version 1.192, 2015/07/16 16:49:02
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version 1.197, 2015/09/01 18:24:39
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.197 2015/09/01 18:24:39 brouard |
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*** empty log message *** |
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Revision 1.196 2015/08/18 23:17:52 brouard |
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Summary: 0.98q5 |
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Revision 1.195 2015/08/18 16:28:39 brouard |
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Summary: Adding a hack for testing purpose |
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After reading the title, ftol and model lines, if the comment line has |
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a q, starting with #q, the answer at the end of the run is quit. It |
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permits to run test files in batch with ctest. The former workaround was |
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$ echo q | imach foo.imach |
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Revision 1.194 2015/08/18 13:32:00 brouard |
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Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line. |
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Revision 1.193 2015/08/04 07:17:42 brouard |
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Summary: 0.98q4 |
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Revision 1.192 2015/07/16 16:49:02 brouard |
Revision 1.192 2015/07/16 16:49:02 brouard |
Summary: Fixing some outputs |
Summary: Fixing some outputs |
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Line 677 typedef struct {
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Line 697 typedef struct {
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#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ |
#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ |
#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ |
#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ |
#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ |
#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ |
#define codtabm(h,k) 1 & (h-1) >> (k-1) ; |
#define codtabm(h,k) (1 & (h-1) >> (k-1))+1 |
#define MAXN 20000 |
#define MAXN 20000 |
#define YEARM 12. /**< Number of months per year */ |
#define YEARM 12. /**< Number of months per year */ |
#define AGESUP 130 |
#define AGESUP 130 |
#define AGEBASE 40 |
#define AGEBASE 40 |
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#define AGEOVERFLOW 1.e20 |
#define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ |
#define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */ |
#ifdef _WIN32 |
#ifdef _WIN32 |
#define DIRSEPARATOR '\\' |
#define DIRSEPARATOR '\\' |
Line 695 typedef struct {
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Line 716 typedef struct {
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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#include "version.h" |
char version[]="Imach version 0.98q3, July 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; |
char version[]=__IMACH_VERSION__; |
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char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; |
char fullversion[]="$Revision$ $Date$"; |
char fullversion[]="$Revision$ $Date$"; |
char strstart[80]; |
char strstart[80]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
Line 831 int estepm;
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Line 853 int estepm;
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int m,nb; |
int m,nb; |
long *num; |
long *num; |
int firstpass=0, lastpass=4,*cod, *Tage,*cens; |
int firstpass=0, lastpass=4,*cod, *cens; |
int *ncodemax; /* ncodemax[j]= Number of modalities of the j th |
int *ncodemax; /* ncodemax[j]= Number of modalities of the j th |
covariate for which somebody answered excluding |
covariate for which somebody answered excluding |
undefined. Usually 2: 0 and 1. */ |
undefined. Usually 2: 0 and 1. */ |
Line 851 double **covar; /**< covar[j,i], value
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Line 873 double **covar; /**< covar[j,i], value
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* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ |
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ |
double idx; |
double idx; |
int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ |
int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ |
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int *Tage; |
int *Ndum; /** Freq of modality (tricode */ |
int *Ndum; /** Freq of modality (tricode */ |
int **codtab; /**< codtab=imatrix(1,100,1,10); */ |
int **codtab; /**< codtab=imatrix(1,100,1,10); */ |
int **Tvard, *Tprod, cptcovprod, *Tvaraff; |
int **Tvard, *Tprod, cptcovprod, *Tvaraff; |
Line 1889 double **prevalim(double **prlim, int nl
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Line 1912 double **prevalim(double **prlim, int nl
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cov[3]= agefin*agefin;; |
cov[3]= agefin*agefin;; |
