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version 1.70, 2003/02/05 12:40:38
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version 1.77, 2003/05/16 16:49:47
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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 . |
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|
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Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach |
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or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so |
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| **********************************************************************/ |
**********************************************************************/ |
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/* |
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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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|
| #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 0.92, February 2003, 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
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Line 141 double jmean; /* Mean space between 2 wa
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| 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
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Line 224 static int split( char *path, char *dirc
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| 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
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| } |
} |
| |
|
| /************************ivector *******************************/ |
/************************ivector *******************************/ |
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char *cvector(long nl,long nh) |
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{ |
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char *v; |
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v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char))); |
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if (!v) nrerror("allocation failure in cvector"); |
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return v-nl+NR_END; |
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} |
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|
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/******************free ivector **************************/ |
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void free_cvector(char *v, long nl, long nh) |
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{ |
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free((FREE_ARG)(v+nl-NR_END)); |
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} |
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|
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/************************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
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Line 410 double **matrix(long nrl, long nrh, long
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|
| 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]) |
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*/ |
| } |
} |
| |
|
| /*************************free matrix ************************/ |
/*************************free matrix ************************/ |
|
Line 404 double ***ma3x(long nrl, long nrh, long
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Line 451 double ***ma3x(long nrl, long nrh, long
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| 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]) |
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&(m[i][j][k]) <=> *((*(m+i) + j)+k) |
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*/ |
| } |
} |
| |
|
| /*************************free ma3x ************************/ |
/*************************free ma3x ************************/ |
|
Line 612 void powell(double p[], double **xi, int
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Line 662 void powell(double p[], double **xi, int
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| 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]); |
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fprintf(ficrespow," %.12lf", p[i]); |
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} |
| 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 972 double func( double *x)
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Line 1026 double func( double *x)
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| * is higher than the multiple of stepm and negative otherwise. |
* 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]));*/ |
/* 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]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ |
if( s2 > nlstate){ |
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/* i.e. if s2 is a death state and if the date of death is known then the contribution |
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to the likelihood is the probability to die between last step unit time and current |
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step unit time, which is also the differences between probability to die before dh |
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and probability to die before dh-stepm . |
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In version up to 0.92 likelihood was computed |
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as if date of death was unknown. Death was treated as any other |
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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 |
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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 |
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introduced the exact date of death then we should have modified |
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the contribution of an exact death to the likelihood. This new |
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contribution is smaller and very dependent of the step unit |
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stepm. It is no more the probability to die between last interview |
