version 1.131, 2009/06/20 16:22:47
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version 1.135, 2009/10/29 15:33:14
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.135 2009/10/29 15:33:14 brouard |
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(Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. |
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Revision 1.134 2009/10/29 13:18:53 brouard |
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(Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. |
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Revision 1.133 2009/07/06 10:21:25 brouard |
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just nforces |
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Revision 1.132 2009/07/06 08:22:05 brouard |
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Many tings |
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Revision 1.131 2009/06/20 16:22:47 brouard |
Revision 1.131 2009/06/20 16:22:47 brouard |
Some dimensions resccaled |
Some dimensions resccaled |
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Line 168
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Line 180
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The same imach parameter file can be used but the option for mle should be -3. |
The same imach parameter file can be used but the option for mle should be -3. |
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Agnès, who wrote this part of the code, tried to keep most of the |
Agnès, who wrote this part of the code, tried to keep most of the |
former routines in order to include the new code within the former code. |
former routines in order to include the new code within the former code. |
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The output is very simple: only an estimate of the intercept and of |
The output is very simple: only an estimate of the intercept and of |
Line 301
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Line 313
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Also this programme outputs the covariance matrix of the parameters but also |
Also this programme outputs the covariance matrix of the parameters but also |
of the life expectancies. It also computes the period (stable) prevalence. |
of the life expectancies. It also computes the period (stable) prevalence. |
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Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). |
Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). |
Institut national d'études démographiques, Paris. |
Institut national d'études démographiques, Paris. |
This software have been partly granted by Euro-REVES, a concerted action |
This software have been partly granted by Euro-REVES, a concerted action |
from the European Union. |
from the European Union. |
It is copyrighted identically to a GNU software product, ie programme and |
It is copyrighted identically to a GNU software product, ie programme and |
Line 400 extern int errno;
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Line 412 extern int errno;
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite "; |
char version[]="Imach version 0.98l, October 2009, INED-EUROREVES-Institut de longevite "; |
char fullversion[]="$Revision$ $Date$"; |
char fullversion[]="$Revision$ $Date$"; |
char strstart[80]; |
char strstart[80]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH]; |
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ |
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ |
int nvar=0; |
int nvar=0, nforce=0; /* Number of variables, number of forces */ |
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */ |
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */ |
int npar=NPARMAX; |
int npar=NPARMAX; |
int nlstate=2; /* Number of live states */ |
int nlstate=2; /* Number of live states */ |
Line 597 void replace_back_to_slash(char *s, char
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Line 609 void replace_back_to_slash(char *s, char
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} |
} |
} |
} |
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char *trimbb(char *out, char *in) |
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{ /* Trim multiple blanks in line */ |
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char *s; |
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s=out; |
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while (*in != '\0'){ |
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while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){ |
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in++; |
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} |
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*out++ = *in++; |
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} |
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*out='\0'; |
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return s; |
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} |
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int nbocc(char *s, char occ) |
int nbocc(char *s, char occ) |
{ |
{ |
int i,j=0; |
int i,j=0; |
Line 1692 double funcone( double *x)
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Line 1718 double funcone( double *x)
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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; |
printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); |
/*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ |
if(globpr){ |
if(globpr){ |
fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ |
fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ |
%11.6f %11.6f %11.6f ", \ |
%11.6f %11.6f %11.6f ", \ |
Line 1897 double hessii(double x[], double delta,
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Line 1923 double hessii(double x[], double delta,
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int i; |
int i; |
int l=1, lmax=20; |
int l=1, lmax=20; |
double k1,k2; |
double k1,k2; |
double p2[NPARMAX+1]; |
double p2[MAXPARM+1]; /* identical to x */ |
double res; |
double res; |
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; |
double fx; |
double fx; |
Line 1918 double hessii(double x[], double delta,
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Line 1944 double hessii(double x[], double delta,
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/*res= (k1-2.0*fx+k2)/delt/delt; */ |
/*res= (k1-2.0*fx+k2)/delt/delt; */ |
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */ |
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#ifdef DEBUG |
#ifdef DEBUGHESS |
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx); |
#endif |
#endif |
Line 1944 double hessij( double x[], double delti[
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Line 1970 double hessij( double x[], double delti[
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int i; |
int i; |
int l=1, l1, lmax=20; |
int l=1, l1, lmax=20; |
double k1,k2,k3,k4,res,fx; |
double k1,k2,k3,k4,res,fx; |
double p2[NPARMAX+1]; |
double p2[MAXPARM+1]; |
int k; |
int k; |
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fx=func(x); |
fx=func(x); |
Line 2155 void freqsummary(char fileres[], int ia
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Line 2181 void freqsummary(char fileres[], int ia
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pos += freq[jk][m][i]; |
pos += freq[jk][m][i]; |
if(pp[jk]>=1.e-10){ |
if(pp[jk]>=1.e-10){ |
if(first==1){ |
if(first==1){ |
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
} |
} |
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); |
}else{ |
}else{ |
Line 2464 void tricode(int *Tvar, int **nbcode, in
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Line 2490 void tricode(int *Tvar, int **nbcode, in
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} |
} |
