--- imach/src/imach.c 2022/06/02 04:45:11 1.319 +++ imach/src/imach.c 2022/08/03 17:29:54 1.329 @@ -1,6 +1,41 @@ -/* $Id: imach.c,v 1.319 2022/06/02 04:45:11 brouard Exp $ +/* $Id: imach.c,v 1.329 2022/08/03 17:29:54 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.329 2022/08/03 17:29:54 brouard + * imach.c (Module): Many errors in graphs fixed with Vn*age covariates. + + Revision 1.328 2022/07/27 17:40:48 brouard + Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage + + Revision 1.327 2022/07/27 14:47:35 brouard + Summary: Still a problem for one-step probabilities in case of quantitative variables + + Revision 1.326 2022/07/26 17:33:55 brouard + Summary: some test with nres=1 + + Revision 1.325 2022/07/25 14:27:23 brouard + Summary: r30 + + * imach.c (Module): Error cptcovn instead of nsd in bmij (was + coredumped, revealed by Feiuno, thank you. + + Revision 1.324 2022/07/23 17:44:26 brouard + *** empty log message *** + + Revision 1.323 2022/07/22 12:30:08 brouard + * imach.c (Module): Output of Wald test in the htm file and not only in the log. + + Revision 1.322 2022/07/22 12:27:48 brouard + * imach.c (Module): Output of Wald test in the htm file and not only in the log. + + Revision 1.321 2022/07/22 12:04:24 brouard + Summary: r28 + + * imach.c (Module): Output of Wald test in the htm file and not only in the log. + + Revision 1.320 2022/06/02 05:10:11 brouard + *** empty log message *** + Revision 1.319 2022/06/02 04:45:11 brouard * imach.c (Module): Adding the Wald tests from the log to the main htm for better display of the maximum likelihood estimators. @@ -855,7 +890,7 @@ The same imach parameter file can be used but the option for mle should be -3. - 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. The output is very simple: only an estimate of the intercept and of @@ -1034,13 +1069,13 @@ Important routines - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities) and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually. - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables - o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if + o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless. - Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). - Institut national d'études démographiques, Paris. + Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). + Institut national d'études démographiques, Paris. This software have been partly granted by Euro-REVES, a concerted action from the European Union. It is copyrighted identically to a GNU software product, ie programme and @@ -1160,7 +1195,7 @@ typedef struct { #define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ -#define FILENAMELENGTH 132 +#define FILENAMELENGTH 256 #define GLOCK_ERROR_NOPATH -1 /* empty path */ #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ @@ -1171,7 +1206,7 @@ typedef struct { #define NINTERVMAX 8 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ -#define NCOVMAX 30 /**< Maximum number of covariates, including generated covariates V1*V2 */ +#define NCOVMAX 30 /**< Maximum number of covariates used in the model, including generated covariates V1*V2 or V1*age */ #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 /*#define decodtabm(h,k,cptcoveff)= (h <= (1<> (k-1)) & 1) +1 : -1)*/ #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 @@ -1195,12 +1230,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.319 2022/06/02 04:45:11 brouard Exp $ */ +/* $Id: imach.c,v 1.329 2022/08/03 17:29:54 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; -char copyright[]="May 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022"; -char fullversion[]="$Revision: 1.319 $ $Date: 2022/06/02 04:45:11 $"; +char copyright[]="July 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022"; +char fullversion[]="$Revision: 1.329 $ $Date: 2022/08/03 17:29:54 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -1422,7 +1457,7 @@ int **nbcode, *Tvar; /**< model=V2 => Tv /* Tage[cptcovage]=k 5 8 */ /* Position in the model of ith cov*age */ /* Tvard[1][1]@4={4,3,1,2} V4*V3 V1*V2 */ /* Position in model of the ith prod without age */ /* TvarF TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1*V2, V1 */ -/* TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod) */ +/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod) */ /* Type */ /* V 1 2 3 4 5 */ /* F F V V V */ @@ -2402,16 +2437,16 @@ void powell(double p[], double **xi, int for (j=1;j<=n;j++) pt[j]=p[j]; rcurr_time = time(NULL); for (*iter=1;;++(*iter)) { - fp=(*fret); /* From former iteration or initial value */ ibig=0; del=0.0; rlast_time=rcurr_time; /* (void) gettimeofday(&curr_time,&tzp); */ rcurr_time = time(NULL); curr_time = *localtime(&rcurr_time); - printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); - fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); + printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); + fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ + fp=(*fret); /* From former iteration or initial value */ for (i=1;i<=n;i++) { fprintf(ficrespow," %.12lf", p[i]); } @@ -2792,8 +2827,8 @@ void powell(double p[], double **xi, int } for (k=1; k<=cptcovprod;k++){ /* For product without age */ /* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */ - if(Dummy[Tvard[k][1]==0]){ - if(Dummy[Tvard[k][2]==0]){ + if(Dummy[Tvard[k][1]]==0){ + if(Dummy[Tvard[k][2]]==0){ cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */ }else{ @@ -2801,7 +2836,7 @@ void powell(double p[], double **xi, int /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */ } }else{ - if(Dummy[Tvard[k][2]==0]){ + if(Dummy[Tvard[k][2]]==0){ cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */ }else{ @@ -2971,14 +3006,14 @@ void powell(double p[], double **xi, int } for (k=1; k<=cptcovprod;k++){ /* For product without age */ /* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */ - if(Dummy[Tvard[k][1]==0]){ - if(Dummy[Tvard[k][2]==0]){ + if(Dummy[Tvard[k][1]]==0){ + if(Dummy[Tvard[k][2]]==0){ cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; }else{ cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; } }else{ - if(Dummy[Tvard[k][2]==0]){ + if(Dummy[Tvard[k][2]]==0){ cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; }else{ cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; @@ -3121,7 +3156,7 @@ double **pmij(double **ps, double *cov, ps[i][i]=1./(s1+1.); /* Computing other pijs */ for(j=1; j0) { fprintf(ficresprob, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); @@ -6906,8 +6959,11 @@ To be simple, these graphs help to under cov[2]=age; if(nagesqr==1) cov[3]= age*age; - for (k=1; k<=cptcovn;k++) { - cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; + /* for (k=1; k<=cptcovn;k++) { */ + /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */ + for (k=1; k<=nsd;k++) { /* For single dummy covariates only */ + /* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */ + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,k)]; /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4 * 1 1 1 1 1 * 2 2 1 1 1 @@ -6918,12 +6974,39 @@ To be simple, these graphs help to under /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */ /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */ /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ - for (k=1; k<=cptcovage;k++) - cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; - for (k=1; k<=cptcovprod;k++) - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; - - + for (k=1; k<=cptcovage;k++){ /* For product with age */ + if(Dummy[Tage[k]]==2){ /* dummy with age */ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,k)]*cov[2]; + /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */ + } else if(Dummy[Tage[k]]==3){ /* quantitative with age */ + printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]); + exit(1); + /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; *\/ */ + /* cov[++k1]=Tqresult[nres][k]; */ + } + /* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */ + } + for (k=1; k<=cptcovprod;k++){/* For product without age */ + if(Dummy[Tvard[k][1]]==0){ + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * nbcode[Tvard[k][2]][codtabm(j1,k)]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + }else{ /* Should we use the mean of the quantitative variables? */ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * Tqresult[nres][k]; + /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */ + } + }else{ + if(Dummy[Tvard[k][2]]==0){ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,k)] * Tqinvresult[nres][Tvard[k][1]]; + /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */ + }else{ + cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; + /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */ + } + } + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */ + } +/* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/ for(theta=1; theta <=npar; theta++){ for(i=1; i<=npar; i++) xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); @@ -7108,6 +7191,7 @@ To be simple, these graphs help to under } /* k12 */ } /*l1 */ }/* k1 */ + } /* loop on nres */ } /* loop on combination of covariates j1 */ free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); @@ -7237,7 +7321,7 @@ void printinghtml(char fileresu[], char } /* if(nqfveff+nqtveff 0) */ /* Test to be done */ - fprintf(fichtm," ************\n
