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| fprintf(ficresprobcov, "**********\n#"); |
fprintf(ficresprobcov, "**********\n#\n"); |
| |
|
| fprintf(ficgp, "\n#********** Variable "); |
fprintf(ficgp, "\n#********** Variable "); |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| fprintf(ficgp, "**********\n#"); |
fprintf(ficgp, "**********\n#\n"); |
| |
|
| |
|
| fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); |
fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); |
|
Line 2364 void varprob(char optionfilefiname[], do
|
Line 2593 void varprob(char optionfilefiname[], do
|
| |
|
| fprintf(ficresprobcor, "\n#********** Variable "); |
fprintf(ficresprobcor, "\n#********** Variable "); |
| for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); |
| fprintf(ficgp, "**********\n#"); |
fprintf(ficresprobcor, "**********\n#"); |
| } |
} |
| |
|
| for (age=bage; age<=fage; age ++){ |
for (age=bage; age<=fage; age ++){ |
|
Line 2383 void varprob(char optionfilefiname[], do
|
Line 2612 void varprob(char optionfilefiname[], do
|
| |
|
| for(theta=1; theta <=npar; theta++){ |
for(theta=1; theta <=npar; theta++){ |
| for(i=1; i<=npar; i++) |
for(i=1; i<=npar; i++) |
| xp[i] = x[i] + (i==theta ?delti[theta]:0); |
xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); |
| |
|
| pmij(pmmij,cov,ncovmodel,xp,nlstate); |
pmij(pmmij,cov,ncovmodel,xp,nlstate); |
| |
|
|
Line 2396 void varprob(char optionfilefiname[], do
|
Line 2625 void varprob(char optionfilefiname[], do
|
| } |
} |
| |
|
| for(i=1; i<=npar; i++) |
for(i=1; i<=npar; i++) |
| xp[i] = x[i] - (i==theta ?delti[theta]:0); |
xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); |
| |
|
| pmij(pmmij,cov,ncovmodel,xp,nlstate); |
pmij(pmmij,cov,ncovmodel,xp,nlstate); |
| k=0; |
k=0; |
|
Line 2408 void varprob(char optionfilefiname[], do
|
Line 2637 void varprob(char optionfilefiname[], do
|
| } |
} |
| |
|
| for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) |
for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) |
| gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; |
gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; |
| } |
} |
| |
|
| for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) |
for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) |
|
Line 2595 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 2824 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
| fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
| } |
} |
| /* Pij */ |
/* Pij */ |
| fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br> |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> |
| <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); |
<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); |
| /* Quasi-incidences */ |
/* Quasi-incidences */ |
| fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> |
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> |
|
Line 2626 health expectancies in states (1) and (2
|
Line 2855 health expectancies in states (1) and (2
|
| - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n |
- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n |
| - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); |
- Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres); |
| |
|
| if(popforecast==1) fprintf(fichtm,"\n |
/* if(popforecast==1) fprintf(fichtm,"\n */ |
| - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n |
/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */ |
| - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n |
/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */ |
| <br>",fileres,fileres,fileres,fileres); |
/* <br>",fileres,fileres,fileres,fileres); */ |
| else |
/* else */ |
| fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); |
/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */ |
| fprintf(fichtm," <ul><li><b>Graphs</b></li><p>"); |
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>"); |
| |
|
| m=cptcoveff; |
m=cptcoveff; |
|
Line 2648 fprintf(fichtm," <ul><li><b>Graphs</b></
|
Line 2877 fprintf(fichtm," <ul><li><b>Graphs</b></
|
| fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">"); |
| } |
} |
| for(cpt=1; cpt<=nlstate;cpt++) { |
for(cpt=1; cpt<=nlstate;cpt++) { |
| fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident |
fprintf(fichtm,"<br>- Observed and period prevalence (with confident |
| interval) in state (%d): v%s%d%d.png <br> |
interval) in state (%d): v%s%d%d.png <br> |
| <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); |
<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); |
| } |
} |
|
Line 2683 m=pow(2,cptcoveff);
|
Line 2912 m=pow(2,cptcoveff);
|
| 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\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1); |
fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1); |
| 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)"); |
| } |
} |
| fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); |
fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); |
| 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 2749 m=pow(2,cptcoveff);
|
Line 2978 m=pow(2,cptcoveff);
|
| } |
} |
| } |
} |
| |
|
| /* CV preval stat */ |
/* CV preval stable (period) */ |
| for (k1=1; k1<= m ; k1 ++) { |
for (k1=1; k1<= m ; k1 ++) { |
| for (cpt=1; cpt<nlstate ; cpt ++) { |
for (cpt=1; cpt<=nlstate ; cpt ++) { |
| k=3; |
k=3; |
| fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); |
fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1); |
| fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1); |
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1); |
| |
|
| for (i=1; i< nlstate ; i ++) |
for (i=1; i<= nlstate ; i ++) |
| fprintf(ficgp,"+$%d",k+i+1); |
fprintf(ficgp,"+$%d",k+i+1); |
| fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); |
fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); |
| |
|
|
Line 2879 int movingaverage(double ***probs, doubl
|
Line 3108 int movingaverage(double ***probs, doubl
|
| |
|
| |
|
| /************** Forecasting ******************/ |
/************** Forecasting ******************/ |
| prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){ |
prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ |
| |
/* proj1, year, month, day of starting projection |
| int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; |
agemin, agemax range of age |
| |
dateprev1 dateprev2 range of dates during which prevalence is computed |
| |
anproj2 year of en of projection (same day and month as proj1). |
| |
*/ |
| |
int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1; |
| int *popage; |
int *popage; |
| double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; |
double agec; /* generic age */ |
| |
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; |
| double *popeffectif,*popcount; |
double *popeffectif,*popcount; |
| double ***p3mat; |
double ***p3mat; |
| double ***mobaverage; |
double ***mobaverage; |
| char fileresf[FILENAMELENGTH]; |
char fileresf[FILENAMELENGTH]; |
| |
|
| agelim=AGESUP; |
agelim=AGESUP; |
| calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; |
prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
| |
|
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); |
|
| |
|
| |
|
| strcpy(fileresf,"f"); |
strcpy(fileresf,"f"); |
| strcat(fileresf,fileres); |
strcat(fileresf,fileres); |
|
Line 2916 prevforecast(char fileres[], double anpr
|
Line 3147 prevforecast(char fileres[], double anpr
|
| |
|
| stepsize=(int) (stepm+YEARM-1)/YEARM; |
stepsize=(int) (stepm+YEARM-1)/YEARM; |
| if (stepm<=12) stepsize=1; |
if (stepm<=12) stepsize=1; |
| |
if(estepm < stepm){ |
| agelim=AGESUP; |
printf ("Problem %d lower than %d\n",estepm, stepm); |
| |
} |
| hstepm=1; |
else hstepm=estepm; |
| |
|
| hstepm=hstepm/stepm; |
hstepm=hstepm/stepm; |
| yp1=modf(dateintmean,&yp); |
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and |
| |
fractional in yp1 */ |
| anprojmean=yp; |
anprojmean=yp; |
| yp2=modf((yp1*12),&yp); |
yp2=modf((yp1*12),&yp); |
| mprojmean=yp; |
mprojmean=yp; |
|
Line 2929 prevforecast(char fileres[], double anpr
|
Line 3162 prevforecast(char fileres[], double anpr
|
| jprojmean=yp; |
jprojmean=yp; |
| if(jprojmean==0) jprojmean=1; |
if(jprojmean==0) jprojmean=1; |
| if(mprojmean==0) jprojmean=1; |
if(mprojmean==0) jprojmean=1; |
| |
|
| |
i1=cptcoveff; |
| |
if (cptcovn < 1){i1=1;} |
| |
|
| fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); |
fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); |
| |
|
