--- imach/src/imach.c 2016/08/26 15:51:03 1.239 +++ imach/src/imach.c 2018/04/27 14:27:04 1.286 @@ -1,6 +1,151 @@ -/* $Id: imach.c,v 1.239 2016/08/26 15:51:03 brouard Exp $ +/* $Id: imach.c,v 1.286 2018/04/27 14:27:04 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.286 2018/04/27 14:27:04 brouard + Summary: some minor bugs + + Revision 1.285 2018/04/21 21:02:16 brouard + Summary: Some bugs fixed, valgrind tested + + Revision 1.284 2018/04/20 05:22:13 brouard + Summary: Computing mean and stdeviation of fixed quantitative variables + + Revision 1.283 2018/04/19 14:49:16 brouard + Summary: Some minor bugs fixed + + Revision 1.282 2018/02/27 22:50:02 brouard + *** empty log message *** + + Revision 1.281 2018/02/27 19:25:23 brouard + Summary: Adding second argument for quitting + + Revision 1.280 2018/02/21 07:58:13 brouard + Summary: 0.99r15 + + New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c + + Revision 1.279 2017/07/20 13:35:01 brouard + Summary: temporary working + + Revision 1.278 2017/07/19 14:09:02 brouard + Summary: Bug for mobil_average=0 and prevforecast fixed(?) + + Revision 1.277 2017/07/17 08:53:49 brouard + Summary: BOM files can be read now + + Revision 1.276 2017/06/30 15:48:31 brouard + Summary: Graphs improvements + + Revision 1.275 2017/06/30 13:39:33 brouard + Summary: Saito's color + + Revision 1.274 2017/06/29 09:47:08 brouard + Summary: Version 0.99r14 + + Revision 1.273 2017/06/27 11:06:02 brouard + Summary: More documentation on projections + + Revision 1.272 2017/06/27 10:22:40 brouard + Summary: Color of backprojection changed from 6 to 5(yellow) + + Revision 1.271 2017/06/27 10:17:50 brouard + Summary: Some bug with rint + + Revision 1.270 2017/05/24 05:45:29 brouard + *** empty log message *** + + Revision 1.269 2017/05/23 08:39:25 brouard + Summary: Code into subroutine, cleanings + + Revision 1.268 2017/05/18 20:09:32 brouard + Summary: backprojection and confidence intervals of backprevalence + + Revision 1.267 2017/05/13 10:25:05 brouard + Summary: temporary save for backprojection + + Revision 1.266 2017/05/13 07:26:12 brouard + Summary: Version 0.99r13 (improvements and bugs fixed) + + Revision 1.265 2017/04/26 16:22:11 brouard + Summary: imach 0.99r13 Some bugs fixed + + Revision 1.264 2017/04/26 06:01:29 brouard + Summary: Labels in graphs + + Revision 1.263 2017/04/24 15:23:15 brouard + Summary: to save + + Revision 1.262 2017/04/18 16:48:12 brouard + *** empty log message *** + + Revision 1.261 2017/04/05 10:14:09 brouard + Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1 + + Revision 1.260 2017/04/04 17:46:59 brouard + Summary: Gnuplot indexations fixed (humm) + + Revision 1.259 2017/04/04 13:01:16 brouard + Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3 + + Revision 1.258 2017/04/03 10:17:47 brouard + Summary: Version 0.99r12 + + Some cleanings, conformed with updated documentation. + + Revision 1.257 2017/03/29 16:53:30 brouard + Summary: Temp + + Revision 1.256 2017/03/27 05:50:23 brouard + Summary: Temporary + + Revision 1.255 2017/03/08 16:02:28 brouard + Summary: IMaCh version 0.99r10 bugs in gnuplot fixed + + Revision 1.254 2017/03/08 07:13:00 brouard + Summary: Fixing data parameter line + + Revision 1.253 2016/12/15 11:59:41 brouard + Summary: 0.99 in progress + + Revision 1.252 2016/09/15 21:15:37 brouard + *** empty log message *** + + Revision 1.251 2016/09/15 15:01:13 brouard + Summary: not working + + Revision 1.250 2016/09/08 16:07:27 brouard + Summary: continue + + 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 *** + + Revision 1.244 2016/09/02 07:17:34 brouard + *** empty log message *** + + Revision 1.243 2016/09/02 06:45:35 brouard + *** empty log message *** + + Revision 1.242 2016/08/30 15:01:20 brouard + Summary: Fixing a lots + + Revision 1.241 2016/08/29 17:17:25 brouard + Summary: gnuplot problem in Back projection to fix + + Revision 1.240 2016/08/29 07:53:18 brouard + Summary: Better + Revision 1.239 2016/08/26 15:51:03 brouard Summary: Improvement in Powell output in order to copy and paste @@ -92,9 +237,7 @@ Author: Nicolas Brouard Revision 1.210 2015/11/18 17:41:20 brouard - Summary: Start working on projected prevalences - - Revision 1.209 2015/11/17 22:12:03 brouard + Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard Summary: Adding ftolpl parameter Author: N Brouard @@ -737,7 +880,7 @@ Back prevalence and projections: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); oldm=oldms;savm=savms; - - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres); Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' months (i.e. until age (in years) age+nhstepm*hstepm*stepm/12) by multiplying @@ -882,7 +1025,7 @@ typedef struct { /* #include */ /* #define _(String) gettext (String) */ -#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ +#define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */ #define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ @@ -905,6 +1048,7 @@ typedef struct { #define YEARM 12. /**< Number of months per year */ /* #define AGESUP 130 */ #define AGESUP 150 +#define AGEINF 0 #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */ #define AGEBASE 40 #define AGEOVERFLOW 1.e20 @@ -919,12 +1063,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.239 2016/08/26 15:51:03 brouard Exp $ */ +/* $Id: imach.c,v 1.286 2018/04/27 14:27:04 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: 1.239 $ $Date: 2016/08/26 15:51:03 $"; +char copyright[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018"; +char fullversion[]="$Revision: 1.286 $ $Date: 2018/04/27 14:27:04 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -996,8 +1140,7 @@ FILE *ficrescveij; char filerescve[FILENAMELENGTH]; FILE *ficresvij; char fileresv[FILENAMELENGTH]; -FILE *ficresvpl; -char fileresvpl[FILENAMELENGTH]; + char title[MAXLINE]; char model[MAXLINE]; /**< The model line */ char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH]; @@ -1037,7 +1180,8 @@ double dval; #define FTOL 1.0e-10 #define NRANSI -#define ITMAX 200 +#define ITMAX 200 +#define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ #define TOL 2.0e-4 @@ -1094,8 +1238,8 @@ double *agedc; double **covar; /**< covar[j,i], value of jth covariate for individual i, * covar=matrix(0,NCOVMAX,1,n); * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ -double **coqvar; /* Fixed quantitative covariate iqv */ -double ***cotvar; /* Time varying covariate itv */ +double **coqvar; /* Fixed quantitative covariate nqv */ +double ***cotvar; /* Time varying covariate ntv */ double ***cotqvar; /* Time varying quantitative covariate itqv */ double idx; int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ @@ -1124,6 +1268,7 @@ int *TvarsQind; #define MAXRESULTLINES 10 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) */ @@ -2066,8 +2211,8 @@ void powell(double p[], double **xi, int void linmin(double p[], double xi[], int n, double *fret, double (*func)(double [])); #else - void linmin(double p[], double xi[], int n, double *fret, - double (*func)(double []),int *flat); + void linmin(double p[], double xi[], int n, double *fret, + double (*func)(double []),int *flat); #endif int i,ibig,j,jk,k; double del,t,*pt,*ptt,*xit; @@ -2107,8 +2252,8 @@ void powell(double p[], double **xi, int printf("\n#model= 1 + age "); fprintf(ficlog,"\n#model= 1 + age "); if(nagesqr==1){ - printf(" + age*age ",Tvar[j]); - fprintf(ficlog," + age*age ",Tvar[j]); + printf(" + age*age "); + fprintf(ficlog," + age*age "); } for(j=1;j <=ncovmodel-2;j++){ if(Typevar[j]==0) { @@ -2131,37 +2276,34 @@ void powell(double p[], double **xi, int if (k != i) { printf("%d%d ",i,k); fprintf(ficlog,"%d%d ",i,k); - fprintf(ficres,"%1d%1d ",i,k); for(j=1; j <=ncovmodel; j++){ printf("%12.7f ",p[jk]); fprintf(ficlog,"%12.7f ",p[jk]); - fprintf(ficres,"%12.7f ",p[jk]); jk++; } printf("\n"); fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); } } } - if(*iter <=3){ + if(*iter <=3 && *iter >1){ tml = *localtime(&rcurr_time); strcpy(strcurr,asctime(&tml)); rforecast_time=rcurr_time; itmp = strlen(strcurr); if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ - strcurr[itmp-1]='\0'; + strcurr[itmp-1]='\0'; printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); for(niterf=10;niterf<=30;niterf+=10){ - rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); - forecast_time = *localtime(&rforecast_time); - strcpy(strfor,asctime(&forecast_time)); - itmp = strlen(strfor); - if(strfor[itmp-1]=='\n') - strfor[itmp-1]='\0'; - printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); - fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); + rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); + forecast_time = *localtime(&rforecast_time); + strcpy(strfor,asctime(&forecast_time)); + itmp = strlen(strfor); + if(strfor[itmp-1]=='\n') + strfor[itmp-1]='\0'; + printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); + fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr); } } for (i=1;i<=n;i++) { /* For each direction i */ @@ -2215,7 +2357,8 @@ void powell(double p[], double **xi, int /* printf("\n"); */ /* fprintf(ficlog,"\n"); */ } - if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ + /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */ + if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */ /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */ /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */ @@ -2261,7 +2404,7 @@ void powell(double p[], double **xi, int free_vector(pt,1,n); return; } /* enough precision */ - if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); + if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */ ptt[j]=2.0*p[j]-pt[j]; xit[j]=p[j]-pt[j]; @@ -2358,8 +2501,8 @@ void powell(double p[], double **xi, int flatd++; } if(flatd >0){ - printf("%d flat directions\n",flatd); - fprintf(ficlog,"%d flat directions\n",flatd); + printf("%d flat directions: ",flatd); + fprintf(ficlog,"%d flat directions :",flatd); for (j=1;j<=n;j++) { if(flatdir[j]>0){ printf("%d ",j); @@ -2399,15 +2542,18 @@ void powell(double p[], double **xi, int double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres) { - /* Computes the prevalence limit in each live state at age x and for covariate combination ij - (and selected quantitative values in nres) - by left multiplying the unit - matrix by transitions matrix until convergence is reached with precision ftolpl */ - /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */ - /* Wx is row vector: population in state 1, population in state 2, population dead */ - /* or prevalence in state 1, prevalence in state 2, 0 */ - /* newm is the matrix after multiplications, its rows are identical at a factor */ - /* Initial matrix pimij */ + /**< Computes the prevalence limit in each live state at age x and for covariate combination ij + * (and selected quantitative values in nres) + * by left multiplying the unit + * matrix by transitions matrix until convergence is reached with precision ftolpl + * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I + * Wx is row vector: population in state 1, population in state 2, population dead + * or prevalence in state 1, prevalence in state 2, 0 + * newm is the matrix after multiplications, its rows are identical at a factor. + * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl. + * Output is prlim. + * Initial matrix pimij + */ /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */ /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */ /* 0, 0 , 1} */ @@ -2541,9 +2687,9 @@ Earliest age to start was %d-%d=%d, ncvl /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */ /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */ - double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij) + double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres) { - /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit + /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit matrix by transitions matrix until convergence is reached with precision ftolpl */ /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */ /* Wx is row vector: population in state 1, population in state 2, population dead */ @@ -2564,6 +2710,7 @@ 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(); @@ -2578,12 +2725,12 @@ Earliest age to start was %d-%d=%d, ncvl max=vector(1,nlstate); meandiff=vector(1,nlstate); - dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms; - oldm=oldms; savm=savms; - - /* Starting with matrix unity */ - for (ii=1;ii<=nlstate+ndeath;ii++) - for (j=1;j<=nlstate+ndeath;j++){ + dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms; + oldm=oldms; savm=savms; + + /* Starting with matrix unity */ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ oldm[ii][j]=(ii==j ? 1.0 : 0.0); } @@ -2600,15 +2747,49 @@ Earliest age to start was %d-%d=%d, ncvl cov[2]=agefin; if(nagesqr==1) cov[3]= agefin*agefin;; - for (k=1; k<=cptcovn;k++) { - /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ - cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; - /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */ - } - for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; - for (k=1; k<=cptcovprod;k++) /* Useless */ - /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; + for (k=1; k<=nsd;k++) { /* For single dummy covariates only */ + /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */ + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)]; + /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */ + } + /* for (k=1; k<=cptcovn;k++) { */ + /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */ + /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */ + /* /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */ + /* } */ + for (k=1; k<=nsq;k++) { /* For single varying covariates only */ + /* Here comes the value of quantitative after renumbering k with single quantitative covariates */ + cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; + /* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */ + } + /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */ + /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */ + /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */ + /* 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[Tvar[Tage[k]]]){ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; + } else{ + cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; + } + /* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */ + } + 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]){ + 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]){ + 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]]; + } + } + } /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ @@ -2623,8 +2804,27 @@ Earliest age to start was %d-%d=%d, ncvl /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */ /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */ + /* if((int)age == 86 || (int)age == 87){ */ + /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */ + /* for(i=1; i<=nlstate+ndeath; i++) { */ + /* printf("%d newm= ",i); */ + /* for(j=1;j<=nlstate+ndeath;j++) { */ + /* printf("%f ",newm[i][j]); */ + /* } */ + /* printf("oldm * "); */ + /* for(j=1;j<=nlstate+ndeath;j++) { */ + /* printf("%f ",oldm[i][j]); */ + /* } */ + /* printf(" bmmij "); */ + /* for(j=1;j<=nlstate+ndeath;j++) { */ + /* printf("%f ",pmmij[i][j]); */ + /* } */ + /* printf("\n"); */ + /* } */ + /* } */ savm=oldm; oldm=newm; + for(j=1; j<=nlstate; j++){ max[j]=0.; min[j]=1.; @@ -2643,9 +2843,9 @@ Earliest age to start was %d-%d=%d, ncvl meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */ 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); */ - } /* j loop */ + } /* i loop */ *ncvyear= -( (int)age- (int)agefin); - /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/ + /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */ if(maxmax < ftolpl){ /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */ free_vector(min,1,nlstate); @@ -2655,7 +2855,12 @@ 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); @@ -2670,7 +2875,7 @@ Oldest age to start was %d-%d=%d, ncvloo double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) { /* According to parameters values stored in x and the covariate's values stored in cov, - computes the probability to be observed in state j being in state i by appying the + computes the probability to be observed in state j (after stepm years) being in state i by appying the model to the ncovmodel covariates (including constant and age). lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] and, according on how parameters are entered, the position of the coefficient xij(nc) of the @@ -2679,8 +2884,9 @@ double **pmij(double **ps, double *cov, j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. - Outputs ps[i][j] the probability to be observed in j being in j according to + Outputs ps[i][j] or probability to be observed in j being in i according to the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] + Sum on j ps[i][j] should equal to 1. */ double s1, lnpijopii; /*double t34;*/ @@ -2744,7 +2950,7 @@ double **pmij(double **ps, double *cov, /* for(i=1; i<= npar; i++) printf("%f ",x[i]); goto end;*/ - return ps; + return ps; /* Pointer is unchanged since its call */ } /*************** backward transition probabilities ***************/ @@ -2753,15 +2959,15 @@ double **pmij(double **ps, double *cov, /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */ double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij ) { - /* Computes the backward probability at age agefin and covariate ij - * and returns in **ps as well as **bmij. + /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too. + * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij. */ int i, ii, j,k; double **out, **pmij(); double sumnew=0.; double agefin; - + double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */ double **dnewm, **dsavm, **doldm; double **bbmij; @@ -2770,43 +2976,68 @@ double **pmij(double **ps, double *cov, dsavm=ddsavms; 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 - the observed prevalence (with this covariate ij) */ - dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); - /* We do have the matrix Px in savm and we need pij */ + the observed prevalence (with this covariate ij) at beginning of transition */ + /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ + + /* P_x */ + pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */ + /* outputs pmmij which is a stochastic matrix in row */ + + /* Diag(w_x) */ + /* Problem with prevacurrent which can be zero */ + sumnew=0.; + /*for (ii=1;ii<=nlstate+ndeath;ii++){*/ + for (ii=1;ii<=nlstate;ii++){ /* Only on live states */ + /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */ + sumnew+=prevacurrent[(int)agefin][ii][ij]; + } + if(sumnew >0.01){ /* At least some value in the prevalence */ + for (ii=1;ii<=nlstate+ndeath;ii++){ + for (j=1;j<=nlstate+ndeath;j++) + doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0); + } + }else{ + for (ii=1;ii<=nlstate+ndeath;ii++){ + for (j=1;j<=nlstate+ndeath;j++) + doldm[ii][j]=(ii==j ? 1./nlstate : 0.0); + } + /* if(sumnew <0.9){ */ + /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */ + /* } */ + } + k3=0.0; /* We put the last diagonal to 0 */ + for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){ + doldm[ii][ii]= k3; + } + /* End doldm, At the end doldm is diag[(w_i)] */ + + /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */ + bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */ + + /* Diag(Sum_i w^i_x p^ij_x */ + /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */ for (j=1;j<=nlstate+ndeath;j++){ - sumnew=0.; /* w1 p11 + w2 p21 only on live states */ + sumnew=0.; for (ii=1;ii<=nlstate;ii++){ - sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; + /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */ + sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */ } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */ for (ii=1;ii<=nlstate+ndeath;ii++){ - if(sumnew >= 1.e-10){ /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */ - /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */ + /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */ /* }else if(agefin >= agemaxpar+stepm/YEARM){ */ - /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */ + /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */ /* }else */ - doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); - }else{ - printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); - } + dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); } /*End ii */ - } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */ - /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */ - bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */ - /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */ - /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */ - /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */ - /* left Product of this matrix by diag matrix of prevalences (savm) */ - for (j=1;j<=nlstate+ndeath;j++){ - for (ii=1;ii<=nlstate+ndeath;ii++){ - dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0); - } - } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */ - ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */ - /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */ + } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */ + + ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */ + /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */ /* end bmij */ - return ps; + return ps; /*pointer is unchanged */ } /*************** transition probabilities ***************/ @@ -3019,20 +3250,20 @@ double ***hpxij(double ***po, int nhstep } for(i=1; i<=nlstate+ndeath; i++) for(j=1;j<=nlstate+ndeath;j++) { - po[i][j][h]=newm[i][j]; - /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ + po[i][j][h]=newm[i][j]; + /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ } /*printf("h=%d ",h);*/ } /* end h */ - /* printf("\n H=%d \n",h); */ + /* printf("\n H=%d \n",h); */ return po; } /************* Higher Back Matrix Product ***************/ /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */ -double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij ) +double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres ) { - /* Computes the transition matrix starting at age 'age' over + /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' months (i.e. until age (in years) age+nhstepm*hstepm*stepm/12) by multiplying nhstepm*hstepm matrices. @@ -3040,18 +3271,19 @@ double ***hbxij(double ***po, int nhstep (typically every 2 years instead of every month which is too big for the memory). Model is determined by parameters x and covariates have to be - included manually here. - + included manually here. Then we use a call to bmij(x and cov) + The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output */ int i, j, d, h, k; - double **out, cov[NCOVMAX+1]; - double **newm; + double **out, cov[NCOVMAX+1], **bmij(); + double **newm, ***newmm; double agexact; double agebegin, ageend; double **oldm, **savm; - oldm=oldms;savm=savms; + newmm=po; /* To be saved */ + oldm=oldms;savm=savms; /* Global pointers */ /* Hstepm could be zero and should return the unit matrix */ for (i=1;i<=nlstate+ndeath;i++) for (j=1;j<=nlstate+ndeath;j++){ @@ -3064,27 +3296,38 @@ double ***hbxij(double ***po, int nhstep newm=savm; /* Covariates have to be included here again */ cov[1]=1.; - agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */ + 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 *\/ */ cov[2]=agexact; if(nagesqr==1) cov[3]= agexact*agexact; - for (k=1; k<=cptcovn;k++) - cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; - /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ - for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ - /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ - cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; - /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */ - for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ + for (k=1; k<=cptcovn;k++){ + /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */ + /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */ + cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)]; + /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */ + } + for (k=1; k<=nsq;k++) { /* For single varying covariates only */ + /* Here comes the value of quantitative after renumbering k with single quantitative covariates */ + cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; + /* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */ + } + for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */ + if(Dummy[Tvar[Tage[k]]]){ + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; + } else{ + cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; + } + /* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */ + } + for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */ cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; - /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */ - - + } /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/ + /* Careful transposed matrix */ - /* age is in cov[2] */ + /* age is in cov[2], prevacurrent at beginning of transition. */ /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */ /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */ out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\ @@ -3109,11 +3352,12 @@ double ***hbxij(double ***po, int nhstep for(i=1; i<=nlstate+ndeath; i++) for(j=1;j<=nlstate+ndeath;j++) { po[i][j][h]=newm[i][j]; - /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/ + /* if(h==nhstepm) */ + /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */ } - /*printf("h=%d ",h);*/ + /* printf("h=%d %.1f ",h, agexact); */ } /* end h */ - /* printf("\n H=%d \n",h); */ + /* printf("\n H=%d nhs=%d \n",h, nhstepm); */ return po; } @@ -3171,7 +3415,7 @@ double func( double *x) Then computes with function pmij which return a matrix p[i][j] giving the elementary probability to be observed in j being in i according to the model. */ - ioffset=2+nagesqr+cptcovage; + ioffset=2+nagesqr ; /* Fixed */ for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */ cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/ @@ -3190,7 +3434,8 @@ double func( double *x) */ for(mi=1; mi<= wav[i]-1; mi++){ for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/ - cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; + /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */ + cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; } for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ @@ -3204,7 +3449,10 @@ 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; } out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); @@ -3486,7 +3734,8 @@ double funcone( double *x) for(k=1; k<=nlstate; k++) ll[k]=0.; ioffset=0; for (i=1,ipmx=0, sw=0.; i<=imx; i++){ - ioffset=2+nagesqr+cptcovage; + /* ioffset=2+nagesqr+cptcovage; */ + ioffset=2+nagesqr; /* Fixed */ /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */ /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */ @@ -3513,52 +3762,57 @@ double funcone( double *x) for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */ /* Wave varying (but not age varying) */ for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/ - cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; - } + /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */ + cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; + } /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */ - /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */ - /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */ - /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */ - /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */ - /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */ + /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */ + /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */ + /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */ + /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */ + /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */ /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */ - /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */ - /* /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */ - /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */ + /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */ + /* /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */ + /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */ /* } */ for (ii=1;ii<=nlstate+ndeath;ii++) - for (j=1;j<=nlstate+ndeath;j++){ - oldm[ii][j]=(ii==j ? 1.0 : 0.0); - savm[ii][j]=(ii==j ? 1.0 : 0.0); - } + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } 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 nlstate && (mle <5) ){ /* Jackson */ - lli=log(out[s1][s2] - savm[s1][s2]); + lli=log(out[s1][s2] - savm[s1][s2]); } else if ( s2==-1 ) { /* alive */ - for (j=1,survp=0. ; j<=nlstate; j++) - survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; - lli= log(survp); + for (j=1,survp=0. ; j<=nlstate; j++) + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + lli= log(survp); }else if (mle==1){ - lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ + lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ } else if(mle==2){ - lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ + lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ } else if(mle==3){ /* exponential inter-extrapolation */ - lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ + lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ } else if (mle==4){ /* mle=4 no inter-extrapolation */ - lli=log(out[s1][s2]); /* Original formula */ + lli=log(out[s1][s2]); /* Original formula */ } else{ /* mle=0 back to 1 */ - lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ - /*lli=log(out[s1][s2]); */ /* Original formula */ + lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ + /*lli=log(out[s1][s2]); */ /* Original formula */ } /* End of if */ ipmx +=1; sw += weight[i]; 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]); */ 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 ", \ - 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]); - for(k=1,llt=0.,l=0.; k<=nlstate; k++){ - llt +=ll[k]*gipmx/gsw; - fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); - } - fprintf(ficresilk," %10.6f\n", -llt); + 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,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); + for(k=1,llt=0.,l=0.; k<=nlstate; k++){ + llt +=ll[k]*gipmx/gsw; + fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw); + } + fprintf(ficresilk," %10.6f\n", -llt); } } /* end of wave */ } /* end of individual */ @@ -3644,7 +3898,7 @@ void likelione(FILE *ficres,double p[], else if(mle >=1) fprintf(fichtm,"\n
File of contributions to the likelihood computed with optimized parameters mle = %d.",mle); fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: %s
\n",subdirf(fileresilk),subdirf(fileresilk)); - + fprintf(fichtm,"\n
Equation of the model: model=1+age+%s
\n",model); for (k=1; k<= nlstate ; k++) { fprintf(fichtm,"
- Probability p%dj by origin %d and destination j. Dot's sizes are related to corresponding weight: %s-p%dj.png
\ @@ -3946,8 +4200,8 @@ double hessij( double x[], double **hess kmax=kmax+10; } 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); - 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); } @@ -4036,7 +4290,16 @@ void ludcmp(double **a, int n, int *indx big=0.0; for (j=1;j<=n;j++) if ((temp=fabs(a[i][j])) > big) big=temp; - if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); + if (big == 0.0){ + printf(" Singular Hessian matrix at row %d:\n",i); + for (j=1;j<=n;j++) { + printf(" a[%d][%d]=%f,",i,j,a[i][j]); + fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]); + } + fflush(ficlog); + fclose(ficlog); + nrerror("Singular matrix in routine ludcmp"); + } vv[i]=1.0/big; } for (j=1;j<=n;j++) { @@ -4102,18 +4365,22 @@ void pstamp(FILE *fichier) fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart); } + + /************ Frequencies ********************/ -void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \ +void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \ int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \ int firstpass, int lastpass, int stepm, int weightopt, char model[]) -{ /* Some frequencies */ +{ /* Some frequencies as well as proposing some starting values */ - int i, m, jk, j1, bool, z1,j, k, iv; + int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1; int iind=0, iage=0; int mi; /* Effective wave */ int first; double ***freq; /* Frequencies */ - double *meanq; + double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */ + int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb); + double *meanq, *stdq, *idq; double **meanqt; double *pp, **prop, *posprop, *pospropt; double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0; @@ -4121,11 +4388,13 @@ void freqsummary(char fileres[], int ia double agebegin, ageend; pp=vector(1,nlstate); - prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); + prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ /* prop=matrix(1,nlstate,iagemin,iagemax+3); */ meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ + stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ + idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ meanqt=matrix(1,lastpass,1,nqtveff); strcpy(fileresp,"P_"); strcat(fileresp,fileresu); @@ -4135,7 +4404,7 @@ void freqsummary(char fileres[], int ia fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); exit(0); } - + strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm")); if((ficresphtm=fopen(fileresphtm,"w"))==NULL) { printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno)); @@ -4145,322 +4414,615 @@ void freqsummary(char fileres[], int ia } else{ fprintf(ficresphtm,"\nIMaCh PHTM_ %s\n %s
%s \ -
\n\ +
\n \ Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } fprintf(ficresphtm,"Current page is file %s
\n\n

Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition

\n",fileresphtm, fileresphtm); - + strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm")); if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) { printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno)); fflush(ficlog); exit(70); - } - else{ + } else{ fprintf(ficresphtmfr,"\nIMaCh PHTM_Frequency table %s\n %s
%s \ -
\n\ +
\n \ Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s
\n",\ fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model); } - fprintf(ficresphtmfr,"Current page is file %s
\n\n

Frequencies of all effective transitions by age at begin of transition

Unknown status is -1
\n",fileresphtmfr, fileresphtmfr); - - freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE); + fprintf(ficresphtmfr,"Current page is file %s
\n\n

Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate)

Unknown status is -1
\n",fileresphtmfr, fileresphtmfr); + + y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE); + x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE); + freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE); j1=0; /* j=ncoveff; /\* Only fixed dummy covariates *\/ */ 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 med_educ V1=1 V2=0, 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 (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]); - scanf("%d", i);*/ - for (i=-5; i<=nlstate+ndeath; i++) - for (jk=-5; jk<=nlstate+ndeath; jk++) - for(m=iagemin; m <= iagemax+3; m++) - freq[i][jk][m]=0; - - for (i=1; i<=nlstate; i++) { - for(m=iagemin; m <= iagemax+3; m++) - prop[i][m]=0; - posprop[i]=0; - pospropt[i]=0; - } - /* for (z1=1; z1<= nqfveff; z1++) { */ - /* meanq[z1]+=0.; */ - /* for(m=1;m<=lastpass;m++){ */ - /* meanqt[m][z1]=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(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++) { */ - /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */ - /* } */ - for (z1=1; z1<=cptcoveff; z1++) { - /* if(Tvaraff[z1] ==-20){ */ - /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */ - /* }else if(Tvaraff[z1] ==-10){ */ - /* /\* sumnew+=coqvar[z1][iind]; *\/ */ - /* }else */ - if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ - /* Tests if this individual iind responded to j1 (V4=1 V3=0) */ - bool=0; - /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", - bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1), - j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/ - /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/ - } /* Onlyf fixed */ - } /* end z1 */ - } /* cptcovn > 0 */ - } /* end any */ - if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */ - /* for(m=firstpass; m<=lastpass; m++){ */ - for(mi=1; mi0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ + for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */ + /* if(Tvaraff[z1] ==-20){ */ + /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */ + /* }else if(Tvaraff[z1] ==-10){ */ + /* /\* sumnew+=coqvar[z1][iind]; *\/ */ + /* }else */ + if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */ + /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */ + bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */ + /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", + bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1), + j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/ + /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/ + } /* Onlyf fixed */ + } /* end z1 */ + } /* cptcovn > 0 */ + } /* end any */ + }/* end j==0 */ + if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */ + /* for(m=firstpass; m<=lastpass; m++){ */ + for(mi=1; mi=firstpass && m <=lastpass){ + k2=anint[m][iind]+(mint[m][iind]/12.); + /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ + if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */ + if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */ + if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */ + prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */ + if (m1) && (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); */ } + }else{ + bool=1; + }/* end bool 2 */ + } /* end m */ + /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */ + /* idq[z1]=idq[z1]+weight[iind]; */ + /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */ + /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */ + /* } */ + } /* end bool */ + } /* end iind = 1 to imx */ + /* prop[s][age] is feeded for any initial and valid live state as well as + freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */ + + + /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ + if(cptcoveff==0 && nj==1) /* no covariate and first pass */ + pstamp(ficresp); + if (cptcoveff>0 && j!=0){ + pstamp(ficresp); + printf( "\n#********** Variable "); + fprintf(ficresp, "\n#********** Variable "); + fprintf(ficresphtm, "\n

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

********** Variable "); + fprintf(ficlog, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++){ + if(!FixedV[Tvaraff[z1]]){ + printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + }else{ + printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + } + } + printf( "**********\n#"); + fprintf(ficresp, "**********\n#"); + fprintf(ficresphtm, "**********

\n"); + fprintf(ficresphtmfr, "**********\n"); + fprintf(ficlog, "**********\n"); + } + /* + Printing means of quantitative variables if any + */ + for (z1=1; z1<= nqfveff; z1++) { + fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]); + fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]); + if(weightopt==1){ + printf(" Weighted mean and standard deviation of"); + fprintf(ficlog," Weighted mean and standard deviation of"); + fprintf(ficresphtmfr," Weighted mean and standard deviation of"); + } + printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1])); + fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1])); + fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)

\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1])); + } + /* for (z1=1; z1<= nqtveff; z1++) { */ + /* for(m=1;m<=lastpass;m++){ */ + /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f

\n", z1, m, meanqt[m][z1]); */ + /* } */ + /* } */ + + fprintf(ficresphtm,""); + if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */ + fprintf(ficresp, " Age"); + if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + for(i=1; i<=nlstate;i++) { + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i); + fprintf(ficresphtm, "",i,i); + } + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n"); + fprintf(ficresphtm, "\n"); + + /* Header of frequency table by age */ + fprintf(ficresphtmfr,"
AgePrev(%d)N(%d)N
"); + fprintf(ficresphtmfr," "); + for(s2=-1; s2 <=nlstate+ndeath; s2++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(s2!=0 && m!=0) + fprintf(ficresphtmfr," ",s2,m); + } + } + fprintf(ficresphtmfr, "\n"); + + /* For each age */ + for(iage=iagemin; iage <= iagemax+3; iage++){ + fprintf(ficresphtm,""); + if(iage==iagemax+1){ + fprintf(ficlog,"1"); + fprintf(ficresphtmfr," "); + }else if(iage==iagemax+2){ + fprintf(ficlog,"0"); + fprintf(ficresphtmfr," "); + }else if(iage==iagemax+3){ + fprintf(ficlog,"Total"); + fprintf(ficresphtmfr," "); + }else{ + if(first==1){ + first=0; + printf("See log file for details...\n"); + } + fprintf(ficresphtmfr," ",iage); + fprintf(ficlog,"Age %d", iage); + } + for(s1=1; s1 <=nlstate ; s1++){ + for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++) + pp[s1] += freq[s1][m][iage]; + } + for(s1=1; s1 <=nlstate ; s1++){ + for(m=-1, pos=0; m <=0 ; m++) + pos += freq[s1][m][iage]; + if(pp[s1]>=1.e-10){ + if(first==1){ + printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]); + } + fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]); + }else{ + if(first==1) + printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1); + fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1); + } + } + + for(s1=1; s1 <=nlstate ; s1++){ + /* posprop[s1]=0; */ + for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */ + pp[s1] += freq[s1][m][iage]; + } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */ + + for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){ + pos += pp[s1]; /* pos is the total number of transitions until this age */ + posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state + from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state + from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + } + + /* Writing ficresp */ + if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + if( iage <= iagemax){ + fprintf(ficresp," %d",iage); + } + }else if( nj==2){ + if( iage <= iagemax){ + fprintf(ficresp," %d",iage); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + } + } + for(s1=1; s1 <=nlstate ; s1++){ + if(pos>=1.e-5){ + if(first==1) + printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos); + fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos); + }else{ + if(first==1) + printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1); + fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1); + } + if( iage <= iagemax){ + if(pos>=1.e-5){ + if(cptcoveff==0 && nj==1){ /* no covariate and first pass */ + fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + }else if( nj==2){ + fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + } + fprintf(ficresphtm,"",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta); + /*probs[iage][s1][j1]= pp[s1]/pos;*/ + /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/ + } else{ + if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta); + fprintf(ficresphtm,"",iage, prop[s1][iage],pospropta); } - }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */ - /* 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] - and mw[mi+1][iind]. dh depends on stepm. */ - agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/ - ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */ - if(m >=firstpass && m <=lastpass){ - k2=anint[m][iind]+(mint[m][iind]/12.); - /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/ - if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */ - if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */ - if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */ - prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */ - if (m1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) { - dateintsum=dateintsum+k2; - k2cpt++; - /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ + /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */ + fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]); } - } /* end bool 2 */ - } /* end m */ - } /* end bool */ - } /* end iind = 1 to imx */ - /* prop[s][age] is feeded for any initial and valid live state as well as - freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */ - - - /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ - pstamp(ficresp); - /* if (ncoveff>0) { */ - if (cptcoveff>0) { - fprintf(ficresp, "\n#********** Variable "); - fprintf(ficresphtm, "\n

