version 1.246, 2016/09/02 08:49:22
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version 1.248, 2016/09/07 14:10:18
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.248 2016/09/07 14:10:18 brouard |
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*** empty log message *** |
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Revision 1.247 2016/09/02 11:11:21 brouard |
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*** empty log message *** |
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Revision 1.246 2016/09/02 08:49:22 brouard |
Revision 1.246 2016/09/02 08:49:22 brouard |
*** empty log message *** |
*** empty log message *** |
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Line 2584 Earliest age to start was %d-%d=%d, ncvl
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Line 2590 Earliest age to start was %d-%d=%d, ncvl
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/* If we start from prlim again, prlim tends to a constant matrix */ |
/* If we start from prlim again, prlim tends to a constant matrix */ |
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int i, ii,j,k; |
int i, ii,j,k; |
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int first=0; |
double *min, *max, *meandiff, maxmax,sumnew=0.; |
double *min, *max, *meandiff, maxmax,sumnew=0.; |
/* double **matprod2(); */ /* test */ |
/* double **matprod2(); */ /* test */ |
double **out, cov[NCOVMAX+1], **bmij(); |
double **out, cov[NCOVMAX+1], **bmij(); |
Line 2709 Earliest age to start was %d-%d=%d, ncvl
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Line 2716 Earliest age to start was %d-%d=%d, ncvl
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} |
} |
} /* age loop */ |
} /* age loop */ |
/* After some age loop it doesn't converge */ |
/* After some age loop it doesn't converge */ |
printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ |
if(first){ |
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first=1; |
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printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\ |
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Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
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} |
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fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\ |
Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear); |
/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ |
/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */ |
free_vector(min,1,nlstate); |
free_vector(min,1,nlstate); |
Line 3596 double funcone( double *x)
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Line 3608 double funcone( double *x)
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agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */ |
agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */ |
ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */ |
ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */ |
for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */ |
for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */ |
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/* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */ |
/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] |
/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] |
and mw[mi+1][i]. dh depends on stepm.*/ |
and mw[mi+1][i]. dh depends on stepm.*/ |
newm=savm; |
newm=savm; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; |
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */ |
cov[2]=agexact; |
cov[2]=agexact; |
if(nagesqr==1) |
if(nagesqr==1) |
cov[3]= agexact*agexact; |
cov[3]= agexact*agexact; |
Line 8833 Dummy[k] 0=dummy (0 1), 1 quantitative (
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Line 8846 Dummy[k] 0=dummy (0 1), 1 quantitative (
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} |
} |
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int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) |
int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) |
{ |
{/* Check ages at death */ |
int i, m; |
int i, m; |
int firstone=0; |
int firstone=0; |
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Line 9877 int main(int argc, char *argv[])
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Line 9890 int main(int argc, char *argv[])
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delti=delti3[1][1]; |
delti=delti3[1][1]; |
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ |
/*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ |
if(mle==-1){ /* Print a wizard for help writing covariance matrix */ |
if(mle==-1){ /* Print a wizard for help writing covariance matrix */ |
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/* We could also provide initial parameters values giving by simple logistic regression |
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* only one way, that is without matrix product. We will have nlstate maximizations */ |
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/* for(i=1;i<nlstate;i++){ */ |
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/* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */ |
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/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */ |
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/* } */ |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); |
printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); |
fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); |
fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso); |
Line 9885 int main(int argc, char *argv[])
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Line 9904 int main(int argc, char *argv[])
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fclose (ficlog); |
fclose (ficlog); |
goto end; |
goto end; |
exit(0); |
exit(0); |
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} else if(mle==-2) { /* Guessing from means */ |
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prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
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printf(" You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso); |
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fprintf(ficlog," You chose mle=-2, look at file %s for a template of covariance matrix \n",filereso); |
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} else if(mle==-5) { /* Main Wizard */ |
} else if(mle==-5) { /* Main Wizard */ |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
prwizard(ncovmodel, nlstate, ndeath, model, ficparo); |
printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso); |
Line 10208 Please run with mle=-1 to get a correct
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Line 10232 Please run with mle=-1 to get a correct
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*/ |
*/ |
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concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); |
/* */ |
/* Concatenates waves */ |
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free_vector(moisdc,1,n); |
free_vector(moisdc,1,n); |
free_vector(andc,1,n); |
free_vector(andc,1,n); |
Line 10411 Interval (in months) between two waves:
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Line 10435 Interval (in months) between two waves:
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/* For mortality only */ |
/* For mortality only */ |
if (mle==-3){ |
if (mle==-3){ |
ximort=matrix(1,NDIM,1,NDIM); |
ximort=matrix(1,NDIM,1,NDIM); |
for(i=1;i<=NDIM;i++) |
for(i=1;i<=NDIM;i++) |
for(j=1;j<=NDIM;j++) |
for(j=1;j<=NDIM;j++) |
ximort[i][j]=0.; |
ximort[i][j]=0.; |
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ |
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ |
cens=ivector(1,n); |
cens=ivector(1,n); |
ageexmed=vector(1,n); |
ageexmed=vector(1,n); |
Line 10649 Please run with mle=-1 to get a correct
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Line 10673 Please run with mle=-1 to get a correct
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printf("\n"); |
printf("\n"); |
if(mle>=1){ /* Could be 1 or 2, Real Maximization */ |
if(mle>=1){ /* Could be 1 or 2, Real Maximization */ |
/* mlikeli uses func not funcone */ |
/* mlikeli uses func not funcone */ |
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/* for(i=1;i<nlstate;i++){ */ |
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/* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */ |
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/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */ |
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/* } */ |
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); |
} |
} |
if(mle==0) {/* No optimization, will print the likelihoods for the datafile */ |
if(mle==0) {/* No optimization, will print the likelihoods for the datafile */ |