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Diff for /imach/src/imach.c between versions 1.246 and 1.247

version 1.246, 2016/09/02 08:49:22	version 1.247, 2016/09/02 11:11:21
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.247 2016/09/02 11:11:21 brouard
	* empty log message *

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 *

Line 2584 Earliest age to start was %d-%d=%d, ncvl	Line 2587 Earliest age to start was %d-%d=%d, ncvl
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k;
	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	Line 2713 Earliest age to start was %d-%d=%d, ncvl
}	}
} /* 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){
	first=1;
	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\
	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);
	}
	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)	Line 3605 double funcone( double *x)
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 */
	/* 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]+dstepm/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 9877 int main(int argc, char *argv[])	Line 9887 int main(int argc, char *argv[])
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 */
	/* We could also provide initial parameters values giving by simple logistic regression
	* only one way, that is without matrix product. We will have nlstate maximizations */
	/* for(i=1;i<nlstate;i++){ */
	/* /\reducing xi for 1 to npar to 1 to ncovmodel; \/ */
	/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
	/* } */
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 10649 Please run with mle=-1 to get a correct	Line 10665 Please run with mle=-1 to get a correct
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 */
	/* for(i=1;i<nlstate;i++){ */
	/* /\reducing xi for 1 to npar to 1 to ncovmodel; \/ */
	/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
	/* } */
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 */

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