--- imach/src/imach.c 2016/08/26 15:51:03 1.239 +++ imach/src/imach.c 2017/04/05 10:14:09 1.261 @@ -1,6 +1,74 @@ -/* $Id: imach.c,v 1.239 2016/08/26 15:51:03 brouard Exp $ +/* $Id: imach.c,v 1.261 2017/04/05 10:14:09 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + 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 +160,7 @@ 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 @@ -882,7 +948,7 @@ 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"*/ @@ -919,12 +985,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.239 2016/08/26 15:51:03 brouard Exp $ */ +/* $Id: imach.c,v 1.261 2017/04/05 10:14:09 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 $"; +char fullversion[]="$Revision: 1.261 $ $Date: 2017/04/05 10:14:09 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -1037,7 +1103,8 @@ 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 @@ -1124,6 +1191,7 @@ 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 +2134,8 @@ 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 +2175,8 @@ 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 +2199,34 @@ 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 +2280,8 @@ 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 +2327,7 @@ 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 +2424,8 @@ 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); @@ -2541,7 +2607,7 @@ 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 matrix by transitions matrix until convergence is reached with precision ftolpl */ @@ -2564,6 +2630,7 @@ 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(); @@ -2600,15 +2667,49 @@ 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<=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 combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,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]]; + } + } } - 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)]; /*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]);*/ @@ -2655,7 +2756,12 @@ 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); @@ -2788,7 +2894,8 @@ double **pmij(double **ps, double *cov, /* }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); + ; + /* 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); */ } } /*End ii */ } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */ @@ -3171,7 +3278,7 @@ 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 +3297,8 @@ 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 +3312,10 @@ 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 +3597,8 @@ 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 *\/ */ @@ -3513,46 +3625,51 @@ 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,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); } } /* end of wave */ } /* end of individual */ @@ -3946,8 +4063,8 @@ 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 +4153,16 @@ 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++) { @@ -4102,17 +4228,84 @@ void pstamp(FILE *fichier) fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart); } +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; /* 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/(ne-2)/(sumx2 - sumx * sumx /ne)); + *sa= *sb * sqrt(sumx2/ne); + + return 0; +} + /************ 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; int iind=0, iage=0; int mi; /* Effective wave */ int first; double ***freq; /* Frequencies */ + double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */ + int no; double *meanq; double **meanqt; double *pp, **prop, *posprop, *pospropt; @@ -4121,7 +4314,7 @@ 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); */ @@ -4135,7 +4328,7 @@ 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)); @@ -4145,318 +4338,463 @@ 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<= nqfveff; z1++) { */ + /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */ + /* } */ + 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 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 or all fixed */ + /* 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 */ + } /* 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 (cptcoveff>0 && j!=0){ + 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"); + } + fprintf(ficresphtm,""); + 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); + } + } + 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(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,"",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,"",iage, prop[jk][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",jk,m,freq[jk][m][iage]); */ + fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][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); - } - } - 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); - } + if(jk!=0 && m!=0) + fprintf(ficresphtmfr," ",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"); + } + if(first==1) + printf("Others in log...\n"); + fprintf(ficlog,"\n"); + } /* end loop age iage */ + fprintf(ficresphtm,""); for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) - pp[jk] += freq[jk][m][iage]; + if(posproptt < 1.e-5){ + fprintf(ficresphtm,"",pospropt[jk],posproptt); + }else{ + fprintf(ficresphtm,"",pospropt[jk]/posproptt,pospropt[jk],posproptt); + } } - 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); - } + fprintf(ficresphtm,"\n"); + fprintf(ficresphtm,"
Age%d%d
0
Unknown
Total
%d%.0f
TotNanq%.0f%.0f%.5f%.0f%.0f
\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{ + fprintf(ficresphtm,"\n

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