for (k=1; k<=cptcovn;k++) { |
for (k=1; k<=cptcovn;k++) { |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; |
/*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/ |
/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/ |
} |
} |
/*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
/*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ |
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; |
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; |
Line 2891 void lubksb(double **a, int n, int *indx
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Line 2914 void lubksb(double **a, int n, int *indx
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void pstamp(FILE *fichier) |
void pstamp(FILE *fichier) |
{ |
{ |
fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); |
fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart); |
} |
} |
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/************ Frequencies ********************/ |
/************ Frequencies ********************/ |
Line 3375 void tricode(int *Tvar, int **nbcode, in
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Line 3398 void tricode(int *Tvar, int **nbcode, in
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nbcode[Tvar[j]][1]=0; |
nbcode[Tvar[j]][1]=0; |
nbcode[Tvar[j]][2]=1; |
nbcode[Tvar[j]][2]=1; |
nbcode[Tvar[j]][3]=2; |
nbcode[Tvar[j]][3]=2; |
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To be continued (not working yet). |
*/ |
*/ |
ij=0; /* ij is similar to i but can jumps over null modalities */ |
ij=0; /* ij is similar to i but can jump over null modalities */ |
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/ |
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ |
if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */ |
if (Ndum[i] == 0) { /* If nobody responded to this modality k */ |
break; |
break; |
} |
} |
ij++; |
ij++; |
nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/ |
nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/ |
cptcode = ij; /* New max modality for covar j */ |
cptcode = ij; /* New max modality for covar j */ |
} /* end of loop on modality i=-1 to 1 or more */ |
} /* end of loop on modality i=-1 to 1 or more */ |
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Line 4211 void varprob(char optionfilefiname[], do
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Line 4235 void varprob(char optionfilefiname[], do
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fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n"); |
fprintf(fichtm,"\n"); |
fprintf(fichtm,"\n"); |
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fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov); |
fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov); |
fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\ |
fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov); |
file %s<br>\n",optionfilehtmcov); |
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \ |
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\ |
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and drawn. It helps understanding how is the covariance between two incidences.\ |
and drawn. It helps understanding how is the covariance between two incidences.\ |
They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n"); |
They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n"); |
fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \ |
fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \ |
Line 4536 fprintf(fichtm," \n<ul><li><b>Graphs</b>
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Line 4559 fprintf(fichtm," \n<ul><li><b>Graphs</b>
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}/* End k1 */ |
}/* End k1 */ |
fprintf(fichtm,"</ul>"); |
fprintf(fichtm,"</ul>"); |
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fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ |
\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\ |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres); |
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \ |
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- 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \ |
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But because parameters are usually highly correlated (a higher incidence of disability \ |
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and a higher incidence of recovery can give very close observed transition) it might \ |
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be very useful to look not only at linear confidence intervals estimated from the \ |
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variances but at the covariance matrix. And instead of looking at the estimated coefficients \ |
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(parameters) of the logistic regression, it might be more meaningful to visualize the \ |
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covariance matrix of the one-step probabilities. \ |
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See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres); |
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fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); |