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

********** Variable "); - for (z1=1; z1<=cptcoveff; z1++){ - fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - } - fprintf(ficresp, "**********\n#"); - fprintf(ficresphtm, "**********

\n"); - fprintf(ficresphtmfr, "**********\n"); - fprintf(ficlog, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); - fprintf(ficlog, "**********\n"); - } - fprintf(ficresphtm,"
Age%d%d
0
Unknown
Total
%d%d%.5f%.0f%.0f%dNaNq%.0f%.0f
"); - for(i=1; i<=nlstate;i++) { - fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); - fprintf(ficresphtm, "",i,i); - } - fprintf(ficresp, "\n"); - fprintf(ficresphtm, "\n"); - - /* Header of frequency table by age */ - fprintf(ficresphtmfr,"
AgePrev(%d)N(%d)N
"); - fprintf(ficresphtmfr," "); - for(jk=-1; jk <=nlstate+ndeath; jk++){ - for(m=-1; m <=nlstate+ndeath; m++){ - if(jk!=0 && m!=0) - fprintf(ficresphtmfr," ",jk,m); + if(s1!=0 && m!=0) + fprintf(ficresphtmfr," ",freq[s1][m][iage]); + } + } /* end loop s1 */ + posproptt=0.; + for(s1=1; s1 <=nlstate; s1++){ + posproptt += pospropt[s1]; + } + fprintf(ficresphtmfr,"\n "); + fprintf(ficresphtm,"\n"); + if((cptcoveff==0 && nj==1)|| nj==2 ) { + if(iage <= iagemax) + fprintf(ficresp,"\n"); + } + if(first==1) + printf("Others in log...\n"); + fprintf(ficlog,"\n"); + } /* end loop age iage */ + + fprintf(ficresphtm,""); + for(s1=1; s1 <=nlstate ; s1++){ + if(posproptt < 1.e-5){ + fprintf(ficresphtm,"",pospropt[s1],posproptt); + }else{ + fprintf(ficresphtm,"",pospropt[s1]/posproptt,pospropt[s1],posproptt); + } } - } - fprintf(ficresphtmfr, "\n"); - - /* For each age */ - for(iage=iagemin; iage <= iagemax+3; iage++){ - fprintf(ficresphtm,""); - if(iage==iagemax+1){ - fprintf(ficlog,"1"); - fprintf(ficresphtmfr," "); - }else if(iage==iagemax+2){ - fprintf(ficlog,"0"); - fprintf(ficresphtmfr," "); - }else if(iage==iagemax+3){ - fprintf(ficlog,"Total"); - fprintf(ficresphtmfr," "); + fprintf(ficresphtm,"\n"); + fprintf(ficresphtm,"
Age%d%d%.0f
TotNanq%.0f%.0f%.5f%.0f%.0f
0
Unknown
Total
\n"); + fprintf(ficresphtmfr,"\n"); + if(posproptt < 1.e-5){ + fprintf(ficresphtm,"\n

This combination (%d) is not valid and no result will be produced

",j1); + fprintf(ficresphtmfr,"\n

This combination (%d) is not valid and no result will be produced

",j1); + fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1); + printf("# This combination (%d) is not valid and no result will be produced\n",j1); + invalidvarcomb[j1]=1; }else{ - if(first==1){ - first=0; - printf("See log file for details...\n"); - } - fprintf(ficresphtmfr,"%d ",iage); - fprintf(ficlog,"Age %d", iage); - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) - pp[jk] += freq[jk][m][iage]; - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pos=0; m <=0 ; m++) - pos += freq[jk][m][iage]; - if(pp[jk]>=1.e-10){ - if(first==1){ - printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); - } - fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]); - }else{ - if(first==1) - printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk); - } - } - - for(jk=1; jk <=nlstate ; jk++){ - /* posprop[jk]=0; */ - for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */ - pp[jk] += freq[jk][m][iage]; - } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */ - - for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){ - pos += pp[jk]; /* pos is the total number of transitions until this age */ - posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state - from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ - pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state - from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ - } - for(jk=1; jk <=nlstate ; jk++){ - if(pos>=1.e-5){ - if(first==1) - printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); - }else{ - if(first==1) - printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); - } - if( iage <= iagemax){ - if(pos>=1.e-5){ - fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta); - fprintf(ficresphtm,"%d%.5f%.0f%.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta); - /*probs[iage][jk][j1]= pp[jk]/pos;*/ - /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/ - } - else{ - fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta); - fprintf(ficresphtm,"%dNaNq%.0f%.0f",iage, prop[jk][iage],pospropta); - } - } - pospropt[jk] +=posprop[jk]; - } /* end loop jk */ - /* pospropt=0.; */ - for(jk=-1; jk <=nlstate+ndeath; jk++){ - for(m=-1; m <=nlstate+ndeath; m++){ - 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]); - } - if(jk!=0 && m!=0) - fprintf(ficresphtmfr,"%.0f ",freq[jk][m][iage]); - } - } /* end loop jk */ - posproptt=0.; - for(jk=1; jk <=nlstate; jk++){ - posproptt += pospropt[jk]; - } - fprintf(ficresphtmfr,"\n "); - if(iage <= iagemax){ - fprintf(ficresp,"\n"); - fprintf(ficresphtm,"\n"); + fprintf(ficresphtm,"\n

This combination (%d) is valid and result will be produced.

",j1); + invalidvarcomb[j1]=0; } - if(first==1) - printf("Others in log...\n"); + fprintf(ficresphtmfr,"\n"); fprintf(ficlog,"\n"); - } /* end loop age iage */ - fprintf(ficresphtm,"Tot"); - for(jk=1; jk <=nlstate ; jk++){ - if(posproptt < 1.e-5){ - fprintf(ficresphtm,"Nanq%.0f%.0f",pospropt[jk],posproptt); - }else{ - fprintf(ficresphtm,"%.5f%.0f%.0f",pospropt[jk]/posproptt,pospropt[jk],posproptt); + if(j!=0){ + printf("#Freqsummary: Starting values for combination j1=%d:\n", j1); + for(i=1,s1=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */ + if(jj==1){ /* Constant case (in fact cste + age) */ + if(j1==1){ /* All dummy covariates to zero */ + freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */ + freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */ + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3])); + fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]); + } + }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */ + for(iage=iagemin; iage <= iagemax+3; iage++){ + x[iage]= (double)iage; + y[iage]= log(freq[i][k][iage]/freq[i][i][iage]); + /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */ + } + /* Some are not finite, but linreg will ignore these ages */ + no=0; + linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */ + pstart[s1]=b; + pstart[s1-1]=a; + }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj) && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ + printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]); + printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]); + pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])); + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4])); + }else{ /* Other cases, like quantitative fixed or varying covariates */ + ; + } + /* printf("%12.7f )", param[i][jj][k]); */ + /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */ + s1++; + } /* end jj */ + } /* end k!= i */ + } /* end k */ + } /* end i, s1 */ + } /* end j !=0 */ + } /* end selected combination of covariate j1 */ + if(j==0){ /* We can estimate starting values from the occurences in each case */ + printf("#Freqsummary: Starting values for the constants:\n"); + fprintf(ficlog,"\n"); + for(i=1,s1=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + for(jj=1; jj <=ncovmodel; jj++){ + pstart[s1]=p[s1]; /* Setting pstart to p values by default */ + if(jj==1){ /* Age has to be done */ + pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]); + printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + } + /* printf("%12.7f )", param[i][jj][k]); */ + /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */ + s1++; + } + printf("\n"); + fprintf(ficlog,"\n"); + } + } + } /* end of state i */ + printf("#Freqsummary\n"); + fprintf(ficlog,"\n"); + for(s1=-1; s1 <=nlstate+ndeath; s1++){ + for(s2=-1; s2 <=nlstate+ndeath; s2++){ + /* param[i]|j][k]= freq[s1][s2][iagemax+3] */ + printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); + fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); + /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */ + /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */ + /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */ + /* } */ + } + } /* end loop s1 */ + + printf("\n"); + fprintf(ficlog,"\n"); + } /* end j=0 */ + } /* end j */ + + if(mle == -2){ /* We want to use these values as starting values */ + for(i=1, jk=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath; j++){ + if(j!=i){ + /*ca[0]= k+'a'-1;ca[1]='\0';*/ + printf("%1d%1d",i,j); + fprintf(ficparo,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + /* printf(" %lf",param[i][j][k]); */ + /* fprintf(ficparo," %lf",param[i][j][k]); */ + p[jk]=pstart[jk]; + printf(" %f ",pstart[jk]); + fprintf(ficparo," %f ",pstart[jk]); + jk++; + } + printf("\n"); + fprintf(ficparo,"\n"); + } } } - fprintf(ficresphtm,"\n"); - fprintf(ficresphtm,"\n"); - fprintf(ficresphtmfr,"\n"); - if(posproptt < 1.e-5){ - fprintf(ficresphtm,"\n

This combination (%d) is not valid and no result will be produced

",j1); - fprintf(ficresphtmfr,"\n

This combination (%d) is not valid and no result will be produced

",j1); - fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1); - invalidvarcomb[j1]=1; - }else{ - fprintf(ficresphtm,"\n

This combination (%d) is valid and result will be produced.