| for(cptcov=1;cptcov<=i2;cptcov++){ |
fprintf(ficresf,"#****** Routine prevforecast **\n"); |
| |
|
| |
/* if (h==(int)(YEARM*yearp)){ */ |
| |
for(cptcov=1, k=0;cptcov<=i1;cptcov++){ |
| for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
| k=k+1; |
k=k+1; |
| fprintf(ficresf,"\n#******"); |
fprintf(ficresf,"\n#******"); |
| for(j=1;j<=cptcoveff;j++) { |
for(j=1;j<=cptcoveff;j++) { |
| fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| } |
} |
| fprintf(ficresf,"******\n"); |
fprintf(ficresf,"******\n"); |
| fprintf(ficresf,"# StartingAge FinalAge"); |
fprintf(ficresf,"# Covariate valuofcovar yearproj age"); |
| for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j); |
for(j=1; j<=nlstate+ndeath;j++){ |
| |
for(i=1; i<=nlstate;i++) |
| |
fprintf(ficresf," p%d%d",i,j); |
| for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { |
fprintf(ficresf," p.%d",j); |
| |
} |
| |
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { |
| fprintf(ficresf,"\n"); |
fprintf(ficresf,"\n"); |
| fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt); |
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); |
| |
|
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ |
for (agec=fage; agec>=(ageminpar-1); agec--){ |
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
nhstepm=(int) rint((agelim-agec)*YEARM/stepm); |
| nhstepm = nhstepm/hstepm; |
nhstepm = nhstepm/hstepm; |
| |
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| oldm=oldms;savm=savms; |
oldm=oldms;savm=savms; |
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); |
| |
|
| for (h=0; h<=nhstepm; h++){ |
for (h=0; h<=nhstepm; h++){ |
| if (h==(int) (calagedate+YEARM*cpt)) { |
if (h*hstepm/YEARM*stepm ==yearp) { |
| fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); |
fprintf(ficresf,"\n"); |
| |
for(j=1;j<=cptcoveff;j++) |
| |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| |
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); |
| } |
} |
| for(j=1; j<=nlstate+ndeath;j++) { |
for(j=1; j<=nlstate+ndeath;j++) { |
| kk1=0.;kk2=0; |
ppij=0.; |
| for(i=1; i<=nlstate;i++) { |
for(i=1; i<=nlstate;i++) { |
| if (mobilav==1) |
if (mobilav==1) |
| kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; |
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; |
| else { |
else { |
| kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; |
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; |
| } |
} |
| |
if (h*hstepm/YEARM*stepm== yearp) { |
| } |
fprintf(ficresf," %.3f", p3mat[i][j][h]); |
| if (h==(int)(calagedate+12*cpt)){ |
} |
| fprintf(ficresf," %.3f", kk1); |
} /* end i */ |
| |
if (h*hstepm/YEARM*stepm==yearp) { |
| |
fprintf(ficresf," %.3f", ppij); |
| } |
} |
| } |
}/* end j */ |
| } |
} /* end h */ |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| } |
} /* end agec */ |
| } |
} /* end yearp */ |
| } |
} /* end cptcod */ |
| } |
} /* end cptcov */ |
| |
|
| if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
|
| fclose(ficresf); |
fclose(ficresf); |
| } |
} |
| /************** Forecasting ******************/ |
|
| |
/************** Forecasting *****not tested NB*************/ |
| populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ |
populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ |
| |
|
| int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; |
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; |
| int *popage; |
int *popage; |
| double calagedate, agelim, kk1, kk2; |
double calagedatem, agelim, kk1, kk2; |
| double *popeffectif,*popcount; |
double *popeffectif,*popcount; |
| double ***p3mat,***tabpop,***tabpopprev; |
double ***p3mat,***tabpop,***tabpopprev; |
| double ***mobaverage; |
double ***mobaverage; |
|
Line 3000 populforecast(char fileres[], double anp
|
Line 3245 populforecast(char fileres[], double anp
|
| tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| agelim=AGESUP; |
agelim=AGESUP; |
| calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; |
calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; |
| |
|
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); |
prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
| |
|
| |
|
| strcpy(filerespop,"pop"); |
strcpy(filerespop,"pop"); |
|
Line 3048 populforecast(char fileres[], double anp