subdirf2(fileres,"prob"),subdirf2(fileres,"prob")); |
fprintf(fichtm,"\ |
fprintf(fichtm,"\ |
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
- Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n", |
Line 4795 plot [%.f:%.f] ", ageminpar, agemaxpar)
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Line 4825 plot [%.f:%.f] ", ageminpar, agemaxpar)
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fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); |
fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); |
ij=1;/* To be checked else nbcode[0][0] wrong */ |
ij=1;/* To be checked else nbcode[0][0] wrong */ |
for(j=3; j <=ncovmodel-nagesqr; j++) { |
for(j=3; j <=ncovmodel-nagesqr; j++) { |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */ |
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ |
fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
if(ij <=cptcovage) { /* Bug valgrind */ |
ij++; |
if((j-2)==Tage[ij]) { /* Bug valgrind */ |
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fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
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ij++; |
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} |
} |
} |
else |
else |
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
Line 4812 plot [%.f:%.f] ", ageminpar, agemaxpar)
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Line 4845 plot [%.f:%.f] ", ageminpar, agemaxpar)
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ij=1; |
ij=1; |
for(j=3; j <=ncovmodel-nagesqr; j++){ |
for(j=3; j <=ncovmodel-nagesqr; j++){ |
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { |
if(ij <=cptcovage) { /* Bug valgrind */ |
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
if((j-2)==Tage[ij]) { /* Bug valgrind */ |
ij++; |
fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); |
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ij++; |
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} |
} |
} |
else |
else |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); |
Line 5433 int readdata(char datafile[], int firsto
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Line 5468 int readdata(char datafile[], int firsto
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if((fic=fopen(datafile,"r"))==NULL) { |
if((fic=fopen(datafile,"r"))==NULL) { |
printf("Problem while opening datafile: %s\n", datafile);return 1; |
printf("Problem while opening datafile: %s\n", datafile);fflush(stdout); |
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; |
fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1; |
} |
} |
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i=1; |
i=1; |
Line 6260 int main(int argc, char *argv[])
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Line 6295 int main(int argc, char *argv[])
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int jj, ll, li, lj, lk; |
int jj, ll, li, lj, lk; |
int numlinepar=0; /* Current linenumber of parameter file */ |
int numlinepar=0; /* Current linenumber of parameter file */ |
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int num_filled; |
int itimes; |
int itimes; |
int NDIM=2; |
int NDIM=2; |
int vpopbased=0; |
int vpopbased=0; |
Line 6269 int main(int argc, char *argv[])
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Line 6305 int main(int argc, char *argv[])
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/* FILE *ficgp;*/ /*Gnuplot File */ |
/* FILE *ficgp;*/ /*Gnuplot File */ |
struct stat info; |
struct stat info; |
double agedeb=0.; |
double agedeb=0.; |
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; |
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double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW; |
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double fret; |
double fret; |
double dum=0.; /* Dummy variable */ |
double dum=0.; /* Dummy variable */ |
Line 6277 int main(int argc, char *argv[])
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Line 6314 int main(int argc, char *argv[])
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double ***mobaverage; |
double ***mobaverage; |
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char line[MAXLINE]; |
char line[MAXLINE]; |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE]; |
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char model[MAXLINE], modeltemp[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
char *tok, *val; /* pathtot */ |
char *tok, *val; /* pathtot */ |
int firstobs=1, lastobs=10; |
int firstobs=1, lastobs=10; |
int c, h , cpt; |
int c, h , cpt, c2; |
int jl=0; |
int jl=0; |
int i1, j1, jk, stepsize=0; |
int i1, j1, jk, stepsize=0; |
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int count=0; |
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int *tab; |
int *tab; |
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; |
Line 6355 int main(int argc, char *argv[])
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Line 6396 int main(int argc, char *argv[])
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getcwd(pathcd, size); |
getcwd(pathcd, size); |
#endif |
#endif |
syscompilerinfo(0); |