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and month of death but the probability to survive from last |
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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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*/ |
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lli=log(out[s1][s2] - savm[s1][s2]); |
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}else{ |
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lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ |
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/* 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]);*/ |
/*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); */ |
| ipmx +=1; |
ipmx +=1; |
| sw += weight[i]; |
sw += weight[i]; |
| 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 */ |
|
Line 1123 double func( double *x)
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Line 1204 double func( double *x)
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| 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"); |
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strcat(filerespow,fileres); |
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if((ficrespow=fopen(filerespow,"w"))==NULL) { |
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printf("Problem with resultfile: %s\n", filerespow); |
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fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
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} |
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fprintf(ficrespow,"# Powell\n# iter -2*LL"); |
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for (i=1;i<=nlstate;i++) |
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for(j=1;j<=nlstate+ndeath;j++) |
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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); |
| |
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(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 1396 void lubksb(double **a, int n, int *indx
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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 1416 void freqsummary(char fileres[], int ag
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Line 1510 void freqsummary(char fileres[], int ag
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| 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 1431 void freqsummary(char fileres[], int ag
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Line 1525 void freqsummary(char fileres[], int ag
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| 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 1447 void freqsummary(char fileres[], int ag
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Line 1545 void freqsummary(char fileres[], int ag
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| 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 1474 void freqsummary(char fileres[], int ag
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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 1506 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 1520 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 1538 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 1549 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, int firstpass, int lastpass) |
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) |
| { |
{ |
| /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people |
/* 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). |
in each health status at the date of interview (if between dateprev1 and dateprev2). |
|
Line 1565 void prevalence(int agemin, float agemax
|
Line 1665 void prevalence(int agemin, float agemax
|
| |
|
| 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; |
double pos,posprop; |
| double y2; /* in fractional years */ |
double y2; /* in fractional years */ |
| |
int iagemin, iagemax; |
| |
|
| pp=vector(1,nlstate); |
iagemin= (int) agemin; |
| |
iagemax= (int) agemax; |
| freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); |
/*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 1581 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++) { /* Each individual */ |
for (i=1; i<=imx; i++) { /* Each individual */ |
| bool=1; |
bool=1; |
|
Line 1597 void prevalence(int agemin, float agemax
|
Line 1699 void prevalence(int agemin, float agemax
|
| for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ |
for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ |
| y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ |
y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ |
| if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ |
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); |
| freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; |
if (s[m][i]>0 && s[m][i]<=nlstate) { |
| freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += 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]]);*/ |
| } |
prop[s[m][i]][(int)agev[m][i]] += weight[i]; |
| |
prop[s[m][i]][iagemax+3] += weight[i]; |
| |
} |
| } |
} |
| } /* end selection of waves */ |
} /* 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(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) |
|
| pp[jk] += freq[jk][m][i]; |
|
| } |
|
| |
|
| for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; |
|
| |
|
| for(jk=1; jk <=nlstate ; jk++){ |
for(jk=1,posprop=0; jk <=nlstate ; jk++) { |
| if( i <= (int) agemax){ |
posprop += prop[jk][i]; |
| if(pos>=1.e-5){ |
} |
| probs[i][jk][j1]= pp[jk]/pos; |
|
| } |
for(jk=1; jk <=nlstate ; jk++){ |
| } |
if( i <= iagemax){ |
| }/* end jk */ |
if(posprop>=1.e-5){ |
| }/* end i */ |
probs[i][jk][j1]= prop[jk][i]/posprop; |
| |
} |
| |
} |
| |
}/* 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 1683 void concatwav(int wav[], int **dh, int
|
Line 1775 void concatwav(int wav[], int **dh, int
|
| wav[i]=mi; |
wav[i]=mi; |
| if(mi==0){ |
if(mi==0){ |
| if(first==0){ |
if(first==0){ |
| printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i); |
printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i); |
| first=1; |
first=1; |
| } |
} |
| if(first==1){ |
if(first==1){ |
| fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i); |
fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i); |
| } |
} |
| } /* end mi==0 */ |
} /* end mi==0 */ |
| } |
} /* End individuals */ |
| |
|
| for(i=1; i<=imx; i++){ |
for(i=1; i<=imx; i++){ |
| for(mi=1; mi<wav[i];mi++){ |
for(mi=1; mi<wav[i];mi++){ |
| if (stepm <=0) |
if (stepm <=0) |
| dh[mi][i]=1; |
dh[mi][i]=1; |
| else{ |
else{ |
| if (s[mw[mi+1][i]][i] > nlstate) { |
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ |
| if (agedc[i] < 2*AGESUP) { |
if (agedc[i] < 2*AGESUP) { |
| j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); |
j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); |
| if(j==0) j=1; /* Survives at least one month after exam */ |
if(j==0) j=1; /* Survives at least one month after exam */ |
|
Line 1705 void concatwav(int wav[], int **dh, int
|
Line 1797 void concatwav(int wav[], int **dh, int
|
| if (j >= jmax) jmax=j; |
if (j >= jmax) jmax=j; |
| 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 %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ |
| |
if(j<0)printf("Warning! Negative delay (%d) between waves %d and %d of individual at line %d who is aged %.1f with statuses %d %d\n ",j,mw[mi][i],mw[mi+1][i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); |
| } |
} |
| } |
} |
| else{ |
else{ |
|
Line 1716 void concatwav(int wav[], int **dh, int
|
Line 1809 void concatwav(int wav[], int **dh, int
|
| 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]);*/ |
| |
if(j<0)printf("Warning! Negative delay (%d to death) between waves %d and %d of individual at line %d who is aged %.1f with statuses %d %d\n ",j,mw[mi][i],mw[mi+1][i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); |
| sum=sum+j; |
sum=sum+j; |
| } |
} |
| jk= j/stepm; |
jk= j/stepm; |
|
Line 1744 void concatwav(int wav[], int **dh, int
|
Line 1839 void concatwav(int wav[], int **dh, int
|
| if(dh[mi][i]==0){ |
if(dh[mi][i]==0){ |
| dh[mi][i]=1; /* At least one step */ |
dh[mi][i]=1; /* At least one step */ |
| bh[mi][i]=ju; /* 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); |
/* 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);*/ |
| } |
} |
| } |
} |
| } /* end if mle */ |
} /* end if mle */ |
|
Line 1829 void evsij(char fileres[], double ***eij
|
Line 1924 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 1878 void evsij(char fileres[], double ***eij
|
Line 1973 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 1917 void evsij(char fileres[], double ***eij
|
Line 2012 void evsij(char fileres[], double ***eij
|
| for(i=1;i<=nlstate;i++){ |
for(i=1;i<=nlstate;i++){ |
| cptj=cptj+1; |
cptj=cptj+1; |
| for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ |
for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ |
| |
|
| gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; |
gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; |
| } |
} |
| } |
} |
| } |
} |
| 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 1929 void evsij(char fileres[], double ***eij
|
Line 2025 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 1971 void evsij(char fileres[], double ***eij
|
Line 2067 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 2279 void varevsij(char optionfilefiname[], d
|
Line 2375 void varevsij(char optionfilefiname[], d
|
| 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)) t \"95\%% interval\" w l 2 ",fileresprobmorprev); |
| fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not 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", estepm,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 2518 void varprob(char optionfilefiname[], do
|
Line 2614 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 2531 void varprob(char optionfilefiname[], do
|
Line 2627 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 2543 void varprob(char optionfilefiname[], do
|
Line 2639 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 2730 fprintf(fichtm," \n<ul><li><b>Graphs</b>
|
Line 2826 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 2761 health expectancies in states (1) and (2
|
Line 2857 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 2783 fprintf(fichtm," <ul><li><b>Graphs</b></
|
Line 2879 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 2884 m=pow(2,cptcoveff);
|
Line 2980 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 3020 prevforecast(char fileres[], double anpr
|
Line 3116 prevforecast(char fileres[], double anpr
|
| dateprev1 dateprev2 range of dates during which prevalence is computed |
dateprev1 dateprev2 range of dates during which prevalence is computed |
| anproj2 year of en of projection (same day and month as proj1). |
anproj2 year of en of projection (same day and month as proj1). |
| */ |
*/ |
| int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h; |
int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1; |
| int *popage; |
int *popage; |
| double agec; /* generic age */ |
double agec; /* generic age */ |
| double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; |
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; |
|
Line 3053 prevforecast(char fileres[], double anpr
|
Line 3149 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){ |
| hstepm=1; |
printf ("Problem %d lower than %d\n",estepm, stepm); |
| |
} |
| |
else hstepm=estepm; |
| |
|
| hstepm=hstepm/stepm; |
hstepm=hstepm/stepm; |
| yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and |
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and |
| fractional in yp1 */ |
fractional in yp1 */ |
|
Line 3065 prevforecast(char fileres[], double anpr
|
Line 3164 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,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); |
fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); |
| |
|
| fprintf(ficresf,"#****** Routine prevforecast **\n"); |
fprintf(ficresf,"#****** Routine prevforecast **\n"); |
| for(cptcov=1, k=0;cptcov<=cptcoveff;cptcov++){ |
|
| |
/* 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#******"); |
|
Line 3083 prevforecast(char fileres[], double anpr
|
Line 3187 prevforecast(char fileres[], double anpr
|
| fprintf(ficresf," p%d%d",i,j); |
fprintf(ficresf," p%d%d",i,j); |
| fprintf(ficresf," p.%d",j); |
fprintf(ficresf," p.%d",j); |
| } |
} |
| for (yearp=0; yearp<=(anproj2-anproj1);yearp++) { |