",j1); + invalidvarcomb[j1]=0; } - - 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] */ + fprintf(ficresphtmfr,"\n"); + fprintf(ficlog,"\n"); + if(j!=0){ + printf("#Freqsummary: Starting values for combination j1=%d:\n", j1); + for(i=1,jk=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */ + 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[jk],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[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])); + pstart[jk]= 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, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */ + } + linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */ + pstart[jk]=b; + pstart[jk-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[jk]= 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("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],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]); */ + jk++; + } /* end jj */ + } /* end k!= i */ + } /* end k */ + } /* end i, jk */ + } /* 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,jk=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[jk]=p[jk]; /* Setting pstart to p values by default */ + if(jj==1){ /* Age has to be done */ + pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]); + printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],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[jk],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]); */ + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + } + } } - 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.; */ + printf("#Freqsummary\n"); + fprintf(ficlog,"\n"); 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]); - } + for(m=-1; m <=nlstate+ndeath; m++){ + /* param[i]|j][k]= freq[jk][m][iagemax+3] */ + printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); + fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); + /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */ + /* printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */ + /* fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */ + /* } */ + } } /* 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"); - } - if(first==1) - printf("Others in log...\n"); + + printf("\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); + } /* 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(meanq,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 */ } @@ -4483,7 +4821,7 @@ 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 +4831,7 @@ 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 +4862,7 @@ 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); } @@ -4561,7 +4899,7 @@ 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 ***************/ @@ -4640,13 +4978,9 @@ 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 +4993,12 @@ 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 +5029,7 @@ 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 +5116,173 @@ 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 */ + 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 */ + /* 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 ****************/ @@ -5405,7 +5739,7 @@ void concatwav(int wav[], int **dh, int 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){ @@ -5437,7 +5771,7 @@ 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); + prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres); if (popbased==1) { if(mobilav ==0){ @@ -5514,7 +5848,7 @@ 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){ @@ -5609,7 +5943,9 @@ 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"); @@ -5695,6 +6031,8 @@ void concatwav(int wav[], int **dh, int 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"); @@ -6053,7 +6391,7 @@ 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 , \ + int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \ double jprev1, double mprev1,double anprev1, double dateprev1, \ double jprev2, double mprev2,double anprev2, double dateprev2){ int jj1, k1, i1, cpt, k4, nres; @@ -6099,8 +6437,8 @@ void printinghtml(char fileresu[], char jj1=0; for(nres=1; nres <= nresult; nres++) /* For each resultline */ - for(k1=1; k1<=m;k1++){ - if(TKresult[nres]!= k1) + 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++){ */ @@ -6127,51 +6465,51 @@ 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 to be in state %d some years earlier, knowing that we will be in state (1 to %d) at different ages. %s_%d-%d-%d.svg
\ +", cpt, cpt, nlstate, 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 to be in state %d at a younger age, knowing that we will be 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) 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-%d.svg
\ +", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),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 +6568,9 @@ 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++; @@ -6253,18 +6591,19 @@ 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); } @@ -6327,10 +6666,10 @@ 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); 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 */ @@ -6339,37 +6678,36 @@ void printinggnuplot(char fileresu[], ch /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */ /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */ - printf(" V%d=%d ",Tvaraff[k],vlv); + /* printf(" V%d=%d ",Tvaraff[k],vlv); */ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); } for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ - printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); + /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } - printf("\n#\n"); + /* printf("\n#\n"); */ fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ + /*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 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*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); @@ -6377,9 +6715,9 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); 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 */ @@ -6394,8 +6732,8 @@ 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++; @@ -6412,7 +6750,7 @@ 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 "); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ @@ -6434,7 +6772,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u 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,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage); @@ -6442,20 +6780,20 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u 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+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," %%lf (%%lf)"); else fprintf(ficgp," %%*lf (%%*lf)"); @@ -6464,7 +6802,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n"); } /* state */ } /* vpopbased */ - fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */ + fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */ } /* end nres */ } /* k1 end 2 eme*/ @@ -6472,11 +6810,11 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /*3eme*/ for (k1=1; k1<= m ; k1 ++){ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= k) + if(m != 1 && TKresult[nres]!