syscompilerinfo(0); |
printf("\n%s\n%s",version,fullversion); |
printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion); |
if(argc <=1){ |
if(argc <=1){ |
printf("\nEnter the parameter file name: "); |
printf("\nEnter the parameter file name: "); |
fgets(pathr,FILENAMELENGTH,stdin); |
fgets(pathr,FILENAMELENGTH,stdin); |
Line 6419 int main(int argc, char *argv[])
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Line 6460 int main(int argc, char *argv[])
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goto end; |
goto end; |
} |
} |
fprintf(ficlog,"Log filename:%s\n",filelog); |
fprintf(ficlog,"Log filename:%s\n",filelog); |
fprintf(ficlog,"\n%s\n%s",version,fullversion); |
fprintf(ficlog,"Version %s %s",version,fullversion); |
fprintf(ficlog,"\nEnter the parameter file name: \n"); |
fprintf(ficlog,"\nEnter the parameter file name: \n"); |
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ |
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ |
path=%s \n\ |
path=%s \n\ |
Line 6427 int main(int argc, char *argv[])
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Line 6468 int main(int argc, char *argv[])
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optionfilext=%s\n\ |
optionfilext=%s\n\ |
optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); |
optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); |
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syscompilerinfo(0); |
syscompilerinfo(1); |
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printf("Local time (at start):%s",strstart); |
printf("Local time (at start):%s",strstart); |
fprintf(ficlog,"Local time (at start): %s",strstart); |
fprintf(ficlog,"Local time (at start): %s",strstart); |
Line 6463 int main(int argc, char *argv[])
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Line 6504 int main(int argc, char *argv[])
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/* Reads comments: lines beginning with '#' */ |
/* Reads comments: lines beginning with '#' */ |
numlinepar=0; |
numlinepar=0; |
while((c=getc(ficpar))=='#' && c!= EOF){ |
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ungetc(c,ficpar); |
/* First parameter line */ |
fgets(line, MAXLINE, ficpar); |
while(fgets(line, MAXLINE, ficpar)) { |
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/* If line starts with a # it is a comment */ |
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if (line[0] == '#') { |
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numlinepar++; |
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fputs(line,stdout); |
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fputs(line,ficparo); |
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fputs(line,ficlog); |
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continue; |
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}else |
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break; |
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} |
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if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \ |
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title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ |
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if (num_filled != 5) { |
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printf("Should be 5 parameters\n"); |
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} |
numlinepar++; |
numlinepar++; |
fputs(line,stdout); |
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); |
fputs(line,ficparo); |
} |
fputs(line,ficlog); |
/* Second parameter line */ |
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while(fgets(line, MAXLINE, ficpar)) { |
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/* If line starts with a # it is a comment */ |
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if (line[0] == '#') { |
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numlinepar++; |
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fputs(line,stdout); |
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fputs(line,ficparo); |
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fputs(line,ficlog); |
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continue; |
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}else |
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break; |
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} |
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if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \ |
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&ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){ |
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if (num_filled != 8) { |
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printf("Not 8\n"); |
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} |
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printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt); |
} |
} |
ungetc(c,ficpar); |
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|
|
fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); |
/* Third parameter line */ |
numlinepar++; |
while(fgets(line, MAXLINE, ficpar)) { |