"); + fprintf(fichtm," (model=%s) ************\n
",model); if(invalidvarcomb[k1]){ fprintf(fichtm,"\n

Combination (%d) ignored because no cases

\n",k1); printf("\nCombination (%d) ignored because no cases \n",k1); @@ -7258,19 +7342,23 @@ divided by h: hPij ",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); /* Survival functions (period) in state j */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
\ -", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres); + fprintf(fichtm,"
\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_")); + fprintf(fichtm,"",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres); } /* State specific survival functions (period) */ for(cpt=1; cpt<=nlstate;cpt++){ fprintf(fichtm,"
\n- Survival functions in state %d and in any other live state (total).\ And probability to be observed in various states (up to %d) being in state %d at different ages. \ - %s_%d-%d-%d.svg
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres); + %s_%d-%d-%d.svg
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_")); + fprintf(fichtm,"",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres); } /* Period (forward stable) prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. %s_%d-%d-%d.svg
\ -", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); + fprintf(fichtm,"
\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. %s_%d-%d-%d.svg
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_")); + fprintf(fichtm,"" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres); } if(prevbcast==1){ /* Backward prevalence in each health state */ @@ -7424,7 +7512,7 @@ See page 'Matrix of variance-covariance fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } - fprintf(fichtm," ************\n
"); + fprintf(fichtm," (model=%s) ************\n
",model); if(invalidvarcomb[k1]){ fprintf(fichtm,"\n

Combination (%d) ignored because no cases

\n",k1); @@ -7560,7 +7648,7 @@ void printinggnuplot(char fileresu[], ch fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres); fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres); /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */ - fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */ /* k1-1 error should be nres-1*/ @@ -7981,8 +8069,8 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,", '' "); /* l=(nlstate+ndeath)*(i-1)+1; */ l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */ - /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */ - /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */ + /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */ + /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */ /* for (j=2; j<= nlstate ; j ++) */ /* fprintf(ficgp,"+$%d",k+l+j-1); */ @@ -8331,41 +8419,49 @@ set ter svg size 640, 480\nunset log y\n /* for(j=3; j <=ncovmodel-nagesqr; j++) { */ for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */ /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ - if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ - if(j==Tage[ij]) { /* Product by age To be looked at!!*/ - if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ - if(DummyV[j]==0){ - fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; - }else{ /* quantitative */ - fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */ - /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + switch(Typevar[j]){ + case 1: + if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ + if(j==Tage[ij]) { /* Product by age To be looked at!!