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+yearp); |
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); |
| |
|
| for (agec=fage; agec>=ageminpar; agec--){ |
for (agec=fage; agec>=(ageminpar-1); agec--){ |
| nhstepm=(int) rint((agelim-agec)*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); |
|
Line 3095 prevforecast(char fileres[], double anpr
|
Line 3199 prevforecast(char fileres[], double anpr
|
| hpxij(p3mat,nhstepm,agec,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) (YEARM*yearp)) { |
if (h*hstepm/YEARM*stepm ==yearp) { |
| fprintf(ficresf,"\n"); |
fprintf(ficresf,"\n"); |
| for(j=1;j<=cptcoveff;j++) |
for(j=1;j<=cptcoveff;j++) |
| fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); |
|
Line 3103 prevforecast(char fileres[], double anpr
|
Line 3207 prevforecast(char fileres[], double anpr
|
| } |
} |
| for(j=1; j<=nlstate+ndeath;j++) { |
for(j=1; j<=nlstate+ndeath;j++) { |
| ppij=0.; |
ppij=0.; |
| for(i=1; i<=nlstate;i++) { |
for(i=1; i<=nlstate;i++) { |
| if (mobilav==1) |
if (mobilav==1) |
| ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec+1][i][cptcod]; |
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; |
| else { |
else { |
| ppij=ppij+p3mat[i][j][h]*probs[(int)(agec+1)][i][cptcod]; |
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; |
| } |
} |
| if (h==(int)(YEARM*yearp)) |
if (h*hstepm/YEARM*stepm== yearp) { |
| fprintf(ficresf," %.3f", p3mat[i][j][h]); |
fprintf(ficresf," %.3f", p3mat[i][j][h]); |
| } |
} |
| if (h==(int)(YEARM*yearp)){ |
} /* end i */ |
| |
if (h*hstepm/YEARM*stepm==yearp) { |
| fprintf(ficresf," %.3f", ppij); |
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); |
| |
|
|
Line 3295 populforecast(char fileres[], double anp
|
Line 3400 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 3317 int main(int argc, char *argv[])
|
Line 3422 int main(int argc, char *argv[])
|
| int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ |
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; |
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 3332 int main(int argc, char *argv[])
|
Line 3438 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 3479 int main(int argc, char *argv[])
|
Line 3585 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 3496 int main(int argc, char *argv[])
|
Line 3602 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 3615 int main(int argc, char *argv[])
|
Line 3724 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 3707 int main(int argc, char *argv[])
|
Line 3820 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, you must set an arbitrary year of death or he/she is skipped and results are biased\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, you must set an arbitrary year of death or he/she is skipped and results are biased\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("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); |
| |
fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); |
| |
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; |
|
Line 3736 int main(int argc, char *argv[])
|
Line 3858 int main(int argc, char *argv[])
|
| years but with the precision of a |
years but with the precision of a |
| month */ |
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 3760 int main(int argc, char *argv[])
|
Line 3882 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 3769 int main(int argc, char *argv[])
|
Line 3891 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 3982 int main(int argc, char *argv[])
|
Line 4111 int main(int argc, char *argv[])
|
| |
|
| 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); |
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,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
| printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobilaverage=%d\n",&prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj); |
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 mobilaverage=%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 mobilaverage=%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.*/ |
/* day and month of proj2 are not used but only year anproj2.*/ |
| |
|
| while((c=getc(ficpar))=='#' && c!= EOF){ |
while((c=getc(ficpar))=='#' && c!= EOF){ |
|
Line 3999 int main(int argc, char *argv[])
|
Line 4128 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 4026 int main(int argc, char *argv[])
|
Line 4156 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 (selected) 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 4158 Interval (in months) between two waves:
|
Line 4289 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); |
| |
|
|
Line 4166 Interval (in months) between two waves:
|
Line 4297 Interval (in months) between two waves:
|
| /*---------- Forecasting ------------------*/ |
/*---------- Forecasting ------------------*/ |
| /*if((stepm == 1) && (strcmp(model,".")==0)){*/ |
/*if((stepm == 1) && (strcmp(model,".")==0)){*/ |
| if(prevfcast==1){ |
if(prevfcast==1){ |
| if(stepm ==1){ |
/* if(stepm ==1){*/ |
| prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); |
prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); |
| if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); |
/* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ |
| } |
/* } */ |
| else{ |
/* else{ */ |
| erreur=108; |
/* 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); |
/* 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); |
/* 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 4208 Interval (in months) between two waves:
|
Line 4339 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); |
| |
|
| prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); |
/* 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); |
| |
/* 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 4335 Interval (in months) between two waves:
|
Line 4470 Interval (in months) between two waves:
|
| |
|
| free_matrix(covar,0,NCOVMAX,1,n); |
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 4346 Interval (in months) between two waves:
|
Line 4484 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 4377 Interval (in months) between two waves:
|
Line 4514 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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