",j1); - invalidvarcomb[j1]=0; - } - fprintf(ficresphtmfr,"\n"); - } /* end selected combination of covariate j1 */ + } /* end mle=-2 */ dateintmean=dateintsum/k2cpt; - + fclose(ficresp); fclose(ficresphtm); fclose(ficresphtmfr); + free_vector(idq,1,nqfveff); free_vector(meanq,1,nqfveff); + free_vector(stdq,1,nqfveff); free_matrix(meanqt,1,lastpass,1,nqtveff); - free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE); + free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE); + free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE); free_vector(pospropt,1,nlstate); free_vector(posprop,1,nlstate); - free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE); + free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE); free_vector(pp,1,nlstate); /* End of freqsummary */ } +/* Simple linear regression */ +int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) { + + /* y=a+bx regression */ + double sumx = 0.0; /* sum of x */ + double sumx2 = 0.0; /* sum of x**2 */ + double sumxy = 0.0; /* sum of x * y */ + double sumy = 0.0; /* sum of y */ + double sumy2 = 0.0; /* sum of y**2 */ + double sume2 = 0.0; /* sum of square or residuals */ + double yhat; + + double denom=0; + int i; + int ne=*no; + + for ( i=ifi, ne=0;i<=ila;i++) { + if(!isfinite(x[i]) || !isfinite(y[i])){ + /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */ + continue; + } + ne=ne+1; + sumx += x[i]; + sumx2 += x[i]*x[i]; + sumxy += x[i] * y[i]; + sumy += y[i]; + sumy2 += y[i]*y[i]; + denom = (ne * sumx2 - sumx*sumx); + /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */ + } + + denom = (ne * sumx2 - sumx*sumx); + if (denom == 0) { + // vertical, slope m is infinity + *b = INFINITY; + *a = 0; + if (r) *r = 0; + return 1; + } + + *b = (ne * sumxy - sumx * sumy) / denom; + *a = (sumy * sumx2 - sumx * sumxy) / denom; + if (r!=NULL) { + *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */ + sqrt((sumx2 - sumx*sumx/ne) * + (sumy2 - sumy*sumy/ne)); + } + *no=ne; + for ( i=ifi, ne=0;i<=ila;i++) { + if(!isfinite(x[i]) || !isfinite(y[i])){ + /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */ + continue; + } + ne=ne+1; + yhat = y[i] - *a -*b* x[i]; + sume2 += yhat * yhat ; + + denom = (ne * sumx2 - sumx*sumx); + /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */ + } + *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne)); + *sa= *sb * sqrt(sumx2/ne); + + return 0; +} + /************ Prevalence ********************/ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) { @@ -4483,7 +5045,7 @@ void prevalence(double ***probs, double iagemin= (int) agemin; iagemax= (int) agemax; /*pp=vector(1,nlstate);*/ - prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); + prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ j1=0; @@ -4493,7 +5055,7 @@ void prevalence(double ***probs, double first=1; for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */ for (i=1; i<=nlstate; i++) - for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++) + for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++) prop[i][iage]=0.0; printf("Prevalence combination of varying and fixed dummies %d\n",j1); /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */ @@ -4524,7 +5086,7 @@ void prevalence(double ***probs, double if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ if(agev[m][i]==0) agev[m][i]=iagemax+1; if(agev[m][i]==1) agev[m][i]=iagemax+2; - if((int)agev[m][i] iagemax+3+AGEMARGE){ + if((int)agev[m][i] iagemax+4+AGEMARGE){ printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); exit(1); } @@ -4550,7 +5112,10 @@ void prevalence(double ***probs, double } else{ if(first==1){ first=0; - printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]); + printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); + fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); + }else{ + fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]); } } } @@ -4561,7 +5126,7 @@ void prevalence(double ***probs, double /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ /*free_vector(pp,1,nlstate);*/ - free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE); + free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE); } /* End of prevalence */ /************* Waves Concatenation ***************/ @@ -4610,10 +5175,10 @@ void concatwav(int wav[], int **dh, int #else if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ 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 pi. .\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); + 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; } - 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 pi. .\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); + 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; mli=m; } @@ -4640,13 +5205,9 @@ void concatwav(int wav[], int **dh, int /* if(mi==0) never been interviewed correctly before death */ /* Only death is a correct wave */ mw[mi][i]=m; - } + } /* else not in a death state */ #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE - else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */ - /* m++; */ - /* mi++; */ - /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */ - /* mw[mi][i]=m; */ + else if ((int) andc[i] != 9999) { /* Date of death is known */ if ((int)anint[m][i]!= 9999) { /* date of last interview is known */ if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */ nbwarn++; @@ -4659,12 +5220,12 @@ void concatwav(int wav[], int **dh, int }else{ /* Death occured afer last wave potential bias */ nberr++; if(firstwo==0){ - printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); firstwo=1; } - fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); } - }else{ /* end date of interview is known */ + }else{ /* if date of interview is unknown */ /* death is known but not confirmed by death status at any wave */ if(firstfour==0){ printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); @@ -4695,7 +5256,7 @@ void concatwav(int wav[], int **dh, int if (stepm <=0) dh[mi][i]=1; else{ - if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ + if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */ if (agedc[i] < 2*AGESUP) { j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); if(j==0) j=1; /* Survives at least one month after exam */ @@ -4782,173 +5343,176 @@ void concatwav(int wav[], int **dh, int /*********** Tricode ****************************/ void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum) -{ - /**< Uses cptcovn+2*cptcovprod as the number of covariates */ - /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 - * Boring subroutine which should only output nbcode[Tvar[j]][k] - * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable - * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually); - */ + { + /**< Uses cptcovn+2*cptcovprod as the number of covariates */ + /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 + * Boring subroutine which should only output nbcode[Tvar[j]][k] + * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable + * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually); + */ - int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; - int modmaxcovj=0; /* Modality max of covariates j */ - int cptcode=0; /* Modality max of covariates j */ - int modmincovj=0; /* Modality min of covariates j */ + int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; + int modmaxcovj=0; /* Modality max of covariates j */ + int cptcode=0; /* Modality max of covariates j */ + int modmincovj=0; /* Modality min of covariates j */ - /* cptcoveff=0; */ - /* *cptcov=0; */ + /* cptcoveff=0; */ + /* *cptcov=0; */ - for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ - - /* Loop on covariates without age and products and no quantitative variable */ - /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */ - for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */ - for (j=-1; (j < maxncov); j++) Ndum[j]=0; - if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ - switch(Fixed[k]) { - case 0: /* Testing on fixed dummy covariate, simple or product of fixed */ - for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/ - ij=(int)(covar[Tvar[k]][i]); - /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i - * If product of Vn*Vm, still boolean *: - * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables - * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ - /* Finds for covariate j, n=Tvar[j] of Vn . ij is the - modality of the nth covariate of individual i. */ - if (ij > modmaxcovj) - modmaxcovj=ij; - else if (ij < modmincovj) - modmincovj=ij; - if ((ij < -1) && (ij > NCOVMAX)){ - printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); - exit(1); - }else - Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ - /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ - /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ - /* getting the maximum value of the modality of the covariate - (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and - female ies 1, then modmaxcovj=1. - */ - } /* end for loop on individuals i */ - printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj); - fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj); - cptcode=modmaxcovj; - /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ - /*for (i=0; i<=cptcode; i++) {*/ - for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */ - printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]); - fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]); - if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */ - if( j != -1){ - ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th - covariate for which somebody answered excluding - undefined. Usually 2: 0 and 1. */ - } - ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th - covariate for which somebody answered including - undefined. Usually 3: -1, 0 and 1. */ - } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for - * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ - } /* Ndum[-1] number of undefined modalities */ + for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ + for (k=1; k <= maxncov; k++) + for(j=1; j<=2; j++) + nbcode[k][j]=0; /* Valgrind */ + + /* Loop on covariates without age and products and no quantitative variable */ + /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */ + for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */ + for (j=-1; (j < maxncov); j++) Ndum[j]=0; + if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ + switch(Fixed[k]) { + case 0: /* Testing on fixed dummy covariate, simple or product of fixed */ + for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/ + ij=(int)(covar[Tvar[k]][i]); + /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i + * If product of Vn*Vm, still boolean *: + * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables + * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */ + /* Finds for covariate j, n=Tvar[j] of Vn . ij is the + modality of the nth covariate of individual i. */ + if (ij > modmaxcovj) + modmaxcovj=ij; + else if (ij < modmincovj) + modmincovj=ij; + if ((ij < -1) && (ij > NCOVMAX)){ + printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX ); + exit(1); + }else + Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/ + /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */ + /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/ + /* getting the maximum value of the modality of the covariate + (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and + female ies 1, then modmaxcovj=1. + */ + } /* end for loop on individuals i */ + printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj); + fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj); + cptcode=modmaxcovj; + /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */ + /*for (i=0; i<=cptcode; i++) {*/ + for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */ + printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]); + fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]); + if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */ + if( j != -1){ + ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th + covariate for which somebody answered excluding + undefined. Usually 2: 0 and 1. */ + } + ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th + covariate for which somebody answered including + undefined. Usually 3: -1, 0 and 1. */ + } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for + * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ + } /* Ndum[-1] number of undefined modalities */ - /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ - /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */ - /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */ - /* modmincovj=3; modmaxcovj = 7; */ - /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */ - /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */ - /* defining two dummy variables: variables V1_1 and V1_2.*/ - /* nbcode[Tvar[j]][ij]=k; */ - /* nbcode[Tvar[j]][1]=0; */ - /* nbcode[Tvar[j]][2]=1; */ - /* nbcode[Tvar[j]][3]=2; */ - /* To be continued (not working yet). */ - ij=0; /* ij is similar to i but can jump over null modalities */ - for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ - if (Ndum[i] == 0) { /* If nobody responded to this modality k */ - break; - } - ij++; - nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/ - cptcode = ij; /* New max modality for covar j */ - } /* end of loop on modality i=-1 to 1 or more */ - break; - case 1: /* Testing on varying covariate, could be simple and - * should look at waves or product of fixed * - * varying. No time to test -1, assuming 0 and 1 only */ - ij=0; - for(i=0; i<=1;i++){ - nbcode[Tvar[k]][++ij]=i; - } - break; - default: - break; - } /* end switch */ - } /* end dummy test */ - - /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ - /* /\*recode from 0 *\/ */ - /* k is a modality. If we have model=V1+V1*sex */ - /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ - /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ - /* } */ - /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ - /* if (ij > ncodemax[j]) { */ - /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ - /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ - /* break; */ - /* } */ - /* } /\* end of loop on modality k *\/ */ - } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ - - for (k=-1; k< maxncov; k++) Ndum[k]=0; - /* Look at fixed dummy (single or product) covariates to check empty modalities */ - for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ - /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ - ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ - Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */ - /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */ - } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */ - - ij=0; - /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */ - for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ - /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ - /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */ - if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */ - /* If product not in single variable we don't print results */ - /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ - ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */ - Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/ - Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */ - TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */ - if(Fixed[k]!=0) - anyvaryingduminmodel=1; - /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */ - /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */ - /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */ - /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */ - /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */ - /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */ - } - } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */ - /* ij--; */ - /* cptcoveff=ij; /\*Number of total covariates*\/ */ - *cptcov=ij; /*Number of total real effective covariates: effective - * because they can be excluded from the model and real - * if in the model but excluded because missing values, but how to get k from ij?*/ - for(j=ij+1; j<= cptcovt; j++){ - Tvaraff[j]=0; - Tmodelind[j]=0; - } - for(j=ntveff+1; j<= cptcovt; j++){ - TmodelInvind[j]=0; - } - /* To be sorted */ - ; -} + /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ + /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */ + /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */ + /* modmincovj=3; modmaxcovj = 7; */ + /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */ + /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */ + /* defining two dummy variables: variables V1_1 and V1_2.*/ + /* nbcode[Tvar[j]][ij]=k; */ + /* nbcode[Tvar[j]][1]=0; */ + /* nbcode[Tvar[j]][2]=1; */ + /* nbcode[Tvar[j]][3]=2; */ + /* To be continued (not working yet). */ + ij=0; /* ij is similar to i but can jump over null modalities */ + for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/ + if (Ndum[i] == 0) { /* If nobody responded to this modality k */ + break; + } + ij++; + nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/ + cptcode = ij; /* New max modality for covar j */ + } /* end of loop on modality i=-1 to 1 or more */ + break; + case 1: /* Testing on varying covariate, could be simple and + * should look at waves or product of fixed * + * varying. No time to test -1, assuming 0 and 1 only */ + ij=0; + for(i=0; i<=1;i++){ + nbcode[Tvar[k]][++ij]=i; + } + break; + default: + break; + } /* end switch */ + } /* end dummy test */ + + /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */ + /* /\*recode from 0 *\/ */ + /* k is a modality. If we have model=V1+V1*sex */ + /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ + /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */ + /* } */ + /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */ + /* if (ij > ncodemax[j]) { */ + /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ + /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */ + /* break; */ + /* } */ + /* } /\* end of loop on modality k *\/ */ + } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/ + + for (k=-1; k< maxncov; k++) Ndum[k]=0; + /* Look at fixed dummy (single or product) covariates to check empty modalities */ + for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ + /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ + ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ + Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */ + /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */ + } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */ + + ij=0; + /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */ + for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ + /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ + /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */ + if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */ + /* If product not in single variable we don't print results */ + /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ + ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */ + Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/ + Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */ + TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */ + if(Fixed[k]!=0) + anyvaryingduminmodel=1; + /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */ + /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */ + /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */ + /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */ + /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */ + /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */ + } + } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */ + /* ij--; */ + /* cptcoveff=ij; /\*Number of total covariates*\/ */ + *cptcov=ij; /*Number of total real effective covariates: effective + * because they can be excluded from the model and real + * if in the model but excluded because missing values, but how to get k from ij?*/ + for(j=ij+1; j<= cptcovt; j++){ + Tvaraff[j]=0; + Tmodelind[j]=0; + } + for(j=ntveff+1; j<= cptcovt; j++){ + TmodelInvind[j]=0; + } + /* To be sorted */ + ; + } /*********** Health Expectancies ****************/ @@ -4994,7 +5558,7 @@ void concatwav(int wav[], int **dh, int /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. nhstepm is the number of hstepm from age to agelim nstepm is the number of stepm from age to agelin. - Look at hpijx to understand the reason of that which relies in memory size + Look at hpijx to understand the reason which relies in memory size consideration and note for a fixed period like estepm months */ /* We decided (b) to get a life expectancy respecting the most precise curvature of the survival function given by stepm (the optimization length). Unfortunately it @@ -5225,7 +5789,8 @@ void concatwav(int wav[], int **dh, int /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ } - + + /* Standard deviation of expectancies ij */ fprintf(ficresstdeij,"%3.0f",age ); for(i=1; i<=nlstate;i++){ eip=0.; @@ -5240,6 +5805,7 @@ void concatwav(int wav[], int **dh, int } fprintf(ficresstdeij,"\n"); + /* Variance of expectancies ij */ fprintf(ficrescveij,"%3.0f",age ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ @@ -5273,10 +5839,11 @@ void concatwav(int wav[], int **dh, int /************ Variance ******************/ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres) { - /* Variance of health expectancies */ - /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ - /* double **newm;*/ - /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ + /** Variance of health expectancies + * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl); + * double **newm; + * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav) + */ /* int movingaverage(); */ double **dnewm,**doldm; @@ -5284,11 +5851,11 @@ void concatwav(int wav[], int **dh, int int i, j, nhstepm, hstepm, h, nstepm ; int k; double *xp; - double **gp, **gm; /* for var eij */ - double ***gradg, ***trgradg; /*for var eij */ - double **gradgp, **trgradgp; /* for var p point j */ - double *gpp, *gmp; /* for var p point j */ - double **varppt; /* for var p point j nlstate to nlstate+ndeath */ + double **gp, **gm; /**< for var eij */ + double ***gradg, ***trgradg; /**< for var eij */ + double **gradgp, **trgradgp; /**< for var p point j */ + double *gpp, *gmp; /**< for var p point j */ + double **varppt; /**< for var p point j nlstate to nlstate+ndeath */ double ***p3mat; double age,agelim, hf; /* double ***mobaverage; */ @@ -5349,7 +5916,7 @@ void concatwav(int wav[], int **dh, int /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ fprintf(fichtm,"\n

  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); fprintf(fichtm,"\n
    %s
    \n",digitp); - /* } */ + varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); pstamp(ficresvij); fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); @@ -5404,9 +5971,12 @@ void concatwav(int wav[], int **dh, int for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ xp[i] = x[i] + (i==theta ?delti[theta]:0); } - - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nresult); - + /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and + * returns into prlim . + */ + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres); + + /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */ if (popbased==1) { if(mobilav ==0){ for(i=1; i<=nlstate;i++) @@ -5416,28 +5986,33 @@ void concatwav(int wav[], int **dh, int prlim[i][i]=mobaverage[(int)age][i][ij]; } } - - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */ + /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h. + */ + hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */ + /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability + * at horizon h in state j including mortality. + */ for(j=1; j<= nlstate; j++){ for(h=0; h<=nhstepm; h++){ for(i=1, gp[h][j]=0.;i<=nlstate;i++) gp[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - /* Next for computing probability of death (h=1 means + /* Next for computing shifted+ probability of death (h=1 means computed over hstepm matrices product = hstepm*stepm months) - as a weighted average of prlim. + as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 . */ for(j=nlstate+1;j<=nlstate+ndeath;j++){ for(i=1,gpp[j]=0.; i<= nlstate; i++) gpp[j] += prlim[i][i]*p3mat[i][j][1]; - } - /* end probability of death */ + } + + /* Again with minus shift */ for(i=1; i<=npar; i++) /* Computes gradient x - delta */ xp[i] = x[i] - (i==theta ?delti[theta]:0); - prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nresult); + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres); if (popbased==1) { if(mobilav ==0){ @@ -5465,19 +6040,23 @@ void concatwav(int wav[], int **dh, int for(i=1,gmp[j]=0.; i<= nlstate; i++) gmp[j] += prlim[i][i]*p3mat[i][j][1]; } - /* end probability of death */ - + /* end shifting computations */ + + /**< Computing gradient matrix at horizon h + */ for(j=1; j<= nlstate; j++) /* vareij */ for(h=0; h<=nhstepm; h++){ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; } - - for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ + /**< Gradient of overall mortality p.3 (or p.j) + */ + for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */ gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; } } /* End theta */ - + + /* We got the gradient matrix for each theta and state j */ trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */ for(h=0; h<=nhstepm; h++) /* veij */ @@ -5488,13 +6067,19 @@ void concatwav(int wav[], int **dh, int for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ for(theta=1; theta <=npar; theta++) trgradgp[j][theta]=gradgp[theta][j]; - + /**< as well as its transposed matrix + */ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ for(i=1;i<=nlstate;i++) for(j=1;j<=nlstate;j++) vareij[i][j][(int)age] =0.; - + + /* Computing trgradg by matcov by gradg at age and summing over h + * and k (nhstepm) formula 15 of article + * Lievre-Brouard-Heathcote + */ + for(h=0;h<=nhstepm;h++){ for(k=0;k<=nhstepm;k++){ matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov); @@ -5505,7 +6090,11 @@ void concatwav(int wav[], int **dh, int } } - /* pptj */ + /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of + * p.j overall mortality formula 49 but computed directly because + * we compute the grad (wix pijx) instead of grad (pijx),even if + * wix is independent of theta. + */ matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); for(j=nlstate+1;j<=nlstate+ndeath;j++) @@ -5514,7 +6103,7 @@ void concatwav(int wav[], int **dh, int /* end ppptj */ /* x centered again */ - prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nresult); + prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres); if (popbased==1) { if(mobilav ==0){ @@ -5593,12 +6182,12 @@ void concatwav(int wav[], int **dh, int } /* end varevsij */ /************ Variance of prevlim ******************/ - void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres) + void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres) { /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ - double **dnewm,**doldm; + double **dnewmpar,**doldm; int i, j, nhstepm, hstepm; double *xp; double *gp, *gm; @@ -5609,13 +6198,15 @@ void concatwav(int wav[], int **dh, int pstamp(ficresvpl); fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); - fprintf(ficresvpl,"# Age"); + fprintf(ficresvpl,"# Age "); + if(nresult >=1) + fprintf(ficresvpl," Result# "); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %1d-%1d",i,i); fprintf(ficresvpl,"\n"); xp=vector(1,npar); - dnewm=matrix(1,nlstate,1,npar); + dnewmpar=matrix(1,nlstate,1,npar); doldm=matrix(1,nlstate,1,nlstate); hstepm=1*YEARM; /* Every year of age */ @@ -5685,16 +6276,18 @@ void concatwav(int wav[], int **dh, int for(i=1;i<=nlstate;i++) varpl[i][(int)age] =0.; if((int)age==79 ||(int)age== 80 ||(int)age== 81){ - matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); + matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg); }else{ - matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg); + matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg); } for(i=1;i<=nlstate;i++) varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ fprintf(ficresvpl,"%.0f ",age ); + if(nresult >=1) + fprintf(ficresvpl,"%d ",nres ); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age])); fprintf(ficresvpl,"\n"); @@ -5708,7 +6301,132 @@ void concatwav(int wav[], int **dh, int free_vector(xp,1,npar); free_matrix(doldm,1,nlstate,1,npar); - free_matrix(dnewm,1,nlstate,1,nlstate); + free_matrix(dnewmpar,1,nlstate,1,nlstate); + +} + + +/************ Variance of backprevalence limit ******************/ + void varbrevlim(char fileresvbl[], FILE *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres) +{ + /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/ + /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ + + double **dnewmpar,**doldm; + int i, j, nhstepm, hstepm; + double *xp; + double *gp, *gm; + double **gradg, **trgradg; + double **mgm, **mgp; + double age,agelim; + int theta; + + pstamp(ficresvbl); + fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n"); + fprintf(ficresvbl,"# Age "); + if(nresult >=1) + fprintf(ficresvbl," Result# "); + for(i=1; i<=nlstate;i++) + fprintf(ficresvbl," %1d-%1d",i,i); + fprintf(ficresvbl,"\n"); + + xp=vector(1,npar); + dnewmpar=matrix(1,nlstate,1,npar); + doldm=matrix(1,nlstate,1,nlstate); + + hstepm=1*YEARM; /* Every year of age */ + hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ + agelim = AGEINF; + for (age=fage; age>=bage; age --){ /* If stepm=6 months */ + nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + if (stepm >= YEARM) hstepm=1; + nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ + gradg=matrix(1,npar,1,nlstate); + mgp=matrix(1,npar,1,nlstate); + mgm=matrix(1,npar,1,nlstate); + gp=vector(1,nlstate); + gm=vector(1,nlstate); + + for(theta=1; theta <=npar; theta++){ + for(i=1; i<=npar; i++){ /* Computes gradient */ + xp[i] = x[i] + (i==theta ?delti[theta]:0); + } + if(mobilavproj > 0 ) + bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres); + else + bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres); + for(i=1;i<=nlstate;i++){ + gp[i] = bprlim[i][i]; + mgp[theta][i] = bprlim[i][i]; + } + for(i=1; i<=npar; i++) /* Computes gradient */ + xp[i] = x[i] - (i==theta ?delti[theta]:0); + if(mobilavproj > 0 ) + bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres); + else + bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres); + for(i=1;i<=nlstate;i++){ + gm[i] = bprlim[i][i]; + mgm[theta][i] = bprlim[i][i]; + } + for(i=1;i<=nlstate;i++) + gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta]; + /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */ + } /* End theta */ + + trgradg =matrix(1,nlstate,1,npar); + + for(j=1; j<=nlstate;j++) + for(theta=1; theta <=npar; theta++) + trgradg[j][theta]=gradg[theta][j]; + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ + /* printf("\nmgm mgp %d ",(int)age); */ + /* for(j=1; j<=nlstate;j++){ */ + /* printf(" %d ",j); */ + /* for(theta=1; theta <=npar; theta++) */ + /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */ + /* printf("\n "); */ + /* } */ + /* } */ + /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */ + /* printf("\n gradg %d ",(int)age); */ + /* for(j=1; j<=nlstate;j++){ */ + /* printf("%d ",j); */ + /* for(theta=1; theta <=npar; theta++) */ + /* printf("%d %lf ",theta,gradg[theta][j]); */ + /* printf("\n "); */ + /* } */ + /* } */ + + for(i=1;i<=nlstate;i++) + varbpl[i][(int)age] =0.; + if((int)age==79 ||(int)age== 80 ||(int)age== 81){ + matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg); + }else{ + matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg); + } + for(i=1;i<=nlstate;i++) + varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */ + + fprintf(ficresvbl,"%.0f ",age ); + if(nresult >=1) + fprintf(ficresvbl,"%d ",nres ); + for(i=1; i<=nlstate;i++) + fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age])); + fprintf(ficresvbl,"\n"); + free_vector(gp,1,nlstate); + free_vector(gm,1,nlstate); + free_matrix(mgm,1,npar,1,nlstate); + free_matrix(mgp,1,npar,1,nlstate); + free_matrix(gradg,1,npar,1,nlstate); + free_matrix(trgradg,1,nlstate,1,npar); + } /* End age */ + + free_vector(xp,1,npar); + free_matrix(doldm,1,nlstate,1,npar); + free_matrix(dnewmpar,1,nlstate,1,nlstate); } @@ -5788,7 +6506,7 @@ void varprob(char optionfilefiname[], do fprintf(fichtm,"\n