= k1) continue; for (cpt=1; cpt<= nlstate ; cpt ++) { - fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt); + fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ @@ -6496,9 +6834,9 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* k=2+nlstate*(2*cpt-2); */ k=2+(nlstate+1)*(cpt-1); - fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1); + fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres); fprintf(ficgp,"set ter svg size 640, 480\n\ -plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt); +plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt); /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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); @@ -6508,11 +6846,11 @@ 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); } } /* end nres */ } /* end kl 3eme */ @@ -6521,7 +6859,7 @@ 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*/ fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt); @@ -6542,7 +6880,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u 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 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; @@ -6567,7 +6905,7 @@ 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 */ 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); @@ -6588,7 +6926,7 @@ set ter svg size 640, 480\nunset log y\n 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 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; @@ -6621,9 +6959,9 @@ 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 */ 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 */ @@ -6643,16 +6981,16 @@ set ter svg size 640, 480\nunset log y\n 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 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); @@ -6668,10 +7006,10 @@ 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 ending state */ + 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 */ @@ -6689,20 +7027,20 @@ set ter svg size 640, 480\nunset log y\n 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 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,"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); *\/ */ @@ -6719,7 +7057,7 @@ 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 */ fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt); @@ -6741,7 +7079,7 @@ 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 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 */ @@ -6850,14 +7188,14 @@ set ter svg size 640, 480\nunset log y\n 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 */ for(nres=1; nres <= nresult; nres++){ /* For each resultline */ - if(TKresult[nres]!= jk) + if(m != 1 && TKresult[nres]!= jk) continue; fprintf(ficgp,"# Combination of dummy jk=%d and ",jk); for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); } 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_"),jk,ng,nres); 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 */ @@ -7212,7 +7550,7 @@ 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); @@ -7832,14 +8170,36 @@ 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 +8501,11 @@ 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 +8825,7 @@ 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 +8850,7 @@ 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 +8864,7 @@ 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 +8875,7 @@ 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 +8891,7 @@ 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 +8903,167 @@ 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]); @@ -8760,7 +9105,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative ( } int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) -{ +{/* Check ages at death */ int i, m; int firstone=0; @@ -8775,16 +9120,16 @@ int calandcheckages(int imx, int maxwav, *nberr = *nberr + 1; if(firstone == 0){ firstone=1; - printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m); + printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m); } - fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m); - s[m][i]=-1; + fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m); + s[m][i]=-1; /* Droping the death status */ } if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>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).\nOther similar cases in log file\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 */ } } } @@ -9097,7 +9442,7 @@ 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 +9539,7 @@ 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 +9578,14 @@ 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); } fprintf(ficresplb,"%.0f ",age ); for(j=1;j<=cptcoveff;j++) @@ -9253,6 +9598,7 @@ 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 +9643,7 @@ 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 +9715,14 @@ 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++) @@ -9403,7 +9749,7 @@ int hPijx(double *p, int bage, int fage) /* 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,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); @@ -9449,6 +9795,7 @@ int main(int argc, char *argv[]) int NDIM=2; int vpopbased=0; int nres=0; + int endishere=0; char ca[32], cb[32]; /* FILE *fichtm; *//* Html File */ @@ -9493,7 +9840,8 @@ 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 */ @@ -9804,6 +10152,12 @@ 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"); @@ -10340,9 +10694,9 @@ 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 +10932,10 @@ 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); */ @@ -10921,7 +11307,7 @@ Please run with mle=-1 to get a correct printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p); } printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \ - model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \ + model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \ jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); /*------------ free_vector -------------*/ @@ -10974,6 +11360,7 @@ Please run with mle=-1 to get a correct 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); @@ -10983,6 +11370,7 @@ Please run with mle=-1 to get a correct /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */ 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); @@ -11045,7 +11433,7 @@ 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#****** "); @@ -11118,11 +11506,11 @@ 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; - 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)]); @@ -11259,7 +11647,7 @@ Please run with mle=-1 to get a correct for(nres=1; nres <= nresult; nres++) /* For each resultline */ for(k=1; k<=i1;k++){ - if(TKresult[nres]!= k) + if(i1 != 1 && TKresult[nres]!= k) continue; fprintf(ficresvpl,"\n#****** "); printf("\n#****** ");