--- imach/src/imach.c 2016/02/17 08:14:50 1.222 +++ imach/src/imach.c 2016/07/12 18:42:34 1.226 @@ -1,6 +1,18 @@ -/* $Id: imach.c,v 1.222 2016/02/17 08:14:50 brouard Exp $ +/* $Id: imach.c,v 1.226 2016/07/12 18:42:34 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.226 2016/07/12 18:42:34 brouard + Summary: temp + + Revision 1.225 2016/07/12 08:40:03 brouard + Summary: saving but not running + + Revision 1.224 2016/07/01 13:16:01 brouard + Summary: Fixes + + Revision 1.223 2016/02/19 09:23:35 brouard + Summary: temporary + Revision 1.222 2016/02/17 08:14:50 brouard Summary: Probably last 0.98 stable version 0.98r6 @@ -680,8 +692,25 @@ Back prevalence and projections: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ - 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); + 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); + +Important routines + +- func (or funcone), computes logit (pij) distinguishing + o fixed variables (single or product dummies or quantitative); + o varying variables by: + (1) wave (single, product dummies, quantitative), + (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be: + % fixed dummy (treated) or quantitative (not done because time-consuming); + % varying dummy (not done) or quantitative (not done); +- Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities) + and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually. +- printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables + o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if + race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless. + + Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). Institut national d'études démographiques, Paris. This software have been partly granted by Euro-REVES, a concerted action @@ -742,9 +771,9 @@ Back prevalence and projections: /* #define DEBUGLINMIN */ /* #define DEBUGHESS */ #define DEBUGHESSIJ -#define LINMINORIGINAL /* Don't use loop on scale in linmin (accepting nan)*/ +/* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */ #define POWELL /* Instead of NLOPT */ -#define POWELLF1F3 /* Skip test */ +#define POWELLNOF3INFF1TEST /* Skip test */ /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ @@ -752,6 +781,7 @@ Back prevalence and projections: #include #include #include +#include #ifdef _WIN32 #include @@ -834,12 +864,12 @@ typedef struct { #define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.222 2016/02/17 08:14:50 brouard Exp $ */ +/* $Id: imach.c,v 1.226 2016/07/12 18:42:34 brouard Exp $ */ /* $State: Exp $ */ #include "version.h" char version[]=__IMACH_VERSION__; -char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; -char fullversion[]="$Revision: 1.222 $ $Date: 2016/02/17 08:14:50 $"; +char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018"; +char fullversion[]="$Revision: 1.226 $ $Date: 2016/07/12 18:42:34 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -847,16 +877,22 @@ int nagesqr=0, nforce=0; /* nagesqr=1 if /* Number of covariates model=V2+V1+ V3*age+V2*V4 */ int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */ int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */ -int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */ +int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */ +int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */ int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */ int cptcovprodnoage=0; /**< Number of covariate products without age */ int cptcoveff=0; /* Total number of covariates to vary for printing results */ +int ncoveff=0; /* Total number of effective covariates in the model */ +int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */ +int ntveff=0; /**< ntveff number of effective time varying variables */ +int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */ int cptcov=0; /* Working variable */ int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */ int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ +int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */ int popbased=0; int *wav; /* Number of waves for this individuual 0 is possible */ @@ -995,8 +1031,14 @@ double *agedc; double **covar; /**< covar[j,i], value of jth covariate for individual i, * covar=matrix(0,NCOVMAX,1,n); * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */ +double **coqvar; /* Fixed quantitative covariate iqv */ +double ***cotvar; /* Time varying covariate itv */ +double ***cotqvar; /* Time varying quantitative covariate itqv */ double idx; int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ +int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */ +int *Fixed; /** Fixed[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ +int *Dummy; /** Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ int *Tage; int *Ndum; /** Freq of modality (tricode */ /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */ @@ -1542,12 +1584,12 @@ double brent(double ax, double bx, doubl etemp=e; e=d; if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) - d=CGOLD*(e=(x >= xm ? a-x : b-x)); + d=CGOLD*(e=(x >= xm ? a-x : b-x)); else { - d=p/q; - u=x+d; - if (u-a < tol2 || b-u < tol2) - d=SIGN(tol1,xm-x); + d=p/q; + u=x+d; + if (u-a < tol2 || b-u < tol2) + d=SIGN(tol1,xm-x); } } else { d=CGOLD*(e=(x >= xm ? a-x : b-x)); @@ -1561,13 +1603,13 @@ double brent(double ax, double bx, doubl } else { if (u < x) a=u; else b=u; if (fu <= fw || w == x) { - v=w; - w=u; - fv=fw; - fw=fu; + v=w; + w=u; + fv=fw; + fw=fu; } else if (fu <= fv || v == x || v == w) { - v=u; - fv=fu; + v=u; + fv=fu; } } } @@ -1608,12 +1650,12 @@ values at the three points, fa, fb , and *cx=(*bx)+GOLD*(*bx-*ax); *fc=(*func)(*cx); #ifdef DEBUG - printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); - fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); + printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc); + fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc); #endif - while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */ + while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/ r=(*bx-*ax)*(*fb-*fc); - q=(*bx-*cx)*(*fb-*fa); + q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */ u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ @@ -1624,8 +1666,8 @@ values at the three points, fa, fb , and double A, fparabu; A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); fparabu= *fa - A*(*ax-u)*(*ax-u); - printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); - fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); + printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r); + fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r); /* And thus,it can be that fu > *fc even if fparabu < *fc */ /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ @@ -1658,9 +1700,12 @@ values at the three points, fa, fb , and /* fu = *fc; */ /* *fc =dum; */ /* } */ -#ifdef DEBUG - printf("mnbrak34 fu < or >= fc \n"); - fprintf(ficlog, "mnbrak34 fu < fc\n"); +#ifdef DEBUGMNBRAK + double A, fparabu; + A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); + fparabu= *fa - A*(*ax-u)*(*ax-u); + printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r); + fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r); #endif dum=u; /* Shifting c and u */ u = *cx; @@ -1671,38 +1716,45 @@ values at the three points, fa, fb , and #endif } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ #ifdef DEBUG - printf("mnbrak2 u after c but before ulim\n"); - fprintf(ficlog, "mnbrak2 u after c but before ulim\n"); + printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx); + fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx); #endif fu=(*func)(u); if (fu < *fc) { #ifdef DEBUG - printf("mnbrak2 u after c but before ulim AND fu < fc\n"); - fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu = 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ #ifdef DEBUG - printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); - fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); + printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx); + fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx); #endif u=ulim; fu=(*func)(u); } else { /* u could be left to b (if r > q parabola has a maximum) */ #ifdef DEBUG - printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); - fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); + printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q); + fprintf(ficlog,"\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q); #endif u=(*cx)+GOLD*(*cx-*bx); fu=(*func)(u); +#ifdef DEBUG + printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx); + fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx); +#endif } /* end tests */ SHFT(*ax,*bx,*cx,u) SHFT(*fa,*fb,*fc,fu) #ifdef DEBUG - printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); - fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); + printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc); + fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc); #endif } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */ } @@ -1717,7 +1769,11 @@ int ncom; double *pcom,*xicom; double (*nrfunc)(double []); +#ifdef LINMINORIGINAL 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) +#endif { double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin); @@ -1761,28 +1817,41 @@ void linmin(double p[], double xi[], int #ifdef LINMINORIGINAL #else if (fx != fx){ - xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ - printf("|"); - fprintf(ficlog,"|"); + xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ + printf("|"); + fprintf(ficlog,"|"); #ifdef DEBUGLINMIN - printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); + printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); #endif } - }while(fx != fx); + }while(fx != fx && xxs > 1.e-5); #endif #ifdef DEBUGLINMIN printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb); #endif +#ifdef LINMINORIGINAL +#else + if(fb == fx){ /* Flat function in the direction */ + xmin=xx; + *flat=1; + }else{ + *flat=0; +#endif + /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */ *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ /* fmin = f(p[j] + xmin * xi[j]) */ /* P+lambda n in that direction (lambdamin), with TOL between abscisses */ /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ #ifdef DEBUG - printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); - fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); + printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin); + fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin); +#endif +#ifdef LINMINORIGINAL +#else + } #endif #ifdef DEBUGLINMIN printf("linmin end "); @@ -1832,17 +1901,33 @@ such that failure to decrease by more th output, p is set to the best point found, xi is the then-current direction set, fret is the returned function value at p , and iter is the number of iterations taken. The routine linmin is used. */ +#ifdef LINMINORIGINAL +#else + int *flatdir; /* Function is vanishing in that direction */ + int flat=0, flatd=0; /* Function is vanishing in that direction */ +#endif void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, double (*func)(double [])) { - void linmin(double p[], double xi[], int