  • Computing and drawing one step probabilities with their confidence intervals

    • \n"); fprintf(fichtm,"\n"); - fprintf(fichtm,"\n

  • Matrix of variance-covariance of one-step probabilities (drawings)

    this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.
    • \n",optionfilehtmcov); + fprintf(fichtm,"\n

  • Matrix of variance-covariance of one-step probabilities (drawings)

    this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s
    • \n",optionfilehtmcov,optionfilehtmcov); fprintf(fichtmcov,"Current page is file %s
    \n\n

    Matrix of variance-covariance of pairs of step probabilities

    \n",optionfilehtmcov, optionfilehtmcov); fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated \ and drawn. It helps understanding how is the covariance between two incidences.\ @@ -5985,7 +6703,12 @@ To be simple, these graphs help to under } /* Eigen vectors */ - v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); + if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){ + printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12); + fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12); + v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12))); + }else + v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); /*v21=sqrt(1.-v11*v11); *//* error */ v21=(lc1-v1)/cv12*v11; v12=-v21; @@ -6005,7 +6728,7 @@ To be simple, these graphs help to under fprintf(ficgp,"\nset parametric;unset label"); fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); fprintf(ficgp,"\nset ter svg size 640, 480"); - fprintf(fichtmcov,"\n
    Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ + fprintf(fichtmcov,"\n


    Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ : \ %s_%d%1d%1d-%1d%1d.svg, ",k1,l1,k2,l2,\ subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \ @@ -6016,16 +6739,16 @@ To be simple, these graphs help to under fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \ - mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \ - mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \ + mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */ }else{ first=0; fprintf(fichtmcov," %d (%.3f),",(int) age, c12); fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2); fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2); fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \ - mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \ - mu2,std,v21,sqrt(lc1),v22,sqrt(lc2)); + mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \ + mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); }/* if first */ } /* age mod 5 */ } /* end loop age */ @@ -6053,9 +6776,9 @@ To be simple, these graphs help to under void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ int imx,int jmin, int jmax, double jmeanint,char rfileres[],\ - int popforecast, int prevfcast, int backcast, int estepm , \ - double jprev1, double mprev1,double anprev1, double dateprev1, \ - double jprev2, double mprev2,double anprev2, double dateprev2){ + int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \ + double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \ + double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){ int jj1, k1, i1, cpt, k4, nres; fprintf(fichtm,"

    • Result files (first order: no variance)\n \ @@ -6091,21 +6814,66 @@ void printinghtml(char fileresu[], char %s
      \n
      • ", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_")); } - fprintf(fichtm," \n
      • Graphs

        • "); m=pow(2,cptcoveff); if (cptcovn < 1) {m=1;ncodemax[1]=1;} + fprintf(fichtm," \n

        • Graphs

          • "); + jj1=0; + fprintf(fichtm," \n

          "); + + jj1=0; + + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k1=1; k1<=m;k1++){ /* For each combination of covariate */ + if(m != 1 && TKresult[nres]!= k1) continue; /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; if (cptcovn > 0) { + fprintf(fichtm,"\n

          "); + fprintf(fichtm,"

