--- imach/src/imach.c 2022/04/11 15:57:42 1.313 +++ imach/src/imach.c 2022/05/24 08:10:59 1.318 @@ -1,6 +1,22 @@ -/* $Id: imach.c,v 1.313 2022/04/11 15:57:42 brouard Exp $ +/* $Id: imach.c,v 1.318 2022/05/24 08:10:59 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.318 2022/05/24 08:10:59 brouard + * imach.c (Module): Some attempts to find a bug of wrong estimates + of confidencce intervals with product in the equation modelC + + Revision 1.317 2022/05/15 15:06:23 brouard + * imach.c (Module): Some minor improvements + + Revision 1.316 2022/05/11 15:11:31 brouard + Summary: r27 + + Revision 1.315 2022/05/11 15:06:32 brouard + *** empty log message *** + + Revision 1.314 2022/04/13 17:43:09 brouard + * imach.c (Module): Adding link to text data files + Revision 1.313 2022/04/11 15:57:42 brouard * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed @@ -1150,7 +1166,7 @@ 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 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ +#define NCOVMAX 30 /**< Maximum number of covariates, including generated covariates V1*V2 */ #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 @@ -1174,12 +1190,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.313 2022/04/11 15:57:42 brouard Exp $ */ +/* $Id: imach.c,v 1.318 2022/05/24 08:10:59 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; -char copyright[]="March 2021,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, INED 2000-2021"; -char fullversion[]="$Revision: 1.313 $ $Date: 2022/04/11 15:57:42 $"; +char copyright[]="May 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022"; +char fullversion[]="$Revision: 1.318 $ $Date: 2022/05/24 08:10:59 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -1360,6 +1376,10 @@ double ***cotvar; /* Time varying covari double ***cotqvar; /* Time varying quantitative covariate itqv */ double idx; int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ +/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1 + # States 1=Coresidence, 2 Living alone, 3 Institution + # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi +*/ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /*k 1 2 3 4 5 6 7 8 9 */ /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */ @@ -1383,17 +1403,21 @@ int *TvarsDind; int *TvarsQ; int *TvarsQind; -#define MAXRESULTLINES 10 +#define MAXRESULTLINESPONE 10+1 int nresult=0; int parameterline=0; /* # of the parameter (type) line */ -int TKresult[MAXRESULTLINES]; -int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */ -int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */ -int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */ -double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */ -double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */ -int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */ - +int TKresult[MAXRESULTLINESPONE]; +int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */ +int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */ +int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */ +double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */ +double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */ +int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */ + +/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1 + # States 1=Coresidence, 2 Living alone, 3 Institution + # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi +*/ /* int *TDvar; /\**< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */ int *TvarF; /**< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ int *TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ @@ -1877,7 +1901,9 @@ char *subdirf(char fileres[]) /*************** function subdirf2 ***********/ char *subdirf2(char fileres[], char *preop) { - + /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte" + Errors in subdirf, 2, 3 while printing tmpout is + rewritten within the same printf. Workaround: many printfs */ /* Caution optionfilefiname is hidden */ strcpy(tmpout,optionfilefiname); strcat(tmpout,"/"); @@ -2248,10 +2274,10 @@ void linmin(double p[], double xi[], int #endif #ifdef LINMINORIGINAL #else - if(fb == fx){ /* Flat function in the direction */ - xmin=xx; + if(fb == fx){ /* Flat function in the direction */ + xmin=xx; *flat=1; - }else{ + }else{ *flat=0; #endif /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */ @@ -2309,10 +2335,10 @@ void linmin(double p[], double xi[], int /*************** powell ************************/ /* -Minimization of a function func of n variables. Input consists of an initial starting point -p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- -rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value -such that failure to decrease by more than this amount on one iteration signals doneness. On +Minimization of a function func of n variables. Input consists in an initial starting point +p[1..n] ; an initial matrix xi[1..n][1..n] whose columns contain the initial set of di- +rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value +such that failure to decrease by more than this amount in one iteration signals doneness. On output, p is set to the best point found, xi is the then-current direction set, fret is the returned function value at p , and iter is the number of iterations taken. The routine