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); |
/* If line starts with a # it is a comment */ |
|
if (line[0] == '#') { |
|
numlinepar++; |
|
fputs(line,stdout); |
|
fputs(line,ficparo); |
|
fputs(line,ficlog); |
|
continue; |
|
}else |
|
break; |
|
} |
|
if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){ |
|
if (num_filled != 1) { |
|
printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); |
|
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); |
|
model[0]='\0'; |
|
goto end; |
|
} |
|
else{ |
|
if (model[0]=='+'){ |
|
for(i=1; i<=strlen(model);i++) |
|
modeltemp[i-1]=model[i]; |
|
} |
|
strcpy(model,modeltemp); |
|
} |
|
printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); |
|
} |
|
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ |
|
/* numlinepar=numlinepar+3; /\* In general *\/ */ |
|
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ |
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ |
if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ |
model[strlen(model)-1]='\0'; |
model[strlen(model)-1]='\0'; |
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); |
fflush(ficlog); |
fflush(ficlog); |
/* if(model[0]=='#'|| model[0]== '\0'){ */ |
/* if(model[0]=='#'|| model[0]== '\0'){ */ |
if(model[0]=='#'){ |
if(model[0]=='#'){ |
Line 6495 int main(int argc, char *argv[])
|
Line 6595 int main(int argc, char *argv[])
|
ungetc(c,ficpar); |
ungetc(c,ficpar); |
fgets(line, MAXLINE, ficpar); |
fgets(line, MAXLINE, ficpar); |
numlinepar++; |
numlinepar++; |
|
if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */ |
|
z[0]=line[1]; |
|
} |
|
/* printf("****line [1] = %c \n",line[1]); */ |
fputs(line, stdout); |
fputs(line, stdout); |
//puts(line); |
//puts(line); |
fputs(line,ficparo); |
fputs(line,ficparo); |
Line 6561 int main(int argc, char *argv[])
|
Line 6665 int main(int argc, char *argv[])
|
if(jj==i) continue; |
if(jj==i) continue; |
j++; |
j++; |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
if ((i1 != i) && (j1 != j)){ |
if ((i1 != i) || (j1 != jj)){ |
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ |
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ |
It might be a problem of design; if ncovcol and the model are correct\n \ |
It might be a problem of design; if ncovcol and the model are correct\n \ |
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); |
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1); |
Line 6569 run imach with mle=-1 to get a correct t
|
Line 6673 run imach with mle=-1 to get a correct t
|
} |
} |
fprintf(ficparo,"%1d%1d",i1,j1); |
fprintf(ficparo,"%1d%1d",i1,j1); |
if(mle==1) |
if(mle==1) |
printf("%1d%1d",i,j); |
printf("%1d%1d",i,jj); |
fprintf(ficlog,"%1d%1d",i,j); |
fprintf(ficlog,"%1d%1d",i,jj); |
for(k=1; k<=ncovmodel;k++){ |
for(k=1; k<=ncovmodel;k++){ |
fscanf(ficpar," %lf",¶m[i][j][k]); |
fscanf(ficpar," %lf",¶m[i][j][k]); |
if(mle==1){ |
if(mle==1){ |
Line 6651 run imach with mle=-1 to get a correct t
|
Line 6755 run imach with mle=-1 to get a correct t
|
for(i=1; i <=npar; i++) |
for(i=1; i <=npar; i++) |
for(j=1; j <=npar; j++) matcov[i][j]=0.; |
for(j=1; j <=npar; j++) matcov[i][j]=0.; |
|
|
|
/* Scans npar lines */ |
for(i=1; i <=npar; i++){ |
for(i=1; i <=npar; i++){ |
fscanf(ficpar,"%s",str); |
count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk); |
|
if(count != 3){ |
|
printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ |
|
This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); |
|
fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ |
|
This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); |
|
exit(1); |
|
}else |
if(mle==1) |
if(mle==1) |
printf("%s",str); |
printf("%1d%1d%1d",i1,j1,jk); |
fprintf(ficlog,"%s",str); |
fprintf(ficlog,"%1d%1d%1d",i1,j1,jk); |
fprintf(ficparo,"%s",str); |
fprintf(ficparo,"%1d%1d%1d",i1,j1,jk); |
for(j=1; j <=i; j++){ |
for(j=1; j <=i; j++){ |
fscanf(ficpar," %le",&matcov[i][j]); |
fscanf(ficpar," %le",&matcov[i][j]); |
if(mle==1){ |
if(mle==1){ |
Line 6672 run imach with mle=-1 to get a correct t
|
Line 6786 run imach with mle=-1 to get a correct t
|
fprintf(ficlog,"\n"); |
fprintf(ficlog,"\n"); |
fprintf(ficparo,"\n"); |
fprintf(ficparo,"\n"); |
} |
} |
|
/* End of read covariance matrix npar lines */ |
for(i=1; i <=npar; i++) |
for(i=1; i <=npar; i++) |
for(j=i+1;j<=npar;j++) |
for(j=i+1;j<=npar;j++) |
matcov[i][j]=matcov[j][i]; |
matcov[i][j]=matcov[j][i]; |
Line 6810 run imach with mle=-1 to get a correct t
|
Line 6925 run imach with mle=-1 to get a correct t
|
|
|
m=pow(2,cptcoveff); |
m=pow(2,cptcoveff); |
|
|
for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ |
|
for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ |
|
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ |
|
for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ |
|
h++; |
|
if (h>m) |
|
h=1; |
|
/**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 |
/**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 |
* For k=4 covariates, h goes from 1 to 2**k |
* For k=4 covariates, h goes from 1 to 2**k |
* codtabm(h,k)= 1 & (h-1) >> (k-1) ; |
* codtabm(h,k)= 1 & (h-1) >> (k-1) ; |
Line 6830 run imach with mle=-1 to get a correct t
|