          ************ Results for covariates"); for (cpt=1; cpt<=cptcoveff;cpt++){ fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); @@ -6127,51 +6895,61 @@ void printinghtml(char fileresu[], char } } /* aij, bij */ - fprintf(fichtm,"
          - Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age:           %s_%d-1.svg
          \ -",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); + fprintf(fichtm,"
          - Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: %s_%d-1-%d.svg
          \ +",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); /* Pij */ - fprintf(fichtm,"
          \n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s_%d-2.svg
          \ -",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); + fprintf(fichtm,"
          \n- Pij or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s_%d-2-%d.svg
          \ +",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); /* Quasi-incidences */ fprintf(fichtm,"
          \n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \ incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \ -divided by h: hPij/h : %s_%d-3.svg
          \ -",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1); +divided by h: hPij/h : %s_%d-3-%d.svg
          \ +",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. Or probability to survive in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
          \ -", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1); + fprintf(fichtm,"
          \n- Survival functions in state %d. Or probability to survive 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); } /* State specific survival functions (period) */ for(cpt=1; cpt<=nlstate;cpt++){ fprintf(fichtm,"
          \n- Survival functions from state %d in each live state and total.\ Or probability to survive in various states (1 to %d) being in state %d at different ages. \ - %s%d_%d.svg
          ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1); + %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); } /* Period (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 to be in state %d being in state (1 to %d) at different ages. %s_%d-%d.svg
          \ -", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1); + 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); } if(backcast==1){ /* Period (stable) back prevalence in each health state */ for(cpt=1; cpt<=nlstate;cpt++){ - fprintf(fichtm,"
          \n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d.svg
          \ -", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1); + fprintf(fichtm,"
          \n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. %s_%d-%d-%d.svg
          \ +", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres); } } if(prevfcast==1){ /* Projection of prevalence up to period (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) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.svg
          \ -", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1); + 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) 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, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres); + } + } + if(backcast==1){ + /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */ + for(cpt=1; cpt<=nlstate;cpt++){ + 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); } } 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.svg
          \ -",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1); + 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); } /* } /\* end i1 *\/ */ }/* End k1 */ @@ -6230,9 +7008,9 @@ See page 'Matrix of variance-covariance jj1=0; - for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ for(k1=1; k1<=m;k1++){ - if(TKresult[nres]!= k1) + if(m != 1 && TKresult[nres]!= k1) continue; /* for(i1=1; i1<=ncodemax[k1];i1++){ */ jj1++; @@ -6253,33 +7031,37 @@ See page 'Matrix of variance-covariance } } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"\n
          - Observed (cross-sectional) and period (incidence based) \ -prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d.svg\n
          \ -",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1); + fprintf(fichtm,"\n
          - Observed (cross-sectional with mov_average=%d) and period (incidence based) \ +prevalence (with 95%% confidence interval) in state (%d): %s_%d-%d-%d.svg\n
          \ +",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres); } fprintf(fichtm,"\n
          - Total life expectancy by age and \ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ true period expectancies (those weighted with period prevalences are also\ drawn in addition to the population based expectancies computed using\ - observed and cahotic prevalences: %s_%d.svg\n
          \ -",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1); + observed and cahotic prevalences: %s_%d-%d.svg\n
          \ +",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres); /* } /\* end i1 *\/ */ }/* End k1 */ + }/* End nres */ fprintf(fichtm,"
        "); fflush(fichtm); } /******************* Gnuplot file **************/ -void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){ +void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){ char dirfileres[132],optfileres[132]; - char gplotcondition[132]; + char gplotcondition[132], gplotlabel[132]; int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0; int lv=0, vlv=0, kl=0; int ng=0; int vpopbased; int ioffset; /* variable offset for columns */ + int iyearc=1; /* variable column for year of projection */ + int iagec=1; /* variable column for age of projection */ int nres=0; /* Index of resultline */ + int istart=1; /* For starting graphs in projections */ /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ /* printf("Problem with file %s",optionfilegnuplot); */ @@ -6291,6 +7073,20 @@ void printinggnuplot(char fileresu[], ch /*#endif */ m=pow(2,cptcoveff); + /* diagram of the model */ + fprintf(ficgp,"\n#Diagram of the model \n"); + fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n"); + fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate); + fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate); + + fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate); + fprintf(ficgp,"\n#show arrow\nunset label\n"); + fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate); + fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate); + fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n"); + fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_")); + fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n"); + /* Contribution to likelihood */ /* Plot the probability implied in the likelihood */ fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); @@ -6327,11 +7123,12 @@ void printinggnuplot(char fileresu[], ch for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ - if(TKresult[nres]!= k1) + if(m != 1 && 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); + strcpy(gplotlabel,"("); 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 */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -6339,47 +7136,78 @@ 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); + sprintf(gplotlabel+strlen(gplotlabel)," 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"); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + /* printf("\n#\n"); */ fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ + /*k1=k1-1;*/ /* To be checked */ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); continue; } - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1); - fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1); - fprintf(ficgp,"set xlabel \"Age\" \n\ -set ylabel \"Probability\" \n \ -set ter svg size 640, 480\n \ -plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1); - + 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 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*/ for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); + fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); + fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); + /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */ + + fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_")); + if(cptcoveff ==0){ + fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt ); + }else{ + kl=0; + for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + kl++; + /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ + /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+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):($5==2000? 3:2) t 'p.1' with line lc variable*/ + if(k==cptcoveff){ + fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ + 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/ + }else{ + fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); + kl++; + } + } /* end covariate */ + } /* end if no covariate */ + if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */ /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%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 */ + fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */ 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{ kl=0; for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ @@ -6394,16 +7222,36 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /*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):($5==2000? 3:2) t 'p.1' with line lc variable*/ if(k==cptcoveff){ - fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ - 4+(cpt-1), cpt ); /* 4 or 6 ?*/ + fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ + 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/ }else{ fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); kl++; } } /* end covariate */ } /* end if no covariate */ + if(backcast == 1){ + fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); + /* k1-1 error should be nres-1*/ + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + fprintf(ficgp,"\" t\"\" w l lt 4"); + } /* end if backprojcast */ } /* end if backcast */ - fprintf(ficgp,"\nset out \n"); + /* fprintf(ficgp,"\nset out ;unset label;\n"); */ + fprintf(ficgp,"\nset out ;unset title;\n"); } /* nres */ } /* k1 */ } /* cpt */ @@ -6412,9 +7260,10 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /*2 eme*/ for (k1=1; k1<= m ; k1 ++){ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k1) + if(m != 1 && TKresult[nres]!= k1) continue; fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files "); + strcpy(gplotlabel,"("); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -6422,40 +7271,44 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); } /* for(k=1; k <= ncovds; k++){ */ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); continue; } - fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1); + fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres); for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ - if(vpopbased==0) + fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel); + if(vpopbased==0){ fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage); - else + }else fprintf(ficgp,"\nreplot "); for (i=1; i<= nlstate+1 ; i ++) { k=2*i; - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i); else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); } fprintf(ficgp,"\" t\"\" w l lt 0,"); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); @@ -6464,7 +7317,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n"); } /* state */ } /* vpopbased */ - fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */ + fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */ } /* end nres */ } /* k1 end 2 eme*/ @@ -6472,11 +7325,12 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /*3eme*/ for (k1=1; k1<= m ; k1 ++){ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k) + if(m != 1 && TKresult[nres]!= k1) continue; for (cpt=1; cpt<= nlstate ; cpt ++) { - fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt); + fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt); + strcpy(gplotlabel,"("); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -6484,10 +7338,13 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); @@ -6496,9 +7353,10 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* k=2+nlstate*(2*cpt-2); */ k=2+(nlstate+1)*(cpt-1); - fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); + fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); fprintf(ficgp,"set ter svg size 640, 480\n\ -plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt); +plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt); /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); fprintf(ficgp,"\" t \"e%d1\" w l",cpt); @@ -6508,12 +7366,13 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u */ for (i=1; i< nlstate ; i ++) { - fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1); + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1); /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/ } - fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt); + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt); } + fprintf(ficgp,"\nunset label;\n"); } /* end nres */ } /* end kl 3eme */ @@ -6521,9 +7380,10 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* Survival functions (period) from state i in state j by initial state i */ for (k1=1; k1<=m; k1++){ /* For each covariate and each value */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k1) + if(m != 1 && TKresult[nres]!= k1) continue; for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/ + strcpy(gplotlabel,"("); fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ @@ -6532,17 +7392,21 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); continue; } - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),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 xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); k=3; @@ -6558,7 +7422,7 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"+$%d",k+l+j-1); fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt); } /* nlstate */ - fprintf(ficgp,"\nset out\n"); + fprintf(ficgp,"\nset out; unset label;\n"); } /* end cpt state*/ } /* end nres */ } /* end covariate k1 */ @@ -6567,9 +7431,10 @@ set ter svg size 640, 480\nunset log y\n /* Survival functions (period) from state i in state j by final state j */ for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k1) + if(m != 1 && TKresult[nres]!= k1) continue; for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */ + strcpy(gplotlabel,"("); fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ @@ -6578,17 +7443,21 @@ set ter svg size 640, 480\nunset log y\n /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); continue; } - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),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 xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); k=3; @@ -6612,7 +7481,7 @@ set ter svg size 640, 480\nunset log y\n else fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt); } - fprintf(ficgp,"\nset out\n"); + fprintf(ficgp,"\nset out; unset label;\n"); } /* end cpt state*/ } /* end covariate */ } /* end nres */ @@ -6621,10 +7490,10 @@ set ter svg size 640, 480\nunset log y\n /* CV preval stable (period) for each covariate */ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k1) + if(m != 1 && TKresult[nres]!= k1) continue; - for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ - + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */ + strcpy(gplotlabel,"("); fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ @@ -6633,32 +7502,36 @@ set ter svg size 640, 480\nunset log y\n /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); continue; } - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),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 xlabel \"Age\" \nset ylabel \"Probability\" \n\ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); k=3; /* Offset */ - for (i=1; i<= nlstate ; i ++){ + for (i=1; i<= nlstate ; i ++){ /* State of origin */ if(i==1) fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); else fprintf(ficgp,", '' "); - l=(nlstate+ndeath)*(i-1)+1; + l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); for (j=2; j<= nlstate ; j ++) fprintf(ficgp,"+$%d",k+l+j-1); fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); } /* nlstate */ - fprintf(ficgp,"\nset out\n"); + fprintf(ficgp,"\nset out; unset label;\n"); } /* end cpt state*/ } /* end covariate */ @@ -6668,10 +7541,11 @@ set ter svg size 640, 480\nunset log y\n /* CV back preval stable (period) for each covariate */ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k1) + if(m != 1 && TKresult[nres]!= k1) continue; - for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ - fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */ + strcpy(gplotlabel,"("); + fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -6679,36 +7553,40 @@ set ter svg size 640, 480\nunset log y\n /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); continue; } - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres); + fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); k=3; /* Offset */ - for (i=1; i<= nlstate ; i ++){ + for (i=1; i<= nlstate ; i ++){ /* State of arrival */ if(i==1) fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_")); else fprintf(ficgp,", '' "); /* l=(nlstate+ndeath)*(i-1)+1; */ - l=(nlstate+ndeath)*(cpt-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",k1,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,"+$%d",k+l+j-1); */ /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */ - fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt); + fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i); } /* nlstate */ - fprintf(ficgp,"\nset out\n"); + fprintf(ficgp,"\nset out; unset label;\n"); } /* end cpt state*/ } /* end covariate */ } /* End if backcast */ @@ -6719,9 +7597,10 @@ set ter svg size 640, 480\nunset log y\n for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k1) + if(m != 1 && TKresult[nres]!= k1) continue; for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ + strcpy(gplotlabel,"("); fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ @@ -6730,10 +7609,13 @@ set ter svg size 640, 480\nunset log y\n /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); @@ -6741,15 +7623,20 @@ set ter svg size 640, 480\nunset log y\n } fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n "); - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),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 xlabel \"Age\" \nset ylabel \"Prevalence\" \n\ set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); - for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */ + + /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */ + istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */ + /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */ + for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */ /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ - if(i==1){ + if(i==istart){ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_")); }else{ fprintf(ficgp,",\\\n '' "); @@ -6761,20 +7648,23 @@ set ter svg size 640, 480\nunset log y\n /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */ fprintf(ficgp," u %d:(", ioffset); - if(i==nlstate+1) - fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \ + if(i==nlstate+1){ + fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt ); - else + fprintf(ficgp,",\\\n '' "); + fprintf(ficgp," u %d:(",ioffset); + fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \ + offyear, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate ); + }else fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt ); }else{ /* more than 2 covariates */ - if(cptcoveff ==1){ - ioffset=4; /* Age is in 4 */ - }else{ - ioffset=6; /* Age is in 6 */ - /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ - /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ - } + ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/ + /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + iyearc=ioffset-1; + iagec=ioffset; fprintf(ficgp," u %d:(",ioffset); kl=0; strcpy(gplotcondition,"("); @@ -6796,19 +7686,140 @@ set ter svg size 640, 480\nunset log y\n /*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*/ if(i==nlstate+1){ - fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \ - ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt ); + fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt ); + fprintf(ficgp,",\\\n '' "); + fprintf(ficgp," u %d:(",iagec); + fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \ + iyearc, iagec, offyear, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc ); +/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/ }else{ fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt ); } } /* end if covariate */ } /* nlstate */ - fprintf(ficgp,"\nset out\n"); + fprintf(ficgp,"\nset out; unset label;\n"); } /* end cpt state*/ } /* end covariate */ } /* End if prevfcast */ + if(backcast==1){ + /* Back projection from cross-sectional to stable (mixed) for each covariate */ + + for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */ + for(nres=1; nres <= nresult; nres++){ /* For each resultline */ + if(m != 1 && TKresult[nres]!= k1) + continue; + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ + strcpy(gplotlabel,"("); + fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt); + for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + strcpy(gplotlabel+strlen(gplotlabel),")"); + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + + fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n "); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres); + fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); + fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\ +set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar); + + /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */ + istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */ + /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */ + for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */ + /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + if(i==istart){ + fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_")); + }else{ + fprintf(ficgp,",\\\n '' "); + } + if(cptcoveff ==0){ /* No covariate */ + ioffset=2; /* Age is in 2 */ + /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */ + /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */ + fprintf(ficgp," u %d:(", ioffset); + if(i==nlstate+1){ + fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt ); + fprintf(ficgp,",\\\n '' "); + fprintf(ficgp," u %d:(",ioffset); + fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \ + offbyear, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1) ); + }else + fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i ); + }else{ /* more than 2 covariates */ + ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/ + /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + iyearc=ioffset-1; + iagec=ioffset; + fprintf(ficgp," u %d:(",ioffset); + kl=0; + strcpy(gplotcondition,"("); + for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */ + kl++; + sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); + kl++; + if(k 1) + sprintf(gplotcondition+strlen(gplotcondition)," && "); + } + strcpy(gplotcondition+strlen(gplotcondition),")"); + /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ + /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+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*/ + if(i==nlstate+1){ + fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt ); + fprintf(ficgp,",\\\n '' "); + fprintf(ficgp," u %d:(",iagec); + /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */ + fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \ + iyearc,iagec,offbyear, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc ); +/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/ + }else{ + /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */ + fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i ); + } + } /* end if covariate */ + } /* nlstate */ + fprintf(ficgp,"\nset out; unset label;\n"); + } /* end cpt state*/ + } /* end covariate */ + } /* End if backcast */ + /* 9eme writing MLE parameters */ fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n"); @@ -6847,17 +7858,33 @@ set ter svg size 640, 480\nunset log y\n fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n"); fprintf(ficgp,"#model=%s \n",model); fprintf(ficgp,"# Type of graphic ng=%d\n",ng); - fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */ - for(jk=1; jk <=m; jk++) /* For each combination of covariate */ + fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */ + for(k1=1; k1 <=m; k1++) /* For each combination of covariate */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= jk) + if(m != 1 && TKresult[nres]!= k1) continue; - fprintf(ficgp,"# Combination of dummy jk=%d and ",jk); + fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1); + strcpy(gplotlabel,"("); + /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/ + for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); + } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } + strcpy(gplotlabel+strlen(gplotlabel),")"); fprintf(ficgp,"\n#\n"); - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres); + fprintf(ficgp,"\nset key outside "); + /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */ + fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel); fprintf(ficgp,"\nset ter svg size 640, 480 "); if (ng==1){ fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */ @@ -6901,43 +7928,47 @@ 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(j==Tage[ij]) { /* Product by age */ - 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(jk,Tvar[j-2])]); */ - } - ij++; - } - }else 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(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,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(jk,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]]); + 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])]); */ } - }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]]); + 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]]); + } } + ijp++; } - ijp++; - } + } /* end Tprod */ } else{ /* simple covariate */ - /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */ + /* 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]]); /* */ }else{ /* quantitative */ 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(jk,Tvar[j-2])]); */ + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */ } } /* end simple */ } /* end j */ @@ -6950,34 +7981,35 @@ set ter svg size 640, 480\nunset log y\n if(ng != 1){ fprintf(ficgp,")/(1"); - for(k1=1; k1 <=nlstate; k1++){ + for(cpt=1; cpt <=nlstate; cpt++){ if(nagesqr==0) - fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); + fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1); else /* nagesqr =1 */ - fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); + 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((j-2)==Tage[ij]) { /* Bug valgrind */ - if(ij <=cptcovage) { /* Bug valgrind */ - fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); - /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ - ij++; - } - } - else - fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */ + 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 */ } fprintf(ficgp,")"); } fprintf(ficgp,")"); if(ng ==2) - fprintf(ficgp," t \"p%d%d\" ", k2,k); + 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," t \"i%d%d\" ", k2,k); + 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 */ if( k !=k2) /* logit p11 is hard to draw */ - fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k); + 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); } if ((k+k2)!= (nlstate*2+ndeath) && ng != 1) fprintf(ficgp,","); @@ -6986,8 +8018,9 @@ set ter svg size 640, 480\nunset log y\n i=i+ncovmodel; } /* end k */ } /* end k2 */ - fprintf(ficgp,"\n set out\n"); - } /* end jk */ + /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */ + fprintf(ficgp,"\n set out; unset title;set key default;\n"); + } /* end k1 */ } /* end ng */ /* avoid: */ fflush(ficgp); @@ -7003,30 +8036,34 @@ set ter svg size 640, 480\nunset log y\n int mobilavrange, mob; int iage=0; - double sum=0.; + double sum=0., sumr=0.; double age; - double *sumnewp, *sumnewm; - double *agemingood, *agemaxgood; /* Currently identical for all covariates */ + double *sumnewp, *sumnewm, *sumnewmr; + double *agemingood, *agemaxgood; + double *agemingoodr, *agemaxgoodr; - /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */ - /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */ + /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */ + /* a covariate has 2 modalities, should be equal to ncovcombmax */ sumnewp = vector(1,ncovcombmax); sumnewm = vector(1,ncovcombmax); + sumnewmr = vector(1,ncovcombmax); agemingood = vector(1,ncovcombmax); + agemingoodr = vector(1,ncovcombmax); agemaxgood = vector(1,ncovcombmax); + agemaxgoodr = vector(1,ncovcombmax); for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ - sumnewm[cptcod]=0.; + sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.; sumnewp[cptcod]=0.; - agemingood[cptcod]=0; - agemaxgood[cptcod]=0; + agemingood[cptcod]=0, agemingoodr[cptcod]=0; + agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0; } if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */ - if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ - if(mobilav==1) mobilavrange=5; /* default */ + if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ + if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */ else mobilavrange=mobilav; for (age=bage; age<=fage; age++) for (i=1; i<=nlstate;i++) @@ -7038,77 +8075,143 @@ set ter svg size 640, 480\nunset log y\n */ for (mob=3;mob <=mobilavrange;mob=mob+2){ for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ - for (i=1; i<=nlstate;i++){ - for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ + for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ + sumnewm[cptcod]=0.; + for (i=1; i<=nlstate;i++){ mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; for (cpt=1;cpt<=(mob-1)/2;cpt++){ mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod]; } mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob; - } - } + sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + } /* end i */ + if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */ + } /* end cptcod */ }/* end age */ }/* end mob */ - }else + }else{ + printf("Error internal in movingaverage, mobilav=%d.\n",mobilav); return -1; - for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ + } + + for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */ /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */ if(invalidvarcomb[cptcod]){ printf("\nCombination (%d) ignored because no cases \n",cptcod); continue; } - agemingood[cptcod]=fage-(mob-1)/2; - for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */ + for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */ sumnewm[cptcod]=0.; + sumnewmr[cptcod]=0.; for (i=1; i<=nlstate;i++){ sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + sumnewmr[cptcod]+=probs[(int)age][i][cptcod]; + } + if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */ + agemingoodr[cptcod]=age; } if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */ - agemingood[cptcod]=age; - }else{ /* bad */ - for (i=1; i<=nlstate;i++){ - mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; - } /* i */ - } /* end bad */ - }/* age */ - sum=0.; - for (i=1; i<=nlstate;i++){ - sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod]; - } - if(fabs(sum - 1.) > 1.e-3) { /* bad */ - printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod); - /* for (i=1; i<=nlstate;i++){ */ - /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */ - /* } /\* i *\/ */ - } /* end bad */ - /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */ - /* From youngest, finding the oldest wrong */ - agemaxgood[cptcod]=bage+(mob-1)/2; - for (age=bage+(mob-1)/2; age<=fage; age++){ + agemingood[cptcod]=age; + } + } /* age */ + for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */ sumnewm[cptcod]=0.; + sumnewmr[cptcod]=0.; for (i=1; i<=nlstate;i++){ sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + sumnewmr[cptcod]+=probs[(int)age][i][cptcod]; + } + if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */ + agemaxgoodr[cptcod]=age; } if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */ agemaxgood[cptcod]=age; - }else{ /* bad */ - for (i=1; i<=nlstate;i++){ - mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; - } /* i */ + } + } /* age */ + /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */ + /* but they will change */ + for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */ + sumnewm[cptcod]=0.; + sumnewmr[cptcod]=0.; + for (i=1; i<=nlstate;i++){ + sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + sumnewmr[cptcod]+=probs[(int)age][i][cptcod]; + } + if(mobilav==-1){ /* Forcing raw ages if good else agemingood */ + if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */ + agemaxgoodr[cptcod]=age; /* age min */ + for (i=1; i<=nlstate;i++) + mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; + }else{ /* bad we change the value with the values of good ages */ + for (i=1; i<=nlstate;i++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod]; + } /* i */ + } /* end bad */ + }else{ + if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */ + agemaxgood[cptcod]=age; + }else{ /* bad we change the value with the values of good ages */ + for (i=1; i<=nlstate;i++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; + } /* i */ + } /* end bad */ + }/* end else */ + sum=0.;sumr=0.; + for (i=1; i<=nlstate;i++){ + sum+=mobaverage[(int)age][i][cptcod]; + sumr+=probs[(int)age][i][cptcod]; + } + if(fabs(sum - 1.) > 1.e-3) { /* bad */ + printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); + } /* end bad */ + /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */ + if(fabs(sumr - 1.) > 1.e-3) { /* bad */ + printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage); } /* end bad */ }/* age */ - sum=0.; - for (i=1; i<=nlstate;i++){ - sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; - } - if(fabs(sum - 1.) > 1.e-3) { /* bad */ - printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod); - /* for (i=1; i<=nlstate;i++){ */ - /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */ - /* } /\* i *\/ */ - } /* end bad */ + + for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */ + sumnewm[cptcod]=0.; + sumnewmr[cptcod]=0.; + for (i=1; i<=nlstate;i++){ + sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod]; + sumnewmr[cptcod]+=probs[(int)age][i][cptcod]; + } + if(mobilav==-1){ /* Forcing raw ages if good else agemingood */ + if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */ + agemingoodr[cptcod]=age; + for (i=1; i<=nlstate;i++) + mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; + }else{ /* bad we change the value with the values of good ages */ + for (i=1; i<=nlstate;i++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod]; + } /* i */ + } /* end bad */ + }else{ + if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */ + agemingood[cptcod]=age; + }else{ /* bad */ + for (i=1; i<=nlstate;i++){ + mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; + } /* i */ + } /* end bad */ + }/* end else */ + sum=0.;sumr=0.; + for (i=1; i<=nlstate;i++){ + sum+=mobaverage[(int)age][i][cptcod]; + sumr+=mobaverage[(int)age][i][cptcod]; + } + if(fabs(sum - 1.) > 1.e-3) { /* bad */ + printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage); + } /* end bad */ + /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */ + if(fabs(sumr - 1.) > 1.e-3) { /* bad */ + printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage); + } /* end bad */ + }/* age */ + for (age=bage; age<=fage; age++){ /* printf("%d %d ", cptcod, (int)age); */ @@ -7123,40 +8226,44 @@ set ter svg size 640, 480\nunset log y\n } /* printf("\n"); */ /* } */ + /* brutal averaging */ - for (i=1; i<=nlstate;i++){ - for (age=1; age<=bage; age++){ - mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; - /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */ - } - for (age=fage; age<=AGESUP; age++){ - mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; - /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */ - } - } /* end i status */ - for (i=nlstate+1; i<=nlstate+ndeath;i++){ - for (age=1; age<=AGESUP; age++){ - /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/ - mobaverage[(int)age][i][cptcod]=0.; - } - } + /* for (i=1; i<=nlstate;i++){ */ + /* for (age=1; age<=bage; age++){ */ + /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */ + /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */ + /* } */ + /* for (age=fage; age<=AGESUP; age++){ */ + /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */ + /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */ + /* } */ + /* } /\* end i status *\/ */ + /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */ + /* for (age=1; age<=AGESUP; age++){ */ + /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */ + /* mobaverage[(int)age][i][cptcod]=0.; */ + /* } */ + /* } */ }/* end cptcod */ - free_vector(sumnewm,1, ncovcombmax); - free_vector(sumnewp,1, ncovcombmax); + free_vector(agemaxgoodr,1, ncovcombmax); free_vector(agemaxgood,1, ncovcombmax); free_vector(agemingood,1, ncovcombmax); + free_vector(agemingoodr,1, ncovcombmax); + free_vector(sumnewmr,1, ncovcombmax); + free_vector(sumnewm,1, ncovcombmax); + free_vector(sumnewp,1, ncovcombmax); return 0; }/* End movingaverage */ /************** Forecasting ******************/ - void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ + void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ /* proj1, year, month, day of starting projection agemin, agemax range of age dateprev1 dateprev2 range of dates during which prevalence is computed anproj2 year of en of projection (same day and month as proj1). */ - int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0; + int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0; double agec; /* generic age */ double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; double *popeffectif,*popcount; @@ -7189,7 +8296,12 @@ set ter svg size 640, 480\nunset log y\n if(estepm < stepm){ printf ("Problem %d lower than %d\n",estepm, stepm); } - else hstepm=estepm; + else{ + hstepm=estepm; + } + if(estepm > stepm){ /* Yes every two year */ + stepsize=2; + } hstepm=hstepm/stepm; yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and @@ -7212,7 +8324,7 @@ set ter svg size 640, 480\nunset log y\n /* if (h==(int)(YEARM*yearp)){ */ for(nres=1; nres <= nresult; nres++) /* For each resultline */ for(k=1; k<=i1;k++){ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; if(invalidvarcomb[k]){ printf("\nCombination (%d) projection ignored because no cases \n",k); @@ -7234,39 +8346,41 @@ set ter svg size 640, 480\nunset log y\n for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { fprintf(ficresf,"\n"); fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); - for (agec=fage; agec>=(ageminpar-1); agec--){ + /* for (agec=fage; agec>=(ageminpar-1); agec--){ */ + for (agec=fage; agec>=(bage); agec--){ nhstepm=(int) rint((agelim-agec)*YEARM/stepm); nhstepm = nhstepm/hstepm; p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); oldm=oldms;savm=savms; + /* We compute pii at age agec over nhstepm);*/ hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres); - + /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */ for (h=0; h<=nhstepm; h++){ if (h*hstepm/YEARM*stepm ==yearp) { - fprintf(ficresf,"\n"); - for(j=1;j<=cptcoveff;j++) - fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); - } - for(j=1; j<=nlstate+ndeath;j++) { - ppij=0.; - for(i=1; i<=nlstate;i++) { - if (mobilav==1) - ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k]; - else { - ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; - } - if (h*hstepm/YEARM*stepm== yearp) { - fprintf(ficresf," %.3f", p3mat[i][j][h]); - } - } /* end i */ - if (h*hstepm/YEARM*stepm==yearp) { - fprintf(ficresf," %.3f", ppij); + break; + } + } + fprintf(ficresf,"\n"); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); + + for(j=1; j<=nlstate+ndeath;j++) { + ppij=0.; + for(i=1; i<=nlstate;i++) { + if (mobilav>=1) + ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k]; + else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */ + ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; } - }/* end j */ - } /* end h */ + fprintf(ficresf," %.3f", p3mat[i][j][h]); + } /* end i */ + fprintf(ficresf," %.3f", ppij); + }/* end j */ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); } /* end agec */ + /* diffyear=(int) anproj1+yearp-ageminpar-1; */ + /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/ } /* end yearp */ } /* end k */ @@ -7276,135 +8390,273 @@ set ter svg size 640, 480\nunset log y\n } -/* /\************** Back Forecasting ******************\/ */ -/* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */ -/* /\* back1, year, month, day of starting backection */ -/* agemin, agemax range of age */ -/* dateprev1 dateprev2 range of dates during which prevalence is computed */ -/* anback2 year of en of backection (same day and month as back1). */ -/* *\/ */ -/* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */ -/* double agec; /\* generic age *\/ */ -/* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */ -/* double *popeffectif,*popcount; */ -/* double ***p3mat; */ -/* /\* double ***mobaverage; *\/ */ -/* char fileresfb[FILENAMELENGTH]; */ - -/* agelim=AGESUP; */ -/* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */ -/* in each health status at the date of interview (if between dateprev1 and dateprev2). */ -/* We still use firstpass and lastpass as another selection. */ -/* *\/ */ -/* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */ -/* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */ -/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ - -/* strcpy(fileresfb,"FB_"); */ -/* strcat(fileresfb,fileresu); */ -/* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */ -/* printf("Problem with back forecast resultfile: %s\n", fileresfb); */ -/* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */ -/* } */ -/* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */ -/* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */ - -/* if (cptcoveff==0) ncodemax[cptcoveff]=1; */ - -/* /\* if (mobilav!=0) { *\/ */ -/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */ -/* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */ -/* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */ -/* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */ -/* /\* } *\/ */ -/* /\* } *\/ */ - -/* stepsize=(int) (stepm+YEARM-1)/YEARM; */ -/* if (stepm<=12) stepsize=1; */ -/* if(estepm < stepm){ */ -/* printf ("Problem %d lower than %d\n",estepm, stepm); */ -/* } */ -/* else hstepm=estepm; */ - -/* hstepm=hstepm/stepm; */ -/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */ -/* fractional in yp1 *\/ */ -/* anprojmean=yp; */ -/* yp2=modf((yp1*12),&yp); */ -/* mprojmean=yp; */ -/* yp1=modf((yp2*30.5),&yp); */ -/* jprojmean=yp; */ -/* if(jprojmean==0) jprojmean=1; */ -/* if(mprojmean==0) jprojmean=1; */ - -/* i1=cptcoveff; */ -/* if (cptcovn < 1){i1=1;} */ +/************** Back Forecasting ******************/ + void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ + /* back1, year, month, day of starting backection + agemin, agemax range of age + dateprev1 dateprev2 range of dates during which prevalence is computed + anback2 year of end of backprojection (same day and month as back1). + prevacurrent and prev are prevalences. + */ + int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0; + double agec; /* generic age */ + double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; + double *popeffectif,*popcount; + double ***p3mat; + /* double ***mobaverage; */ + char fileresfb[FILENAMELENGTH]; + + agelim=AGEINF; + /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people + in each health status at the date of interview (if between dateprev1 and dateprev2). + We still use firstpass and lastpass as another selection. + */ + /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */ + /* firstpass, lastpass, stepm, weightopt, model); */ + + /*Do we need to compute prevalence again?*/ + + /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ -/* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */ + strcpy(fileresfb,"FB_"); + strcat(fileresfb,fileresu); + if((ficresfb=fopen(fileresfb,"w"))==NULL) { + printf("Problem with back forecast resultfile: %s\n", fileresfb); + fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); + } + printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb); + fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb); -/* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */ - -/* /\* if (h==(int)(YEARM*yearp)){ *\/ */ -/* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */ -/* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */ -/* k=k+1; */ -/* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */ -/* for(j=1;j<=cptcoveff;j++) { */ -/* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ -/* } */ -/* fprintf(ficresfb," yearbproj age"); */ -/* for(j=1; j<=nlstate+ndeath;j++){ */ -/* for(i=1; i<=nlstate;i++) */ -/* fprintf(ficresfb," p%d%d",i,j); */ -/* fprintf(ficresfb," p.%d",j); */ -/* } */ -/* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */ -/* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */ -/* fprintf(ficresfb,"\n"); */ -/* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */ -/* for (agec=fage; agec>=(ageminpar-1); agec--){ */ -/* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */ -/* nhstepm = nhstepm/hstepm; */ -/* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ -/* oldm=oldms;savm=savms; */ -/* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */ -/* for (h=0; h<=nhstepm; h++){ */ -/* if (h*hstepm/YEARM*stepm ==yearp) { */ -/* fprintf(ficresfb,"\n"); */ -/* for(j=1;j<=cptcoveff;j++) */ -/* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ -/* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */ -/* } */ -/* for(j=1; j<=nlstate+ndeath;j++) { */ -/* ppij=0.; */ -/* for(i=1; i<=nlstate;i++) { */ -/* if (mobilav==1) */ -/* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */ -/* else { */ -/* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */ -/* } */ -/* if (h*hstepm/YEARM*stepm== yearp) { */ -/* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */ -/* } */ -/* } /\* end i *\/ */ -/* if (h*hstepm/YEARM*stepm==yearp) { */ -/* fprintf(ficresfb," %.3f", ppij); */ -/* } */ -/* }/\* end j *\/ */ -/* } /\* end h *\/ */ -/* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */ -/* } /\* end agec *\/ */ -/* } /\* end yearp *\/ */ -/* } /\* end cptcod *\/ */ -/* } /\* end cptcov *\/ */ - -/* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */ - -/* fclose(ficresfb); */ -/* printf("End of Computing Back forecasting \n"); */ -/* fprintf(ficlog,"End of Computing Back forecasting\n"); */ + if (cptcoveff==0) ncodemax[cptcoveff]=1; + + + stepsize=(int) (stepm+YEARM-1)/YEARM; + if (stepm<=12) stepsize=1; + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else{ + hstepm=estepm; + } + if(estepm >= stepm){ /* Yes every two year */ + stepsize=2; + } + + hstepm=hstepm/stepm; + yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and + fractional in yp1 */ + anprojmean=yp; + yp2=modf((yp1*12),&yp); + mprojmean=yp; + yp1=modf((yp2*30.5),&yp); + jprojmean=yp; + if(jprojmean==0) jprojmean=1; + if(mprojmean==0) jprojmean=1; + + i1=pow(2,cptcoveff); + if (cptcovn < 1){i1=1;} + + fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); + printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); + + fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); + + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ + if(i1 != 1 && TKresult[nres]!= k) + continue; + if(invalidvarcomb[k]){ + printf("\nCombination (%d) projection ignored because no cases \n",k); + continue; + } + fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#"); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ + fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + } + fprintf(ficresfb," yearbproj age"); + for(j=1; j<=nlstate+ndeath;j++){ + for(i=1; i<=nlstate;i++) + fprintf(ficresfb," b%d%d",i,j); + fprintf(ficresfb," b.%d",j); + } + for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { + /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */ + fprintf(ficresfb,"\n"); + fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); + /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */ + /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */ + for (agec=bage; agec<=fage; agec++){ /* testing */ + /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/ + nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/ + nhstepm = nhstepm/hstepm; + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + /* computes hbxij at age agec over 1 to nhstepm */ + /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */ + hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres); + /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */ + /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */ + /* printf(" agec=%.2f\n",agec);fflush(stdout); */ + for (h=0; h<=nhstepm; h++){ + if (h*hstepm/YEARM*stepm ==-yearp) { + break; + } + } + fprintf(ficresfb,"\n"); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm); + for(i=1; i<=nlstate+ndeath;i++) { + ppij=0.;ppi=0.; + for(j=1; j<=nlstate;j++) { + /* if (mobilav==1) */ + ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k]; + ppi=ppi+prevacurrent[(int)agec][j][k]; + /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */ + /* ppi=ppi+mobaverage[(int)agec][j][k]; */ + /* else { */ + /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */ + /* } */ + fprintf(ficresfb," %.3f", p3mat[i][j][h]); + } /* end j */ + if(ppi <0.99){ + printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi); + fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi); + } + fprintf(ficresfb," %.3f", ppij); + }/* end j */ + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + } /* end agec */ + } /* end yearp */ + } /* end k */ + + /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */ + + fclose(ficresfb); + printf("End of Computing Back forecasting \n"); + fprintf(ficlog,"End of Computing Back forecasting\n"); -/* } */ +} + +/* Variance of prevalence limit: varprlim */ + void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){ + /*------- Variance of period (stable) prevalence------*/ + + char fileresvpl[FILENAMELENGTH]; + FILE *ficresvpl; + double **oldm, **savm; + double **varpl; /* Variances of prevalence limits by age */ + int i1, k, nres, j ; + + strcpy(fileresvpl,"VPL_"); + strcat(fileresvpl,fileresu); + if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { + printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); + exit(0); + } + printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); + fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); + + /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ + + i1=pow(2,cptcoveff); + if (cptcovn < 1){i1=1;} + + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ + if(i1 != 1 && TKresult[nres]!= k) + continue; + fprintf(ficresvpl,"\n#****** "); + printf("\n#****** "); + fprintf(ficlog,"\n#****** "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficresvpl,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); + + varpl=matrix(1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres); + free_matrix(varpl,1,nlstate,(int) bage, (int)fage); + /*}*/ + } + + fclose(ficresvpl); + printf("done variance-covariance of period prevalence\n");fflush(stdout); + fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); + + } +/* Variance of back prevalence: varbprlim */ + void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){ + /*------- Variance of back (stable) prevalence------*/ + + char fileresvbl[FILENAMELENGTH]; + FILE *ficresvbl; + + double **oldm, **savm; + double **varbpl; /* Variances of back prevalence limits by age */ + int i1, k, nres, j ; + + strcpy(fileresvbl,"VBL_"); + strcat(fileresvbl,fileresu); + if((ficresvbl=fopen(fileresvbl,"w"))==NULL) { + printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl); + exit(0); + } + printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout); + fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog); + + + i1=pow(2,cptcoveff); + if (cptcovn < 1){i1=1;} + + for(nres=1; nres <= nresult; nres++) /* For each resultline */ + for(k=1; k<=i1;k++){ + if(i1 != 1 && TKresult[nres]!= k) + continue; + fprintf(ficresvbl,"\n#****** "); + printf("\n#****** "); + fprintf(ficlog,"\n#****** "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + } + for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ + printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); + } + fprintf(ficresvbl,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); + + varbpl=matrix(1,nlstate,(int) bage, (int) fage); + oldm=oldms;savm=savms; + + varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres); + free_matrix(varbpl,1,nlstate,(int) bage, (int)fage); + /*}*/ + } + + fclose(ficresvbl); + printf("done variance-covariance of back prevalence\n");fflush(stdout); + fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog); + + } /* End of varbprlim */ /************** Forecasting *****not tested NB*************/ /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */ @@ -7832,14 +9084,36 @@ int readdata(char datafile[], int firsto /*-------- data file ----------*/ FILE *fic; char dummy[]=" "; - int i=0, j=0, n=0, iv=0; + int i=0, j=0, n=0, iv=0, v; int lstra; int linei, month, year,iout; char line[MAXLINE], linetmp[MAXLINE]; char stra[MAXLINE], strb[MAXLINE]; char *stratrunc; + DummyV=ivector(1,NCOVMAX); /* 1 to 3 */ + FixedV=ivector(1,NCOVMAX); /* 1 to 3 */ + for(v=1; v <=ncovcol;v++){ + DummyV[v]=0; + FixedV[v]=0; + } + for(v=ncovcol+1; v <=ncovcol+nqv;v++){ + DummyV[v]=1; + FixedV[v]=0; + } + for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){ + DummyV[v]=0; + FixedV[v]=1; + } + for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){ + DummyV[v]=1; + FixedV[v]=1; + } + for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){ + printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]); + fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]); + } if((fic=fopen(datafile,"r"))==NULL) { printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout); @@ -8141,6 +9415,11 @@ int decoderesult ( char resultline[], in if (strlen(resultsav) >1){ j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */ } + if(j == 0){ /* Resultline but no = */ + TKresult[nres]=0; /* Combination for the nresult and the model */ + return (0); + } + if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */ printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs); @@ -8460,27 +9739,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\ Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); - - for(v=1; v <=ncovcol;v++){ - DummyV[v]=0; - FixedV[v]=0; - } - for(v=ncovcol+1; v <=ncovcol+nqv;v++){ - DummyV[v]=1; - FixedV[v]=0; - } - for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){ - DummyV[v]=0; - FixedV[v]=1; - } - for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){ - DummyV[v]=1; - FixedV[v]=1; - } - for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){ - printf("Decodemodel: V%d, Dummy(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]); - fprintf(ficlog,"Decodemodel: V%d, Dummy(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]); - } + for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;} for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */ if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */ Fixed[k]= 0; @@ -8505,7 +9764,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( TvarFind[ncovf]=k; TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ - }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ /* Only simple fixed quantitative variable */ + }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */ Fixed[k]= 0; Dummy[k]= 1; nqfveff++; @@ -8519,7 +9778,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( TvarFind[ncovf]=k; TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */ - }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */ + }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */ Fixed[k]= 1; Dummy[k]= 0; ntveff++; /* Only simple time varying dummy variable */ @@ -8530,7 +9789,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( TvarsDind[nsd]=k; ncovv++; /* Only simple time varying variables */ TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; + TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */ TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4 TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */ TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */ printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv); @@ -8546,7 +9805,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( TvarsQ[nsq]=Tvar[k]; TvarsQind[nsq]=k; TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; + TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */ TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */ TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */ @@ -8558,167 +9817,167 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( TvarA[ncova]=Tvar[k]; TvarAind[ncova]=k; if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */ - Fixed[k]= 2; - Dummy[k]= 2; - modell[k].maintype= ATYPE; - modell[k].subtype= APFD; - /* ncoveff++; */ + Fixed[k]= 2; + Dummy[k]= 2; + modell[k].maintype= ATYPE; + modell[k].subtype= APFD; + /* ncoveff++; */ }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/ - Fixed[k]= 2; - Dummy[k]= 3; - modell[k].maintype= ATYPE; - modell[k].subtype= APFQ; /* Product age * fixed quantitative */ - /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */ + Fixed[k]= 2; + Dummy[k]= 3; + modell[k].maintype= ATYPE; + modell[k].subtype= APFQ; /* Product age * fixed quantitative */ + /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */ }else if( Tvar[k] <=ncovcol+nqv+ntv ){ - Fixed[k]= 3; - Dummy[k]= 2; - modell[k].maintype= ATYPE; - modell[k].subtype= APVD; /* Product age * varying dummy */ - /* ntveff++; /\* Only simple time varying dummy variable *\/ */ + Fixed[k]= 3; + Dummy[k]= 2; + modell[k].maintype= ATYPE; + modell[k].subtype= APVD; /* Product age * varying dummy */ + /* ntveff++; /\* Only simple time varying dummy variable *\/ */ }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){ - Fixed[k]= 3; - Dummy[k]= 3; - modell[k].maintype= ATYPE; - modell[k].subtype= APVQ; /* Product age * varying quantitative */ - /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */ + Fixed[k]= 3; + Dummy[k]= 3; + modell[k].maintype= ATYPE; + modell[k].subtype= APVQ; /* Product age * varying quantitative */ + /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */ } }else if (Typevar[k] == 2) { /* product without age */ k1=Tposprod[k]; if(Tvard[k1][1] <=ncovcol){ - if(Tvard[k1][2] <=ncovcol){ - Fixed[k]= 1; - Dummy[k]= 0; - modell[k].maintype= FTYPE; - modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */ - ncovf++; /* Fixed variables without age */ - TvarF[ncovf]=Tvar[k]; - TvarFind[ncovf]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv){ - Fixed[k]= 0; /* or 2 ?*/ - Dummy[k]= 1; - modell[k].maintype= FTYPE; - modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */ - ncovf++; /* Varying variables without age */ - TvarF[ncovf]=Tvar[k]; - TvarFind[ncovf]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ - Fixed[k]= 1; - Dummy[k]= 0; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - } + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */ + ncovf++; /* Fixed variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 0; /* or 2 ?*/ + Dummy[k]= 1; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */ + ncovf++; /* Varying variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } }else if(Tvard[k1][1] <=ncovcol+nqv){ - if(Tvard[k1][2] <=ncovcol){ - Fixed[k]= 0; /* or 2 ?*/ - Dummy[k]= 1; - modell[k].maintype= FTYPE; - modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */ - ncovf++; /* Fixed variables without age */ - TvarF[ncovf]=Tvar[k]; - TvarFind[ncovf]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - } + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 0; /* or 2 ?*/ + Dummy[k]= 1; + modell[k].maintype= FTYPE; + modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */ + ncovf++; /* Fixed variables without age */ + TvarF[ncovf]=Tvar[k]; + TvarFind[ncovf]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ - if(Tvard[k1][2] <=ncovcol){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ - Fixed[k]= 1; - Dummy[k]= 0; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - } + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 0; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ - if(Tvard[k1][2] <=ncovcol){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ - Fixed[k]= 1; - Dummy[k]= 1; - modell[k].maintype= VTYPE; - modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */ - ncovv++; /* Varying variables without age */ - TvarV[ncovv]=Tvar[k]; - TvarVind[ncovv]=k; - } + if(Tvard[k1][2] <=ncovcol){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[k]= 1; + Dummy[k]= 1; + modell[k].maintype= VTYPE; + modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */ + ncovv++; /* Varying variables without age */ + TvarV[ncovv]=Tvar[k]; + TvarVind[ncovv]=k; + } }else{ - printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); - fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); - } /* end k1 */ + printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); + fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]); + } /*end k1*/ }else{ printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]); fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]); @@ -8730,11 +9989,12 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( /* Searching for doublons in the model */ for(k1=1; k1<= cptcovt;k1++){ for(k2=1; k2 nlstate){ (*nberr)++; - printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); - fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); - s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ + printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m); + fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m); + s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */ } } } @@ -9045,7 +10305,7 @@ void syscompilerinfo(int logged) #endif #endif - // void main() + // void main () // { #if defined(_MSC_VER) if (IsWow64()){ @@ -9097,7 +10357,7 @@ int prevalence_limit(double *p, double * for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ @@ -9194,7 +10454,7 @@ int back_prevalence_limit(double *p, dou for(nres=1; nres <= nresult; nres++){ /* For each resultline */ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov)); fprintf(ficresplb,"#******"); @@ -9233,14 +10493,16 @@ int back_prevalence_limit(double *p, dou if(mobilavproj > 0){ /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */ /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */ - bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k); + bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres); }else if (mobilavproj == 0){ printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj); fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj); exit(1); }else{ /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */ - bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k); + bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres); + /* printf("TOTOT\n"); */ + /* exit(1); */ } fprintf(ficresplb,"%.0f ",age ); for(j=1;j<=cptcoveff;j++) @@ -9253,6 +10515,7 @@ int back_prevalence_limit(double *p, dou fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp); } /* Age */ /* was end of cptcod */ + /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */ } /* end of any combination */ } /* end of nres */ /* hBijx(p, bage, fage); */ @@ -9297,7 +10560,7 @@ int hPijx(double *p, int bage, int fage) /* k=k+1; */ for(nres=1; nres <= nresult; nres++) /* For each resultline */ for(k=1; k<=i1;k++){ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; fprintf(ficrespij,"\n#****** "); for(j=1;j<=cptcoveff;j++) @@ -9369,14 +10632,14 @@ int hPijx(double *p, int bage, int fage) /* hstepm=1; aff par mois*/ pstamp(ficrespijb); - fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x "); + fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 "); i1= pow(2,cptcoveff); /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ /* k=k+1; */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; fprintf(ficrespijb,"\n#****** "); for(j=1;j<=cptcoveff;j++) @@ -9385,7 +10648,7 @@ int hPijx(double *p, int bage, int fage) fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); } fprintf(ficrespijb,"******\n"); - if(invalidvarcomb[k]){ + if(invalidvarcomb[k]){ /* Is it necessary here? */ fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); continue; } @@ -9398,12 +10661,14 @@ int hPijx(double *p, int bage, int fage) /* nhstepm=nhstepm*YEARM; aff par mois*/ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */ + /* and memory limitations if stepm is small */ + /* oldm=oldms;savm=savms; */ /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */ - hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k); + hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres); /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */ - fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j="); + fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j="); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespijb," %1d-%1d",i,j); @@ -9449,7 +10714,10 @@ int main(int argc, char *argv[]) int NDIM=2; int vpopbased=0; int nres=0; - + int endishere=0; + int noffset=0; + int ncurrv=0; /* Temporary variable */ + char ca[32], cb[32]; /* FILE *fichtm; *//* Html File */ /* FILE *ficgp;*/ /*Gnuplot File */ @@ -9493,17 +10761,20 @@ int main(int argc, char *argv[]) double **prlim; double **bprlim; double ***param; /* Matrix of parameters */ - double *p; + double ***paramstart; /* Matrix of starting parameter values */ + double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */ double **matcov; /* Matrix of covariance */ double **hess; /* Hessian matrix */ double ***delti3; /* Scale */ double *delti; /* Scale */ double ***eij, ***vareij; double **varpl; /* Variances of prevalence limits by age */ + double *epj, vepp; - double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; - double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000; + double dateprev1, dateprev2; + double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0; + double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0; double **ximort; char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; @@ -9581,8 +10852,13 @@ int main(int argc, char *argv[]) if(pathr[0] == '\0') break; /* Dirty */ } } + else if (argc<=2){ + strcpy(pathtot,argv[1]); + } else{ strcpy(pathtot,argv[1]); + strcpy(z,argv[2]); + printf("\nargv[2]=%s z=%c\n",argv[2],z[0]); } /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/ /*cygwin_split_path(pathtot,path,optionfile); @@ -9660,8 +10936,6 @@ int main(int argc, char *argv[]) exit(70); } - - strcpy(filereso,"o"); strcat(filereso,fileresu); if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */ @@ -9670,17 +10944,52 @@ int main(int argc, char *argv[]) fflush(ficlog); goto end; } + /*-------- Rewriting parameter file ----------*/ + strcpy(rfileres,"r"); /* "Rparameterfile */ + strcat(rfileres,optionfilefiname); /* Parameter file first name */ + strcat(rfileres,"."); /* */ + strcat(rfileres,optionfilext); /* Other files have txt extension */ + if((ficres =fopen(rfileres,"w"))==NULL) { + printf("Problem writing new parameter file: %s\n", rfileres);goto end; + fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end; + fflush(ficlog); + goto end; + } + fprintf(ficres,"#IMaCh %s\n",version); + /* Reads comments: lines beginning with '#' */ numlinepar=0; - - /* First parameter line */ + /* Is it a BOM UTF-8 Windows file? */ + /* First parameter line */ while(fgets(line, MAXLINE, ficpar)) { + noffset=0; + if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */ + { + noffset=noffset+3; + printf("# File is an UTF8 Bom.\n"); // 0xBF + } + else if( line[0] == (char)0xFE && line[1] == (char)0xFF) + { + noffset=noffset+2; + printf("# File is an UTF16BE BOM file\n"); + } + else if( line[0] == 0 && line[1] == 0) + { + if( line[2] == (char)0xFE && line[3] == (char)0xFF){ + noffset=noffset+4; + printf("# File is an UTF16BE BOM file\n"); + } + } else{ + ;/*printf(" Not a BOM file\n");*/ + } + /* If line starts with a # it is a comment */ - if (line[0] == '#') { + if (line[noffset] == '#') { numlinepar++; fputs(line,stdout); fputs(line,ficparo); + fputs(line,ficres); fputs(line,ficlog); continue; }else @@ -9690,18 +10999,24 @@ int main(int argc, char *argv[]) title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){ if (num_filled != 5) { printf("Should be 5 parameters\n"); + fprintf(ficlog,"Should be 5 parameters\n"); } numlinepar++; printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); + fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass); } /* Second parameter line */ while(fgets(line, MAXLINE, ficpar)) { - /* If line starts with a # it is a comment */ + /* while(fscanf(ficpar,"%[^\n]", line)) { */ + /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */ if (line[0] == '#') { numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); + printf("%s",line); + fprintf(ficres,"%s",line); + fprintf(ficparo,"%s",line); + fprintf(ficlog,"%s",line); continue; }else break; @@ -9711,8 +11026,19 @@ int main(int argc, char *argv[]) if (num_filled != 11) { printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); printf("but line=%s\n",line); + fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); + fprintf(ficlog,"but line=%s\n",line); + } + if( lastpass > maxwav){ + printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav); + fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav); + fflush(ficlog); + goto end; } - printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); + printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); + fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); + fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt); + fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); } /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ @@ -9721,19 +11047,18 @@ int main(int argc, char *argv[]) /* If line starts with a # it is a comment */ if (line[0] == '#') { numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); + printf("%s",line); + fprintf(ficres,"%s",line); + fprintf(ficparo,"%s",line); + fprintf(ficlog,"%s",line); continue; }else break; } if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ - if (num_filled == 0) - model[0]='\0'; - else if (num_filled != 1){ - printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); - fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line); + if (num_filled != 1){ + printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line); + fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line); model[0]='\0'; goto end; } @@ -9746,20 +11071,23 @@ int main(int argc, char *argv[]) } /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */ printf("model=1+age+%s\n",model);fflush(stdout); + fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout); + fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout); + fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout); } /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ /* numlinepar=numlinepar+3; /\* In general *\/ */ /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); - fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); + /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */ + /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */ fflush(ficlog); /* if(model[0]=='#'|| model[0]== '\0'){ */ if(model[0]=='#'){ - printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ - 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ - 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ + printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \ + 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \ + 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \ if(mle != -1){ - printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); + printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n"); exit(1); } } @@ -9780,9 +11108,9 @@ int main(int argc, char *argv[]) covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ - coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */ - cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/ - cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */ + if(nqv>=1)coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */ + if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */ + if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 v1+v2*age+v2*v3 makes cptcovn = 3 @@ -9804,6 +11132,12 @@ 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;iDatafile=%s Firstpass=%d La /* Calculates basic frequencies. Computes observed prevalence at single age and for any valid combination of covariates and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \ + freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \ firstpass, lastpass, stepm, weightopt, model); fprintf(fichtm,"\n"); - fprintf(fichtm,"
        Total number of observations=%d
        \n\ + fprintf(fichtm,"