|
Line 3293 populforecast(char fileres[], double anp
|
| for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; |
for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; |
| } |
} |
| |
|
| for(cptcov=1;cptcov<=i2;cptcov++){ |
for(cptcov=1,k=0;cptcov<=i2;cptcov++){ |
| for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ |
| k=k+1; |
k=k+1; |
| fprintf(ficrespop,"\n#******"); |
fprintf(ficrespop,"\n#******"); |
|
Line 3063 populforecast(char fileres[], double anp
|
Line 3308 populforecast(char fileres[], double anp
|
| for (cpt=0; cpt<=0;cpt++) { |
for (cpt=0; cpt<=0;cpt++) { |
| fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
| |
|
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ |
for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ |
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
| nhstepm = nhstepm/hstepm; |
nhstepm = nhstepm/hstepm; |
| |
|
|
Line 3072 populforecast(char fileres[], double anp
|
Line 3317 populforecast(char fileres[], double anp
|
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
| |
|
| for (h=0; h<=nhstepm; h++){ |
for (h=0; h<=nhstepm; h++){ |
| if (h==(int) (calagedate+YEARM*cpt)) { |
if (h==(int) (calagedatem+YEARM*cpt)) { |
| fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
| } |
} |
| for(j=1; j<=nlstate+ndeath;j++) { |
for(j=1; j<=nlstate+ndeath;j++) { |
|
Line 3084 populforecast(char fileres[], double anp
|
Line 3329 populforecast(char fileres[], double anp
|
| kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; |
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; |
| } |
} |
| } |
} |
| if (h==(int)(calagedate+12*cpt)){ |
if (h==(int)(calagedatem+12*cpt)){ |
| tabpop[(int)(agedeb)][j][cptcod]=kk1; |
tabpop[(int)(agedeb)][j][cptcod]=kk1; |
| /*fprintf(ficrespop," %.3f", kk1); |
/*fprintf(ficrespop," %.3f", kk1); |
| if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ |
if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ |
|
Line 3095 populforecast(char fileres[], double anp
|
Line 3340 populforecast(char fileres[], double anp
|
| for(j=1; j<=nlstate;j++){ |
for(j=1; j<=nlstate;j++){ |
| kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; |
kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; |
| } |
} |
| tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)]; |
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; |
| } |
} |
| |
|
| if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) |
if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) |
| fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); |
fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); |
| } |
} |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
Line 3109 populforecast(char fileres[], double anp
|
Line 3354 populforecast(char fileres[], double anp
|
| |
|
| for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { |
for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { |
| fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); |
| for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ |
for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ |
| nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); |
| nhstepm = nhstepm/hstepm; |
nhstepm = nhstepm/hstepm; |
| |
|
|
Line 3117 populforecast(char fileres[], double anp
|
Line 3362 populforecast(char fileres[], double anp
|
| oldm=oldms;savm=savms; |
oldm=oldms;savm=savms; |
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
| for (h=0; h<=nhstepm; h++){ |
for (h=0; h<=nhstepm; h++){ |
| if (h==(int) (calagedate+YEARM*cpt)) { |
if (h==(int) (calagedatem+YEARM*cpt)) { |
| fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); |
| } |
} |
| for(j=1; j<=nlstate+ndeath;j++) { |
for(j=1; j<=nlstate+ndeath;j++) { |
|
Line 3125 populforecast(char fileres[], double anp
|
Line 3370 populforecast(char fileres[], double anp
|
| for(i=1; i<=nlstate;i++) { |
for(i=1; i<=nlstate;i++) { |
| kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; |
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; |
| } |
} |
| if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); |
if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); |
| } |
} |
| } |
} |
| free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
|