*//* Bug valgrind */ + if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */ + if(DummyV[j]==0){/* Bug valgrind */ + fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; + }else{ /* quantitative */ + fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + ij++; } - ij++; } - } - }else if(cptcovprod >0){ - if(j==Tprod[ijp]) { /* */ - /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */ - if(ijp <=cptcovprod) { /* Product */ - if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */ - if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */ - /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */ - fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); - }else{ /* Vn is dummy and Vm is quanti */ - /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */ - fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); - } - }else{ /* Vn*Vm Vn is quanti */ - if(DummyV[Tvard[ijp][2]]==0){ - fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); - }else{ /* Both quanti */ - fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } + break; + case 2: + if(cptcovprod >0){ + if(j==Tprod[ijp]) { /* */ + /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */ + if(ijp <=cptcovprod) { /* Product */ + if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */ + if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */ + /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */ + fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); + }else{ /* Vn is dummy and Vm is quanti */ + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */ + fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } + }else{ /* Vn*Vm Vn is quanti */ + if(DummyV[Tvard[ijp][2]]==0){ + fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); + }else{ /* Both quanti */ + fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + } } + ijp++; } - ijp++; - } - } /* end Tprod */ - } else{ /* simple covariate */ + } /* end Tprod */ + } + break; + case 0: + /* simple covariate */ /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */ if(Dummy[j]==0){ fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */ @@ -8373,12 +8469,17 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */ /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ } - } /* end simple */ + /* end simple */ + break; + default: + break; + } /* end switch */ } /* end j */ - }else{ - i=i-ncovmodel; - if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */ - fprintf(ficgp," (1."); + }else{ /* k=k2 */ + if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */ + fprintf(ficgp," (1.");i=i-ncovmodel; + }else + i=i-ncovmodel; } if(ng != 1){ @@ -8391,17 +8492,78 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr); ij=1; - for(j=3; j <=ncovmodel-nagesqr; j++){ - if(cptcovage >0){ - if((j-2)==Tage[ij]) { /* Bug valgrind */ - if(ij <=cptcovage) { /* Bug valgrind */ - fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); - /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ - ij++; - } - } - }else - fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */ + ijp=1; + /* for(j=3; j <=ncovmodel-nagesqr; j++){ */ + for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */ + switch(Typevar[j]){ + case 1: + if(cptcovage >0){ + if(j==Tage[ij]) { /* Bug valgrind */ + if(ij <=cptcovage) { /* Bug valgrind */ + if(DummyV[j]==0){/* Bug valgrind */ + /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); */ + /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); */ + fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); + /* fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */ + /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + }else{ /* quantitative */ + /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */ + fprintf(ficgp,"+p%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */ + /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + ij++; + } + } + } + break; + case 2: + if(cptcovprod >0){ + if(j==Tprod[ijp]) { /* */ + /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */ + if(ijp <=cptcovprod) { /* Product */ + if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */ + if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */ + /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */ + fprintf(ficgp,"+p%d*%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); + /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */ + }else{ /* Vn is dummy and Vm is quanti */ + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */ + fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */ + } + }else{ /* Vn*Vm Vn is quanti */ + if(DummyV[Tvard[ijp][2]]==0){ + fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); + /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */ + }else{ /* Both quanti */ + fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); + /* fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */ + } + } + ijp++; + } + } /* end Tprod */ + } /* end if */ + break; + case 0: + /* simple covariate */ + /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */ + if(Dummy[j]==0){ + /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\* *\/ */ + fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /* */ + /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\* *\/ */ + }else{ /* quantitative */ + fprintf(ficgp,"+p%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */ + /* fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* *\/ */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ + } + /* end simple */ + /* fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode *\/ */ + break; + default: + break; + } /* end switch */ } fprintf(ficgp,")"); } @@ -8410,7 +8572,7 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); else /* ng= 3 */ fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); - }else{ /* end ng <> 1 */ + }else{ /* end ng <> 1 */ if( k !=k2) /* logit p11 is hard to draw */ fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k); } @@ -9524,6 +9686,10 @@ int readdata(char datafile[], int firsto DummyV=ivector(1,NCOVMAX); /* 1 to 3 */ FixedV=ivector(1,NCOVMAX); /* 1 to 3 */ + for(v=1;v16 */ ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ @@ -11925,7 +12092,9 @@ Please run with mle=-1 to get a correct Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age 4 covariates (3 plus signs) Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 - */ + */ + for(i=1;i> (k-1)) + 1; * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1 - * h\k 1 2 3 4 - *______________________________ - * 1 i=1 1 i=1 1 i=1 1 i=1 1 - * 2 2 1 1 1 - * 3 i=2 1 2 1 1 - * 4 2 2 1 1 - * 5 i=3 1 i=2 1 2 1 - * 6 2 1 2 1 - * 7 i=4 1 2 2 1 - * 8 2 2 2 1 - * 9 i=5 1 i=3 1 i=2 1 2 - * 10 2 1 1 2 - * 11 i=6 1 2 1 2 - * 12 2 2 1 2 - * 13 i=7 1 i=4 1 2 2 - * 14 2 1 2 2 - * 15 i=8 1 2 2 2 - * 16 2 2 2 2 - */ + * h\k 1 2 3 4 * h-1\k-1 4 3 2 1 + *______________________________ *______________________ + * 1 i=1 1 i=1 1 i=1 1 i=1 1 * 0 0 0 0 0 + * 2 2 1 1 1 * 1 0 0 0 1 + * 3 i=2 1 2 1 1 * 2 0 0 1 0 + * 4 2 2 1 1 * 3 0 0 1 1 + * 5 i=3 1 i=2 1 2 1 * 4 0 1 0 0 + * 6 2 1 2 1 * 5 0 1 0 1 + * 7 i=4 1 2 2 1 * 6 0 1 1 0 + * 8 2 2 2 1 * 7 0 1 1 1 + * 9 i=5 1 i=3 1 i=2 1 2 * 8 1 0 0 0 + * 10 2 1 1 2 * 9 1 0 0 1 + * 11 i=6 1 2 1 2 * 10 1 0 1 0 + * 12 2 2 1 2 * 11 1 0 1 1 + * 13 i=7 1 i=4 1 2 2 * 12 1 1 0 0 + * 14 2 1 2 2 * 13 1 1 0 1 + * 15 i=8 1 2 2 2 * 14 1 1 1 0 + * 16 2 2 2 2 * 15 1 1 1 1 + */ /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */ /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4 * and the value of each covariate? @@ -12138,7 +12307,7 @@ Title=%s
Datafile=%s Firstpass=%d La optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(fichtm,"\n\n\nIMaCh %s\n IMaCh for Interpolated Markov Chain
\nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
\ + fprintf(fichtm,"\n\n\nIMaCh %s\n IMaCh for Interpolated Markov Chain
\nSponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
\
\n\ IMaCh-%s
%s \
\n\ @@ -12548,6 +12717,7 @@ Please run with mle=-1 to get a correct hesscov(matcov, hess, p, npar, delti, ftolhess, func); printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); + fprintf(fichtm, "\n

The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n
Parameters, Wald tests and Wald-based confidence intervals\n
W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n
And Wald-based confidence intervals plus and minus 1.96 * W \n
It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities and its graphs'.\n
",optionfilehtmcov); fprintf(fichtm,"\n"); fprintf(fichtm, "\n"); if(nagesqr==1){ @@ -12581,12 +12751,11 @@ Please run with mle=-1 to get a correct printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); if(fabs(wald) > 1.96){ - fprintf(fichtm, "", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); jk++; } @@ -13188,9 +13357,9 @@ Please run with mle=-1 to get a correct for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ if(i1 != 1 && TKresult[nres]!= k) continue; - printf("\n#****** Result for:"); - fprintf(ficrest,"\n#****** Result for:"); - fprintf(ficlog,"\n#****** Result for:"); + printf("\n# model %s \n#****** Result for:", model); + fprintf(ficrest,"\n# model %s \n#****** Result for:", model); + fprintf(ficlog,"\n# model %s \n#****** Result for:", model); for(j=1;j<=cptcoveff;j++){ printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Model=1+ age%12.7f (%12.7f)
",p[jk],sqrt(matcov[jk][jk])); - fprintf(fichtm,"W=%8.3f
",wald); + fprintf(fichtm, "		%12.7f
(%12.7f)
",p[jk],sqrt(matcov[jk][jk])); }else{ fprintf(fichtm, "		%12.7f (%12.7f)
",p[jk],sqrt(matcov[jk][jk])); - fprintf(fichtm,"W=%8.3f
",wald); } + fprintf(fichtm,"W=%8.3f
",wald); fprintf(fichtm,"[%12.7f;%12.7f]