version 1.244, 2016/09/02 07:17:34
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version 1.247, 2016/09/02 11:11:21
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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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 |
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*** empty log message *** |
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Revision 1.245 2016/09/02 07:25:01 brouard |
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*** empty log message *** |
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Revision 1.244 2016/09/02 07:17:34 brouard |
Revision 1.244 2016/09/02 07:17:34 brouard |
*** empty log message *** |
*** empty log message *** |
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Line 2578 Earliest age to start was %d-%d=%d, ncvl
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Line 2587 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 2703 Earliest age to start was %d-%d=%d, ncvl
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Line 2713 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 3590 double funcone( double *x)
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Line 3605 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 3646 double funcone( double *x)
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Line 3662 double funcone( double *x)
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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,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ |
fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ |
%11.6f %11.6f %11.6f ", \ |
%11.6f %11.6f %11.6f ", \ |
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw, |
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw, |
2*weight[i]*lli,out[s1][s2],savm[s1][s2]); |
2*weight[i]*lli,out[s1][s2],savm[s1][s2]); |
Line 4004 double hessij( double x[], double **hess
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Line 4020 double hessij( double x[], double **hess
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kmax=kmax+10; |
kmax=kmax+10; |
} |
} |
if(kmax >=10 || firstime ==1){ |
if(kmax >=10 || firstime ==1){ |
printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol); |
printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol); |
fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol); |
fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol); |
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); |
} |
} |
Line 6398 void printinggnuplot(char fileresu[], ch
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Line 6414 void printinggnuplot(char fileresu[], ch
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if(TKresult[nres]!= k1) |
if(TKresult[nres]!= k1) |
continue; |
continue; |
/* We are interested in selected combination by the resultline */ |
/* We are interested in selected combination by the resultline */ |
printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); |
/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */ |
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); |
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); |
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */ |
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */ |
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ |
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ |
Line 6407 void printinggnuplot(char fileresu[], ch
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Line 6423 void printinggnuplot(char fileresu[], ch
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/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ |
vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */ |
vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */ |
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */ |
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */ |
printf(" V%d=%d ",Tvaraff[k],vlv); |
/* printf(" V%d=%d ",Tvaraff[k],vlv); */ |
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); |
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); |
} |
} |
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ |
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ |
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); |
/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */ |
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); |
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); |
} |
} |
printf("\n#\n"); |
/* printf("\n#\n"); */ |
fprintf(ficgp,"\n#\n"); |
fprintf(ficgp,"\n#\n"); |
if(invalidvarcomb[k1]){ |
if(invalidvarcomb[k1]){ |
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); |
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); |
Line 6444 void printinggnuplot(char fileresu[], ch
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Line 6460 void printinggnuplot(char fileresu[], ch
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/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */ |
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */ |
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */ |
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */ |
if(cptcoveff ==0){ |
if(cptcoveff ==0){ |
fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt ); |
fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt ); |
}else{ |
}else{ |
kl=0; |
kl=0; |
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ |
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ |
Line 6459 void printinggnuplot(char fileresu[], ch
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Line 6475 void printinggnuplot(char fileresu[], ch
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/*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ |
/*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ |
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ |
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ |
if(k==cptcoveff){ |
if(k==cptcoveff){ |
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ |
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ |
2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/ |
2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/ |
}else{ |
}else{ |
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); |
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); |
Line 9871 int main(int argc, char *argv[])
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Line 9887 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 10643 Please run with mle=-1 to get a correct
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Line 10665 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 */ |