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for (i=0; i<=cptcode; i++) { /* i=-1 ?*/ |
for (i=0; i<=cptcode; i++) { /* i=-1 ?*/ |
if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariate. In fact ncodemax[j]=2 (dichotom. variables only) but it can be more */ |
if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j |
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th covariate. In fact |
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ncodemax[j]=2 |
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(dichotom. variables only) but |
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it can be more */ |
} /* Ndum[-1] number of undefined modalities */ |
} /* Ndum[-1] number of undefined modalities */ |
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ij=1; |
ij=1; |
Line 3458 To be simple, these graphs help to under
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Line 3488 To be simple, these graphs help to under
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/* Computing eigen value of matrix of covariance */ |
/* Computing eigen value of matrix of covariance */ |
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; |
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if ((lc2 <0) || (lc1 <0) ){ |
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printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor); |
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fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog); |
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lc1=fabs(lc1); |
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lc2=fabs(lc2); |
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} |
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/* Eigen vectors */ |
/* Eigen vectors */ |
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); |
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); |
/*v21=sqrt(1.-v11*v11); *//* error */ |
/*v21=sqrt(1.-v11*v11); *//* error */ |
Line 4431 int main(int argc, char *argv[])
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Line 4468 int main(int argc, char *argv[])
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double ***mobaverage; |
double ***mobaverage; |
int *indx; |
int *indx; |
char line[MAXLINE], linepar[MAXLINE]; |
char line[MAXLINE], linepar[MAXLINE]; |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; |
char linetmp[MAXLINE]; |
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char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
char **bp, *tok, *val; /* pathtot */ |
char **bp, *tok, *val; /* pathtot */ |
int firstobs=1, lastobs=10; |
int firstobs=1, lastobs=10; |
Line 4635 int main(int argc, char *argv[])
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Line 4673 int main(int argc, char *argv[])
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covar=matrix(0,NCOVMAX,1,n); |
covar=matrix(0,NCOVMAX,1,n); |
cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ |
cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ |
if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; |
if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; |
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/* where is ncovprod ?*/ |
ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */ |
ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/ |
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ |
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ |
npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ |
nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ |
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npar= nforce*ncovmodel; /* Number of parameters like aij*/ |
if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ |
if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ |
printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); |
printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); |
fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); |
fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX); |
Line 4858 run imach with mle=-1 to get a correct t
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Line 4897 run imach with mle=-1 to get a correct t
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printf("Comment line\n%s\n",line); |
printf("Comment line\n%s\n",line); |
continue; |
continue; |
} |
} |
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trimbb(linetmp,line); /* Trims multiple blanks in line */ |
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for (j=0; line[j]!='\0';j++){ |
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line[j]=linetmp[j]; |
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} |
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for (j=maxwav;j>=1;j--){ |
for (j=maxwav;j>=1;j--){ |
cutv(stra, strb,line,' '); |
cutv(stra, strb,line,' '); |
Line 4914 run imach with mle=-1 to get a correct t
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Line 4958 run imach with mle=-1 to get a correct t
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month=99; |
month=99; |
year=9999; |
year=9999; |
}else{ |
}else{ |
printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j); |
printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line); |
fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);fflush(ficlog); |
fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); |
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goto end; |
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} |
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if (year==9999) { |
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printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line); |
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fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog); |
goto end; |
goto end; |
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} |
} |
annais[i]=(double)(year); |
annais[i]=(double)(year); |
moisnais[i]=(double)(month); |
moisnais[i]=(double)(month); |
Line 5040 run imach with mle=-1 to get a correct t
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Line 5090 run imach with mle=-1 to get a correct t
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cptcovprod--; |
cptcovprod--; |
cutv(strb,stre,strd,'V'); |
cutv(strb,stre,strd,'V'); |
Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */ |
Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */ |
cptcovage++; /* Sum the number of covariates including ages as a product */ |
cptcovage++; /* Sums the number of covariates including age as a product */ |
Tage[cptcovage]=i; /* Tage[1] =2 */ |
Tage[cptcovage]=i; /* Tage[1] =2 */ |
/*printf("stre=%s ", stre);*/ |
/*printf("stre=%s ", stre);*/ |
} |
} |
Line 5141 run imach with mle=-1 to get a correct t
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Line 5191 run imach with mle=-1 to get a correct t
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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]; |
/*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/ |
printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin); |
} |
} |
else if(agev[m][i] >agemax){ |
else if(agev[m][i] >agemax){ |
agemax=agev[m][i]; |
agemax=agev[m][i]; |
Line 5436 Interval (in months) between two waves:
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Line 5486 Interval (in months) between two waves:
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} /* Endof if mle==-3 */ |
} /* Endof if mle==-3 */ |
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else{ /* For mle >=1 */ |
else{ /* For mle >=1 */ |
globpr=1;/* debug */ |
globpr=0;/* debug */ |
/* likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone);*/ /* Prints the contributions to the likelihood */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); |
for (k=1; k<=npar;k++) |
for (k=1; k<=npar;k++) |
printf(" %d %8.5f",k,p[k]); |
printf(" %d %8.5f",k,p[k]); |