linmin is used. */ @@ -2793,8 +2819,16 @@ void powell(double p[], double **xi, int if(!first){ first=1; printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + }else if (first >=1 && first <10){ + fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + first++; + }else if (first ==10){ + fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); + printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n"); + fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n"); + first++; } - fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax); /* 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); @@ -2963,7 +2997,7 @@ void powell(double p[], double **xi, int maxmax=0.; for(i=1; i<=nlstate; i++){ - meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */ + meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column, could be nan! */ maxmax=FMAX(maxmax,meandiff[i]); /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */ } /* i loop */ @@ -3097,7 +3131,9 @@ double **pmij(double **ps, double *cov, doldm=ddoldms; /* global pointers */ dnewm=ddnewms; dsavm=ddsavms; - + + /* Debug */ + /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */ agefin=cov[2]; /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */ /* bmij *//* age is cov[2], ij is included in cov, but we need for @@ -3421,6 +3457,8 @@ double ***hbxij(double ***po, int nhstep cov[1]=1.; agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */ /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */ + /* Debug */ + /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */ cov[2]=agexact; if(nagesqr==1) cov[3]= agexact*agexact; @@ -3572,10 +3610,10 @@ double func( double *x) if(nagesqr==1) cov[3]= agexact*agexact; /* Should be changed here */ for (kk=1; kk<=cptcovage;kk++) { - if(!FixedV[Tvar[Tage[kk]]]) - cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ - else - cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact; + if(!FixedV[Tvar[Tage[kk]]]) + cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */ + else + cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact; } out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); @@ -5316,12 +5354,20 @@ void concatwav(int wav[], int **dh, int #ifdef UNKNOWNSTATUSNOTCONTRIBUTING break; #else - if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* case -2 (vital status unknown is warned later */ + if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */ if(firsthree == 0){ printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); firsthree=1; + }else if(firsthree >=1 && firsthree < 10){ + fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); + firsthree++; + }else if(firsthree == 10){ + printf("Information, too many Information flags: no more reported to log either\n"); + fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n"); + firsthree++; + }else{ + firsthree++; } - fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath); mw[++mi][i]=m; /* Valid transition with unknown status */ mli=m; } @@ -5394,7 +5440,10 @@ void concatwav(int wav[], int **dh, int } /* End individuals */ /* wav and mw are no more changed */ - + printf("Information, you have to check %d informations which haven't been logged!\n",firsthree); + fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree); + + for(i=1; i<=imx; i++){ for(mi=1; mi
  • Graphs

    • "); + fprintf(fichtm," \n

    "); + fprintf(fichtm," \n"); jj1=0; @@ -7089,8 +7138,10 @@ divided by h: hPij if(prevfcast==1){ /* Projection of prevalence up to period (forward stable) prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
    \n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg
    \ -", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); + fprintf(fichtm,"
    \n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
    ",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_")); + fprintf(fichtm,"", + subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); } } if(prevbcast==1){ @@ -7099,14 +7150,16 @@ divided by h: hPij fprintf(fichtm,"
    \n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \ from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \ account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \ -with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg
    \ - ", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres); +with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
    ",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_")); + fprintf(fichtm," ", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres); } } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"\n
    - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d-%d-%d.svg
    \ -",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); + fprintf(fichtm,"\n
    - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): %s_%d-%d-%d.svg",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); + fprintf(fichtm," (data from text file %s.txt)\n
    ",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_")); + fprintf(fichtm,"", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres ); } /* } /\* end i1 *\/ */ }/* End k1 */ @@ -7158,11 +7211,47 @@ See page 'Matrix of variance-covariance /* else */ /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)

    \n",popforecast, stepm, model); */ fflush(fichtm); - fprintf(fichtm,"