Line 3153 populforecast(char fileres[], double anp
|
Line 3398 populforecast(char fileres[], double anp
|
| int main(int argc, char *argv[]) |
int main(int argc, char *argv[]) |
| { |
{ |
| 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,m,size,cptcode, cptcod; |
int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; |
| double agedeb, agefin,hf; |
double agedeb, agefin,hf; |
| double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; |
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; |
| |
|
|
Line 3172 int main(int argc, char *argv[])
|
Line 3417 int main(int argc, char *argv[])
|
| int ju,jl, mi; |
int ju,jl, mi; |
| int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; |
int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; |
| int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; |
int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; |
| |
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ |
| int mobilav=0,popforecast=0; |
int mobilav=0,popforecast=0; |
| int hstepm, nhstepm; |
int hstepm, nhstepm; |
| double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; |
double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; |
| |
double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; |
| |
|
| double bage, fage, age, agelim, agebase; |
double bage, fage, age, agelim, agebase; |
| double ftolpl=FTOL; |
double ftolpl=FTOL; |
|
Line 3189 int main(int argc, char *argv[])
|
Line 3436 int main(int argc, char *argv[])
|
| double **varpl; /* Variances of prevalence limits by age */ |
double **varpl; /* Variances of prevalence limits by age */ |
| double *epj, vepp; |
double *epj, vepp; |
| double kk1, kk2; |
double kk1, kk2; |
| double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; |
double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; |
| |
|
| char *alph[]={"a","a","b","c","d","e"}, str[4]; |
char *alph[]={"a","a","b","c","d","e"}, str[4]; |
| |
|
|
Line 3336 int main(int argc, char *argv[])
|
Line 3583 int main(int argc, char *argv[])
|
| ungetc(c,ficpar); |
ungetc(c,ficpar); |
| |
|
| delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); |
| delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ |
/* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */ |
| for(i=1; i <=nlstate; i++){ |
for(i=1; i <=nlstate; i++){ |
| for(j=1; j <=nlstate+ndeath-1; j++){ |
for(j=1; j <=nlstate+ndeath-1; j++){ |
| fscanf(ficpar,"%1d%1d",&i1,&j1); |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
|
Line 3353 int main(int argc, char *argv[])
|
Line 3600 int main(int argc, char *argv[])
|
| } |
} |
| } |
} |
| delti=delti3[1][1]; |
delti=delti3[1][1]; |
| |
|
| |
|
| |
/* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ |
| |
|
| /* Reads comments: lines beginning with '#' */ |
/* Reads comments: lines beginning with '#' */ |
| while((c=getc(ficpar))=='#' && c!= EOF){ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
|
Line 3472 int main(int argc, char *argv[])
|
Line 3722 int main(int argc, char *argv[])
|
| if (s[4][i]==9) s[4][i]=-1; |
if (s[4][i]==9) s[4][i]=-1; |
| printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ |
printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ |
| |
|
| |
for (i=1; i<=imx; i++) |
| |
|
| |
/*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08; |
| |
else weight[i]=1;*/ |
| |
|
| /* Calculation of the number of parameter from char model*/ |
/* Calculation of the number of parameter from char model*/ |
| Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ |
Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ |
| Tprod=ivector(1,15); |
Tprod=ivector(1,15); |
|
Line 3564 int main(int argc, char *argv[])
|
Line 3818 int main(int argc, char *argv[])
|
| |
|
| for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { |
| for(m=2; (m<= maxwav); m++) { |
for(m=2; (m<= maxwav); m++) { |
| if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ |
if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ |
| anint[m][i]=9999; |
anint[m][i]=9999; |
| s[m][i]=-1; |
s[m][i]=-1; |
| } |
} |
| if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; |
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ |
| |
printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown %d, set an arbitrary year of death\n",(int)moisdc[i],(int)andc[i],num[i],i); |
