--- imach/src/imach.c 2016/09/02 07:25:01 1.245 +++ imach/src/imach.c 2016/09/07 17:14:18 1.249 @@ -1,6 +1,18 @@ -/* $Id: imach.c,v 1.245 2016/09/02 07:25:01 brouard Exp $ +/* $Id: imach.c,v 1.249 2016/09/07 17:14:18 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.249 2016/09/07 17:14:18 brouard + Summary: Starting values from frequencies + + Revision 1.248 2016/09/07 14:10:18 brouard + *** empty log message *** + + Revision 1.247 2016/09/02 11:11:21 brouard + *** empty log message *** + + Revision 1.246 2016/09/02 08:49:22 brouard + *** empty log message *** + Revision 1.245 2016/09/02 07:25:01 brouard *** empty log message *** @@ -937,12 +949,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.245 2016/09/02 07:25:01 brouard Exp $ */ +/* $Id: imach.c,v 1.249 2016/09/07 17:14:18 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018"; -char fullversion[]="$Revision: 1.245 $ $Date: 2016/09/02 07:25:01 $"; +char fullversion[]="$Revision: 1.249 $ $Date: 2016/09/07 17:14:18 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -2581,6 +2593,7 @@ Earliest age to start was %d-%d=%d, ncvl /* If we start from prlim again, prlim tends to a constant matrix */ int i, ii,j,k; + int first=0; double *min, *max, *meandiff, maxmax,sumnew=0.; /* double **matprod2(); */ /* test */ double **out, cov[NCOVMAX+1], **bmij(); @@ -2706,7 +2719,12 @@ Earliest age to start was %d-%d=%d, ncvl } } /* age loop */ /* 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); /* 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); @@ -3593,10 +3611,11 @@ double funcone( double *x) 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 */ for(d=0; d=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); - 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); + 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 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); 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); } @@ -4233,7 +4252,6 @@ Title=%s
Datafile=%s Firstpass=%d La j=cptcoveff; /* Only dummy covariates of the model */ if (cptcovn<1) {j=1;ncodemax[1]=1;} - first=1; /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels: reference=low_education V1=0,V2=0 @@ -4241,7 +4259,11 @@ Title=%s
Datafile=%s Firstpass=%d La high_educ V1=0 V2=1 Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff */ - + dateintsum=0; + k2cpt=0; + + for (j = 0; j <= cptcoveff; j+=cptcoveff){ + first=1; for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */ posproptt=0.; /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); @@ -4264,11 +4286,13 @@ Title=%s
Datafile=%s Firstpass=%d La /* } */ /* } */ - dateintsum=0; - k2cpt=0; + /* dateintsum=0; */ + /* k2cpt=0; */ + /* For that combination of covariate j1, we count and print the frequencies in one pass */ for (iind=1; iind<=imx; iind++) { /* For each individual iind */ bool=1; + if(j !=0){ if(anyvaryingduminmodel==0){ /* If All fixed covariates */ if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ /* for (z1=1; z1<= nqfveff; z1++) { */ @@ -4291,16 +4315,18 @@ Title=%s
Datafile=%s Firstpass=%d La } /* end z1 */ } /* cptcovn > 0 */ } /* end any */ + }/* end j==0 */ if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */ /* for(m=firstpass; m<=lastpass; m++){ */ for(mi=1; miDatafile=%s Firstpass=%d La } } }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */ + } /* end j==0 */ /* bool =0 we keep that guy which corresponds to the combination of dummy values */ if(bool==1){ /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind] @@ -4331,8 +4358,8 @@ Title=%s
Datafile=%s Firstpass=%d La freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */ } } /* end if between passes */ - if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) { - dateintsum=dateintsum+k2; + if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) { + dateintsum=dateintsum+k2; /* on all covariates ?*/ k2cpt++; /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ } @@ -4346,7 +4373,7 @@ Title=%s
Datafile=%s Firstpass=%d La /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ pstamp(ficresp); - if (cptcoveff>0){ + if (cptcoveff>0 && j!=0){ fprintf(ficresp, "\n#********** Variable "); fprintf(ficresphtm, "\n

********** Variable "); fprintf(ficresphtmfr, "\n

********** Variable "); @@ -4512,6 +4539,20 @@ Title=%s
Datafile=%s Firstpass=%d La } fprintf(ficresphtmfr,"\n"); } /* end selected combination of covariate j1 */ + if(j==0){ /* We can estimate starting values from the occurences in each case */ + for(jk=-1; jk <=nlstate+ndeath; jk++){ + for(m=-1; m <=nlstate+ndeath; m++){ + /* param[i]|j][k]= freq[jk][m][iagemax+3] */ + if(freq[jk][m][iage] !=0 ) { /* minimizing output */ + if(first==1){ + printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); + } + fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]); + } + } + } /* end loop jk */ + } + } /* end j */ dateintmean=dateintsum/k2cpt; fclose(ficresp); @@ -6401,7 +6442,7 @@ void printinggnuplot(char fileresu[], ch if(TKresult[nres]!= k1) continue; /* 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); 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 */ @@ -6410,14 +6451,14 @@ void printinggnuplot(char fileresu[], ch /* 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 */ /* 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); } 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]); } - printf("\n#\n"); + /* printf("\n#\n"); */ fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); @@ -8830,7 +8871,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( } int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) -{ +{/* Check ages at death */ int i, m; int firstone=0; @@ -9874,6 +9915,12 @@ int main(int argc, char *argv[]) delti=delti3[1][1]; /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/ 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=1){ /* Could be 1 or 2, Real Maximization */ /* mlikeli uses func not funcone */ + /* for(i=1;i