Line 6938 run imach with mle=-1 to get a correct t
|
* 6 2 1 2 1 |
* 6 2 1 2 1 |
* 7 i=4 1 2 2 1 |
* 7 i=4 1 2 2 1 |
* 8 2 2 2 1 |
* 8 2 2 2 1 |
* 9 i=5 1 i=3 1 i=2 1 1 |
* 9 i=5 1 i=3 1 i=2 1 2 |
* 10 2 1 1 1 |
* 10 2 1 1 2 |
* 11 i=6 1 2 1 1 |
* 11 i=6 1 2 1 2 |
* 12 2 2 1 1 |
* 12 2 2 1 2 |
* 13 i=7 1 i=4 1 2 1 |
* 13 i=7 1 i=4 1 2 2 |
* 14 2 1 2 1 |
* 14 2 1 2 2 |
* 15 i=8 1 2 2 1 |
* 15 i=8 1 2 2 2 |
* 16 2 2 2 1 |
* 16 2 2 2 2 |
*/ |
*/ |
codtab[h][k]=j; |
for(h=1; h <=100 ;h++){ |
/* codtab[12][3]=1; */ |
/* printf("h=%2d ", h); */ |
/*codtab[h][Tvar[k]]=j;*/ |
for(k=1; k <=10; k++){ |
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); |
/* printf("k=%d %d ",k,codtabm(h,k)); */ |
} |
codtab[h][k]=codtabm(h,k); |
} |
} |
} |
/* printf("\n"); */ |
} |
} |
|
/* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */ |
|
/* for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/ */ |
|
/* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */ |
|
/* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */ |
|
/* h++; */ |
|
/* if (h>m) */ |
|
/* h=1; */ |
|
/* codtab[h][k]=j; */ |
|
/* /\* codtab[12][3]=1; *\/ */ |
|
/* /\*codtab[h][Tvar[k]]=j;*\/ */ |
|
/* /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */ |
|
/* } */ |
|
/* } */ |
|
/* } */ |
|
/* } */ |
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); |
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); |
codtab[1][2]=1;codtab[2][2]=2; */ |
codtab[1][2]=1;codtab[2][2]=2; */ |
/* for(i=1; i <=m ;i++){ |
/* for(i=1; i <=m ;i++){ */ |
for(k=1; k <=cptcovn; k++){ |
/* for(k=1; k <=cptcovn; k++){ */ |
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); |
/* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */ |
} |
/* } */ |
printf("\n"); |
/* printf("\n"); */ |
} |
/* } */ |
scanf("%d",i);*/ |
/* scanf("%d",i);*/ |
|
|
free_ivector(Ndum,-1,NCOVMAX); |
free_ivector(Ndum,-1,NCOVMAX); |
|
|
Line 7111 Interval (in months) between two waves:
|
Line 7234 Interval (in months) between two waves:
|
} |
} |
|
|
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); |
for (i=1;i<=NDIM;i++) |
for (i=1;i<=NDIM;i++) { |
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
|
fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); |
|
} |
lsurv=vector(1,AGESUP); |
lsurv=vector(1,AGESUP); |
lpop=vector(1,AGESUP); |
lpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
Line 7145 Interval (in months) between two waves:
|
Line 7269 Interval (in months) between two waves:
|
|
|
|
|
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){ |
|
printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
}else |
|
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ |
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ |
stepm, weightopt,\ |
stepm, weightopt,\ |
model,imx,p,matcov,agemortsup); |
model,imx,p,matcov,agemortsup); |
Line 7210 Interval (in months) between two waves:
|
Line 7341 Interval (in months) between two waves:
|
ftolhess=ftol; /* Usually correct */ |
ftolhess=ftol; /* Usually correct */ |
hesscov(matcov, p, npar, delti, ftolhess, func); |
hesscov(matcov, p, npar, delti, ftolhess, func); |
} |
} |
|
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
|
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); |
|
for(i=1,jk=1; i <=nlstate; i++){ |
|
for(k=1; k <=(nlstate+ndeath); k++){ |
|
if (k != i) { |
|
printf("%d%d ",i,k); |
|
fprintf(ficlog,"%d%d ",i,k); |
|
for(j=1; j <=ncovmodel; j++){ |
|
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
|
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); |
|
jk++; |
|
} |
|
printf("\n"); |
|
fprintf(ficlog,"\n"); |
|
} |
|
} |
|
} |
|
|
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
printf("# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); |
Line 7366 Interval (in months) between two waves:
|
Line 7515 Interval (in months) between two waves:
|
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.; |
|
|
fscanf(ficpar,"pop_based=%d\n",&popbased); |
fscanf(ficpar,"pop_based=%d\n",&popbased); |
|
fprintf(ficlog,"pop_based=%d\n",popbased); |
fprintf(ficparo,"pop_based=%d\n",popbased); |
fprintf(ficparo,"pop_based=%d\n",popbased); |
fprintf(ficres,"pop_based=%d\n",popbased); |
fprintf(ficres,"pop_based=%d\n",popbased); |
|
|
Line 7390 Interval (in months) between two waves:
|
Line 7540 Interval (in months) between two waves:
|
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ |
|
|
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ |
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){ |
|
printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\ |
|
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ |
|
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); |
|
}else |
|
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
|
|
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ |
model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\ |
Line 7793 Interval (in months) between two waves:
|
Line 7951 Interval (in months) between two waves:
|
} |
} |
end: |
end: |
while (z[0] != 'q') { |
while (z[0] != 'q') { |
printf("\nType q for exiting: "); |
printf("\nType q for exiting: "); fflush(stdout); |
scanf("%s",z); |
scanf("%s",z); |
} |
} |
} |
} |