        Parameter line 2

        • Tolerance for the convergence of the likelihood: ftol=%g \n
        • Interval for the elementary matrix (in month): stepm=%d",\ + ftol, stepm); + fprintf(fichtm,"\n
        • Number of fixed dummy covariates: ncovcol=%d ", ncovcol); + ncurrv=1; + for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i); + fprintf(fichtm,"\n
        • Number of fixed quantitative variables: nqv=%d ", nqv); + ncurrv=i; + for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i); + fprintf(fichtm,"\n
        • Number of time varying (wave varying) covariates: ntv=%d ", ntv); + ncurrv=i; + for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i); + fprintf(fichtm,"\n
        • Number of quantitative time varying covariates: nqtv=%d ", nqtv); + ncurrv=i; + for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i); + fprintf(fichtm,"\n
        • Weights column \n
          Number of alive states: nlstate=%d
          Number of death states (not really implemented): ndeath=%d \n
        • Number of waves: maxwav=%d \n
        • Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n
        • Does the weight column be taken into account (1), or not (0): weight=%d
        \n", \ + nlstate, ndeath, maxwav, mle, weightopt); + + fprintf(fichtm,"

        Diagram of states %s_.svg

        \n\ +", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_")); + + + fprintf(fichtm,"\n

        Some descriptive statistics

        \n
        Total number of observations=%d
        \n\ Youngest age at first (selected) pass %.2f, oldest age %.2f
        \n\ Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
        \n",\ - imx,agemin,agemax,jmin,jmax,jmean); + imx,agemin,agemax,jmin,jmax,jmean); pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ + oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ + oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ /* For Powell, parameters are in a vector p[] starting at p[1] so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ @@ -10340,9 +11685,9 @@ Interval (in months) between two waves: /* For mortality only */ if (mle==-3){ ximort=matrix(1,NDIM,1,NDIM); - for(i=1;i<=NDIM;i++) - for(j=1;j<=NDIM;j++) - ximort[i][j]=0.; + for(i=1;i<=NDIM;i++) + for(j=1;j<=NDIM;j++) + ximort[i][j]=0.; /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ cens=ivector(1,n); ageexmed=vector(1,n); @@ -10578,6 +11923,10 @@ Please run with mle=-1 to get a correct printf("\n"); if(mle>=1){ /* Could be 1 or 2, Real Maximization */ /* mlikeli uses func not funcone */ + /* for(i=1;i MAXRESULTLINES){ + printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); + fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult); + goto end; + } + decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */ + fprintf(ficparo,"result: %s\n",resultline); + fprintf(ficres,"result: %s\n",resultline); + fprintf(ficlog,"result: %s\n",resultline); + break; + case 14: + if(ncovmodel >2 && nresult==0 ){ + printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line); + goto end; + } + break; + default: + nresult=1; + decoderesult(".",nresult ); /* No covariate */ + } + } /* End switch parameterline */ + }while(endishere==0); /* End do */ /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ @@ -10918,11 +12300,12 @@ Please run with mle=-1 to get a correct This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar); }else{ - printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p); + /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */ + printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage); } printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \ - model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \ - jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); + model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \ + jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2); /*------------ free_vector -------------*/ /* chdir(path); */ @@ -10958,44 +12341,49 @@ Please run with mle=-1 to get a correct k=1; varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); - /* Prevalence for each covariates in probs[age][status][cov] */ - probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); - for(i=1;i<=AGESUP;i++) + /* Prevalence for each covariate combination in probs[age][status][cov] */ + probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); + for(i=AGEINF;i<=AGESUP;i++) for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */ for(k=1;k<=ncovcombmax;k++) probs[i][j][k]=0.; - prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); + prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, + ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); if (mobilav!=0 ||mobilavproj !=0 ) { - mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); - for(i=1;i<=AGESUP;i++) - for(j=1;j<=nlstate;j++) + mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); + for(i=AGEINF;i<=AGESUP;i++) + for(j=1;j<=nlstate+ndeath;j++) for(k=1;k<=ncovcombmax;k++) mobaverages[i][j][k]=0.; mobaverage=mobaverages; if (mobilav!=0) { printf("Movingaveraging observed prevalence\n"); + fprintf(ficlog,"Movingaveraging observed prevalence\n"); if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); printf(" Error in movingaverage mobilav=%d\n",mobilav); } - } - /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */ - /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ - else if (mobilavproj !=0) { + } else if (mobilavproj !=0) { printf("Movingaveraging projected observed prevalence\n"); + fprintf(ficlog,"Movingaveraging projected observed prevalence\n"); if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){ fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj); printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj); } + }else{ + printf("Internal error moving average\n"); + fflush(stdout); + exit(1); } }/* end if moving average */ /*---------- Forecasting ------------------*/ - /*if((stepm == 1) && (strcmp(model,".")==0)){*/ if(prevfcast==1){ /* if(stepm ==1){*/ - prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); + prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); } + + /* Backcasting */ if(backcast==1){ ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath); @@ -11004,20 +12392,24 @@ Please run with mle=-1 to get a correct /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/ bprlim=matrix(1,nlstate,1,nlstate); + back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj); fclose(ficresplb); hBijx(p, bage, fage, mobaverage); fclose(ficrespijb); - free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */ - /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj, - bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */ + prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, + mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); + varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff); + + + free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */ free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath); free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath); free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath); - } - + } /* end Backcasting */ + /* ------ Other prevalence ratios------------ */ @@ -11045,7 +12437,7 @@ Please run with mle=-1 to get a correct for(nres=1; nres <= nresult; nres++) /* For each resultline */ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; fprintf(ficreseij,"\n#****** "); printf("\n#****** "); @@ -11069,10 +12461,10 @@ Please run with mle=-1 to get a correct fclose(ficreseij); printf("done evsij\n");fflush(stdout); fprintf(ficlog,"done evsij\n");fflush(ficlog); + /*---------- State-specific expectancies and variances ------------*/ - strcpy(filerest,"T_"); strcat(filerest,fileresu); if((ficrest=fopen(filerest,"w"))==NULL) { @@ -11081,8 +12473,6 @@ Please run with mle=-1 to get a correct } printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout); fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog); - - strcpy(fileresstde,"STDE_"); strcat(fileresstde,fileresu); if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { @@ -11110,19 +12500,16 @@ Please run with mle=-1 to get a correct printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout); fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog); - /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ - i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */ if (cptcovn < 1){i1=1;} for(nres=1; nres <= nresult; nres++) /* For each resultline */ for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; - printf("\n#****** Selected:"); - fprintf(ficrest,"\n#****** Selected:"); - fprintf(ficlog,"\n#****** Selected:"); + printf("\n#****** Result for:"); + fprintf(ficrest,"\n#****** Result for:"); + fprintf(ficlog,"\n#****** Result for:"); 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)]); @@ -11174,7 +12561,7 @@ Please run with mle=-1 to get a correct vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); pstamp(ficrest); - + epj=vector(1,nlstate+1); for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ oldm=oldms;savm=savms; /* ZZ Segmentation fault */ cptcod= 0; /* To be deleted */ @@ -11190,7 +12577,6 @@ Please run with mle=-1 to get a correct for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); fprintf(ficrest,"\n"); /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */ - epj=vector(1,nlstate+1); printf("Computing age specific period (stable) prevalences in each health state \n"); fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n"); for(age=bage; age <=fage ;age++){ @@ -11228,66 +12614,20 @@ Please run with mle=-1 to get a correct fprintf(ficrest,"\n"); } } /* End vpopbased */ + free_vector(epj,1,nlstate+1); free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); - free_vector(epj,1,nlstate+1); printf("done selection\n");fflush(stdout); fprintf(ficlog,"done selection\n");fflush(ficlog); - /*}*/ } /* End k selection */ printf("done State-specific expectancies\n");fflush(stdout); fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog); - /*------- Variance of period (stable) prevalence------*/ - - strcpy(fileresvpl,"VPL_"); - strcat(fileresvpl,fileresu); - if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { - printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); - exit(0); - } - printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout); - fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog); - - /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ - - i1=pow(2,cptcoveff); - if (cptcovn < 1){i1=1;} + /* variance-covariance of period prevalence*/ + varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff); - for(nres=1; nres <= nresult; nres++) /* For each resultline */ - for(k=1; k<=i1;k++){ - if(TKresult[nres]!= k) - continue; - fprintf(ficresvpl,"\n#****** "); - printf("\n#****** "); - fprintf(ficlog,"\n#****** "); - for(j=1;j<=cptcoveff;j++) { - fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); - } - for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */ - printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); - fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); - fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); - } - fprintf(ficresvpl,"******\n"); - printf("******\n"); - fprintf(ficlog,"******\n"); - - varpl=matrix(1,nlstate,(int) bage, (int) fage); - oldm=oldms;savm=savms; - varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres); - free_matrix(varpl,1,nlstate,(int) bage, (int)fage); - /*}*/ - } - - fclose(ficresvpl); - printf("done variance-covariance of period prevalence\n");fflush(stdout); - fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog); free_vector(weight,1,n); free_imatrix(Tvard,1,NCOVMAX,1,2); @@ -11305,8 +12645,8 @@ Please run with mle=-1 to get a correct /*---------- End : free ----------------*/ if (mobilav!=0 ||mobilavproj !=0) - free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */ - free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); + free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */ + free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); } /* mle==-3 arrives here for freeing */ @@ -11314,15 +12654,16 @@ Please run with mle=-1 to get a correct free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); - free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n); - free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n); - free_matrix(coqvar,1,maxwav,1,n); + if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n); + if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n); + if(nqv>=1)free_matrix(coqvar,1,nqv,1,n); free_matrix(covar,0,NCOVMAX,1,n); free_matrix(matcov,1,npar,1,npar); free_matrix(hess,1,npar,1,npar); /*free_vector(delti,1,npar);*/ free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); free_matrix(agev,1,maxwav,1,imx); + free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); free_ivector(ncodemax,1,NCOVMAX); @@ -11399,6 +12740,8 @@ Please run with mle=-1 to get a correct fclose(ficlog); /*------ End -----------*/ + +/* Executes gnuplot */ printf("Before Current directory %s!\n",pathcd); #ifdef WIN32 @@ -11467,4 +12810,6 @@ end: printf("\nType q for exiting: "); fflush(stdout); scanf("%s",z); } + printf("End\n"); + exit(0); }