| |
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown %d, set an arbitrary year of death\n",(int)moisdc[i],(int)andc[i],num[i],i); |
| |
s[m][i]=-1; |
| |
} |
| |
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ |
| |
printf("Warning! Month of death of individual %d on line %d was unknown %2d, we set it to June\n",num[i],i,(int)moisdc[i]); |
| |
fprintf(ficlog,"Warning! Month of death of individual %d on line %d was unknown %f, we set it to June\n",num[i],i,moisdc[i]); |
| |
moisdc[i]=6; |
| |
s[m][i]=-1; |
| |
} |
| } |
} |
| } |
} |
| |
|
| for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { |
| agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); |
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); |
| for(m=1; (m<= maxwav); m++){ |
for(m=firstpass; (m<= lastpass); m++){ |
| if(s[m][i] >0){ |
if(s[m][i] >0){ |
| if (s[m][i] >= nlstate+1) { |
if (s[m][i] >= nlstate+1) { |
| if(agedc[i]>0) |
if(agedc[i]>0) |
| if(moisdc[i]!=99 && andc[i]!=9999) |
if((int)moisdc[i]!=99 && (int)andc[i]!=9999) |
| agev[m][i]=agedc[i]; |
agev[m][i]=agedc[i]; |
| /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ |
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ |
| else { |
else { |
| if (andc[i]!=9999){ |
if ((int)andc[i]!=9999){ |
| printf("Warning negative age at death: %d line:%d\n",num[i],i); |
printf("Warning negative age at death: %d line:%d\n",num[i],i); |
| fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); |
fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); |
| agev[m][i]=-1; |
agev[m][i]=-1; |
| } |
} |
| } |
} |
| } |
} |
| else if(s[m][i] !=9){ /* Should no more exist */ |
else if(s[m][i] !=9){ /* Standard case, age in fractional |
| |
years but with the precision of a |
| |
month */ |
| agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); |
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); |
| if(mint[m][i]==99 || anint[m][i]==9999) |
if((int)mint[m][i]==99 || (int)anint[m][i]==9999) |
| agev[m][i]=1; |
agev[m][i]=1; |
| else if(agev[m][i] <agemin){ |
else if(agev[m][i] <agemin){ |
| agemin=agev[m][i]; |
agemin=agev[m][i]; |
|
Line 3615 int main(int argc, char *argv[])
|
Line 3881 int main(int argc, char *argv[])
|
| |
|
| } |
} |
| for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { |
| for(m=1; (m<= maxwav); m++){ |
for(m=firstpass; (m<=lastpass); m++){ |
| if (s[m][i] > (nlstate+ndeath)) { |
if (s[m][i] > (nlstate+ndeath)) { |
| printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
| fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); |
|
Line 3624 int main(int argc, char *argv[])
|
Line 3890 int main(int argc, char *argv[])
|
| } |
} |
| } |
} |
| |
|
| |
/*for (i=1; i<=imx; i++){ |
| |
for (m=firstpass; (m<lastpass); m++){ |
| |
printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]); |
| |
} |
| |
|
| |
}*/ |
| |
|
| printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); |
printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); |
| fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); |
fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); |
| |
|
|
Line 3808 int main(int argc, char *argv[])
|
Line 4081 int main(int argc, char *argv[])
|
| fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); |
fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); |
| fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
| fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
| |
printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
| |
fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); |
| |
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
| ungetc(c,ficpar); |
ungetc(c,ficpar); |
|
Line 3818 int main(int argc, char *argv[])
|
Line 4093 int main(int argc, char *argv[])
|
| ungetc(c,ficpar); |
ungetc(c,ficpar); |
| |
|
| |
|
| dateprev1=anprev1+mprev1/12.+jprev1/365.; |
dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.; |
| dateprev2=anprev2+mprev2/12.+jprev2/365.; |
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
| |
|
| fscanf(ficpar,"pop_based=%d\n",&popbased); |
fscanf(ficpar,"pop_based=%d\n",&popbased); |
| fprintf(ficparo,"pop_based=%d\n",popbased); |
fprintf(ficparo,"pop_based=%d\n",popbased); |
|
Line 3833 int main(int argc, char *argv[])
|
Line 4108 int main(int argc, char *argv[])
|
| } |
} |
| ungetc(c,ficpar); |
ungetc(c,ficpar); |
| |
|
| fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2); |
fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj); |
| fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); |
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
| fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); |
printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
| |
fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
| |
fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
| |
/* day and month of proj2 are not used but only year anproj2.*/ |
| |
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
| ungetc(c,ficpar); |
ungetc(c,ficpar); |
|
Line 3850 int main(int argc, char *argv[])
|
Line 4127 int main(int argc, char *argv[])
|
| fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); |
fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); |
| fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); |
fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); |
| |
|
| |
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); |
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); |
| |
|
| /*------------ gnuplot -------------*/ |
/*------------ gnuplot -------------*/ |
|
Line 3877 int main(int argc, char *argv[])
|
Line 4155 int main(int argc, char *argv[])
|
| Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n |
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n |
| \n |
\n |
| Total number of observations=%d <br>\n |
Total number of observations=%d <br>\n |
| |
Youngest age at first pass %.2f, oldest age %.2f<br>\n |
| Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n |
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n |
| <hr size=\"2\" color=\"#EC5E5E\"> |
<hr size=\"2\" color=\"#EC5E5E\"> |
| <ul><li><h4>Parameter files</h4>\n |
<ul><li><h4>Parameter files</h4>\n |
| - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n |
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n |
| - Log file of the run: <a href=\"%s\">%s</a><br>\n |
- Log file of the run: <a href=\"%s\">%s</a><br>\n |
| - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); |
- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); |
| fclose(fichtm); |
fclose(fichtm); |
| |
|
| printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); |
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); |
| |
|
|
Line 3896 Interval (in months) between two waves:
|
Line 4175 Interval (in months) between two waves:
|
| free_imatrix(mw,1,lastpass-firstpass+1,1,imx); |
free_imatrix(mw,1,lastpass-firstpass+1,1,imx); |
| free_ivector(num,1,n); |
free_ivector(num,1,n); |
| free_vector(agedc,1,n); |
free_vector(agedc,1,n); |
| 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); |
| fclose(ficres); |
fclose(ficres); |
|
Line 3943 Interval (in months) between two waves:
|
Line 4222 Interval (in months) between two waves:
|
| |
|
| for (age=agebase; age<=agelim; age++){ |
for (age=agebase; age<=agelim; age++){ |
| prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); |
| fprintf(ficrespl,"%.0f",age ); |
fprintf(ficrespl,"%.0f ",age ); |
| |
for(j=1;j<=cptcoveff;j++) |
| |
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
| for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
| fprintf(ficrespl," %.5f", prlim[i][i]); |
fprintf(ficrespl," %.5f", prlim[i][i]); |
| fprintf(ficrespl,"\n"); |
fprintf(ficrespl,"\n"); |
|
Line 3971 Interval (in months) between two waves:
|
Line 4252 Interval (in months) between two waves:
|
| |
|
| /* hstepm=1; aff par mois*/ |
/* hstepm=1; aff par mois*/ |
| |
|
| |
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); |
| 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++){ |
| k=k+1; |
k=k+1; |
|
Line 3988 Interval (in months) between two waves:
|
Line 4270 Interval (in months) between two waves:
|
| p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); |
| oldm=oldms;savm=savms; |
oldm=oldms;savm=savms; |
| hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); |
| fprintf(ficrespij,"# Age"); |
fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); |
| for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
| for(j=1; j<=nlstate+ndeath;j++) |
for(j=1; j<=nlstate+ndeath;j++) |
| fprintf(ficrespij," %1d-%1d",i,j); |
fprintf(ficrespij," %1d-%1d",i,j); |
| fprintf(ficrespij,"\n"); |
fprintf(ficrespij,"\n"); |
| for (h=0; h<=nhstepm; h++){ |
for (h=0; h<=nhstepm; h++){ |
| fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); |
fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); |
| for(i=1; i<=nlstate;i++) |
for(i=1; i<=nlstate;i++) |
| for(j=1; j<=nlstate+ndeath;j++) |
for(j=1; j<=nlstate+ndeath;j++) |
| fprintf(ficrespij," %.5f", p3mat[i][j][h]); |
fprintf(ficrespij," %.5f", p3mat[i][j][h]); |
|
Line 4006 Interval (in months) between two waves:
|
Line 4288 Interval (in months) between two waves:
|
| } |
} |
| } |
} |
| |
|
| varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); |
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax); |
| |
|
| fclose(ficrespij); |
fclose(ficrespij); |
| |
|
| |
|
| /*---------- Forecasting ------------------*/ |
/*---------- Forecasting ------------------*/ |
| if((stepm == 1) && (strcmp(model,".")==0)){ |
/*if((stepm == 1) && (strcmp(model,".")==0)){*/ |
| prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); |
if(prevfcast==1){ |
| if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); |
/* if(stepm ==1){*/ |
| } |
prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); |
| else{ |
/* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ |
| erreur=108; |
/* } */ |
| printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); |
/* else{ */ |
| fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); |
/* erreur=108; */ |
| |
/* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */ |
| |
/* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */ |
| |
/* } */ |
| } |
} |
| |
|
| |
|
|
Line 4053 Interval (in months) between two waves:
|
Line 4338 Interval (in months) between two waves:
|
| printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
| fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); |
| |
|
| calagedate=-1; |
/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ |
| |
prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
| prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); |
/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\ |
| |
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); |
| |
*/ |
| |
|
| if (mobilav!=0) { |
if (mobilav!=0) { |
| mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
|
Line 4179 Interval (in months) between two waves:
|
Line 4466 Interval (in months) between two waves:
|
| 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); |
| |
|
| |
free_matrix(covar,0,NCOVMAX,1,n); |
| free_matrix(matcov,1,npar,1,npar); |
free_matrix(matcov,1,npar,1,npar); |
| free_vector(delti,1,npar); |
/*free_vector(delti,1,npar);*/ |
| |
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
| free_matrix(agev,1,maxwav,1,imx); |
free_matrix(agev,1,maxwav,1,imx); |
| free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); |
| if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); |
| |
|
| free_ivector(ncodemax,1,8); |
free_ivector(ncodemax,1,8); |
| free_ivector(Tvar,1,15); |
free_ivector(Tvar,1,15); |
| free_ivector(Tprod,1,15); |
free_ivector(Tprod,1,15); |
|
Line 4192 Interval (in months) between two waves:
|
Line 4483 Interval (in months) between two waves:
|
| free_ivector(Tage,1,15); |
free_ivector(Tage,1,15); |
| free_ivector(Tcode,1,100); |
free_ivector(Tcode,1,100); |
| |
|
| fprintf(fichtm,"\n</body>"); |
/* fclose(fichtm);*/ |
| fclose(fichtm); |
/* fclose(ficgp);*/ /* ALready done */ |
| fclose(ficgp); |
|
| |
|
| |
|
| if(erreur >0){ |
if(erreur >0){ |
|
Line 4223 Interval (in months) between two waves:
|
Line 4513 Interval (in months) between two waves:
|
| strcpy(plotcmd,GNUPLOTPROGRAM); |
strcpy(plotcmd,GNUPLOTPROGRAM); |
| strcat(plotcmd," "); |
strcat(plotcmd," "); |
| strcat(plotcmd,optionfilegnuplot); |
strcat(plotcmd,optionfilegnuplot); |
| printf("Starting: %s\n",plotcmd);fflush(stdout); |
printf("Starting graphs with: %s",plotcmd);fflush(stdout); |
| system(plotcmd); |
system(plotcmd); |
| |
printf(" Wait..."); |
| |
|
| /*#ifdef windows*/ |
/*#ifdef windows*/ |
| while (z[0] != 'q') { |
while (z[0] != 'q') { |
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