n, double *fret, +#ifdef LINMINORIGINAL + 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); +#endif int i,ibig,j; double del,t,*pt,*ptt,*xit; double directest; double fp,fptt; double *xits; int niterf, itmp; +#ifdef LINMINORIGINAL +#else + + flatdir=ivector(1,n); + for (j=1;j<=n;j++) flatdir[j]=0; +#endif pt=vector(1,n); ptt=vector(1,n); @@ -1876,18 +1961,18 @@ void powell(double p[], double **xi, int 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 */ @@ -1899,27 +1984,32 @@ void powell(double p[], double **xi, int #endif printf("%d",i);fflush(stdout); /* print direction (parameter) i */ fprintf(ficlog,"%d",i);fflush(ficlog); +#ifdef LINMINORIGINAL linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ - /* Outputs are fret(new point p) p is updated and xit rescaled */ +#else + linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ + flatdir[i]=flat; /* Function is vanishing in that direction i */ +#endif + /* Outputs are fret(new point p) p is updated and xit rescaled */ if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */ - /* because that direction will be replaced unless the gain del is small */ - /* in comparison with the 'probable' gain, mu^2, with the last average direction. */ - /* Unless the n directions are conjugate some gain in the determinant may be obtained */ - /* with the new direction. */ - del=fabs(fptt-(*fret)); - ibig=i; + /* because that direction will be replaced unless the gain del is small */ + /* in comparison with the 'probable' gain, mu^2, with the last average direction. */ + /* Unless the n directions are conjugate some gain in the determinant may be obtained */ + /* with the new direction. */ + del=fabs(fptt-(*fret)); + ibig=i; } #ifdef DEBUG printf("%d %.12e",i,(*fret)); fprintf(ficlog,"%d %.12e",i,(*fret)); for (j=1;j<=n;j++) { - xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); - printf(" x(%d)=%.12e",j,xit[j]); - fprintf(ficlog," x(%d)=%.12e",j,xit[j]); + xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5); + printf(" x(%d)=%.12e",j,xit[j]); + fprintf(ficlog," x(%d)=%.12e",j,xit[j]); } for(j=1;j<=n;j++) { - printf(" p(%d)=%.12e",j,p[j]); - fprintf(ficlog," p(%d)=%.12e",j,p[j]); + printf(" p(%d)=%.12e",j,p[j]); + fprintf(ficlog," p(%d)=%.12e",j,p[j]); } printf("\n"); fprintf(ficlog,"\n"); @@ -1928,6 +2018,14 @@ void powell(double p[], double **xi, int /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ /* New value of last point Pn is not computed, P(n-1) */ + for(j=1;j<=n;j++) { + if(flatdir[j] >0){ + printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); + fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]); + } + /* printf("\n"); */ + /* fprintf(ficlog,"\n"); */ + } if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* 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 */ @@ -1936,7 +2034,7 @@ void powell(double p[], double **xi, int /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */ /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */ /* By adding 10 parameters more the gain should be 18.31 */ - + /* Starting the program with initial values given by a former maximization will simply change */ /* the scales of the directions and the directions, because the are reset to canonical directions */ /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */ @@ -1964,7 +2062,10 @@ void powell(double p[], double **xi, int } #endif - +#ifdef LINMINORIGINAL +#else + free_ivector(flatdir,1,n); +#endif free_vector(xit,1,n); free_vector(xits,1,n); free_vector(ptt,1,n); @@ -1978,7 +2079,11 @@ void powell(double p[], double **xi, int pt[j]=p[j]; } fptt=(*func)(ptt); /* f_3 */ -#ifdef POWELLF1F3 +#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */ + if (*iter <=4) { +#else +#endif +#ifdef POWELLNOF3INFF1TEST /* skips test F3 0 */ + /* mu² and del² are equal when f3=f1 */ + /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */ + /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */ + /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */ + /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */ #ifdef NRCORIGINAL t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ #else @@ -2010,57 +2123,86 @@ void powell(double p[], double **xi, int if (t < 0.0) { /* Then we use it for new direction */ #else if (directest*t < 0.0) { /* Contradiction between both tests */ - printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); + printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); - fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); + fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); } if (directest < 0.0) { /* Then we use it for new direction */ #endif #ifdef DEBUGLINMIN - printf("Before linmin in direction P%d-P0\n",n); - for (j=1;j<=n;j++) { - printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); - fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); - if(j % ncovmodel == 0){ - printf("\n"); - fprintf(ficlog,"\n"); - } - } + printf("Before linmin in direction P%d-P0\n",n); + for (j=1;j<=n;j++) { + printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + if(j % ncovmodel == 0){ + printf("\n"); + fprintf(ficlog,"\n"); + } + } #endif - linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ -#ifdef DEBUGLINMIN - for (j=1;j<=n;j++) { - printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); - fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); - if(j % ncovmodel == 0){ - printf("\n"); - fprintf(ficlog,"\n"); - } - } +#ifdef LINMINORIGINAL + linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ +#else + linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ + flatdir[i]=flat; /* Function is vanishing in that direction i */ #endif - for (j=1;j<=n;j++) { - xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ - xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ - } - printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); - fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); +#ifdef DEBUGLINMIN + for (j=1;j<=n;j++) { + printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]); + if(j % ncovmodel == 0){ + printf("\n"); + fprintf(ficlog,"\n"); + } + } +#endif + for (j=1;j<=n;j++) { + xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ + xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ + } +#ifdef LINMINORIGINAL +#else + for (j=1, flatd=0;j<=n;j++) { + if(flatdir[j]>0) + flatd++; + } + if(flatd >0){ + printf("%d flat directions\n",flatd); + fprintf(ficlog,"%d flat directions\n",flatd); + for (j=1;j<=n;j++) { + if(flatdir[j]>0){ + printf("%d ",j); + fprintf(ficlog,"%d ",j); + } + } + printf("\n"); + fprintf(ficlog,"\n"); + } +#endif + printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); + fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); + #ifdef DEBUG - printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); - fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); - for(j=1;j<=n;j++){ - printf(" %.12e",xit[j]); - fprintf(ficlog," %.12e",xit[j]); - } - printf("\n"); - fprintf(ficlog,"\n"); + printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); + fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); + for(j=1;j<=n;j++){ + printf(" %lf",xit[j]); + fprintf(ficlog," %lf",xit[j]); + } + printf("\n"); + fprintf(ficlog,"\n"); #endif } /* end of t or directest negative */ -#ifdef POWELLF1F3 +#ifdef POWELLNOF3INFF1TEST #else } /* end if (fptt < fp) */ #endif +#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */ + } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */ +#else +#endif } /* loop iteration */ } @@ -2334,65 +2476,65 @@ double **pmij(double **ps, double *cov, /*double t34;*/ int i,j, nc, ii, jj; - for(i=1; i<= nlstate; i++){ - for(j=1; ji s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ - } - ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ - } - } + for(i=1; i<= nlstate; i++){ + for(j=1; ji s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ + } + ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ + } + } - for(i=1; i<= nlstate; i++){ - s1=0; - for(j=1; ji} pij/pii=(1-pii)/pii and thus pii is known from s1 */ - ps[i][i]=1./(s1+1.); - /* Computing other pijs */ - for(j=1; ji} pij/pii=(1-pii)/pii and thus pii is known from s1 */ + ps[i][i]=1./(s1+1.); + /* Computing other pijs */ + for(j=1; j(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */ @@ -2916,7 +3085,7 @@ double func( double *x) /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ /*if(lli ==000.0)*/ /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ - ipmx +=1; + ipmx +=1; sw += weight[i]; ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; /* if (lli < log(mytinydouble)){ */ @@ -3079,11 +3248,13 @@ double funcone( double *x) { /* Same as likeli but slower because of a lot of printf and if */ int i, ii, j, k, mi, d, kk; + int ioffset=0; double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1]; double **out; double lli; /* Individual log likelihood */ double llt; int s1, s2; + int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */ double bbh, survp; double agexact; double agebegin, ageend; @@ -3096,10 +3267,24 @@ double funcone( double *x) cov[1]=1.; for(k=1; k<=nlstate; k++) ll[k]=0.; - + ioffset=0; for (i=1,ipmx=0, sw=0.; i<=imx; i++){ - for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; - for(mi=1; mi<= wav[i]-1; mi++){ + ioffset=2+nagesqr+cptcovage; + /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */ + for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed covariates without age* products */ + cov[++ioffset]=covar[Tvar[k]][i]; + } + for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */ + cov[++ioffset]=coqvar[Tvar[iqv]][i]; + } + + for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */ + for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */ + cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i]; + } + for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */ + cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][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); @@ -3119,7 +3304,7 @@ double funcone( double *x) for (kk=1; kk<=cptcovage;kk++) { cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; } - + /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */ /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); @@ -3162,7 +3347,7 @@ double funcone( double *x) 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 %11.6f %8.4f %8.3f\ + fprintf(ficresilk,"%9ld %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]); @@ -3677,325 +3862,345 @@ void pstamp(FILE *fichier) } /************ Frequencies ********************/ - void freqsummary(char fileres[], 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 */ - - int i, m, jk, j1, bool, z1,j; - int iind=0, iage=0; - int mi; /* Effective wave */ - int first; - double ***freq; /* Frequencies */ - double *pp, **prop, *posprop, *pospropt; - double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0; - char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH]; - double agebegin, ageend; - - pp=vector(1,nlstate); - prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+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); */ - strcpy(fileresp,"P_"); - strcat(fileresp,fileresu); - /*strcat(fileresphtm,fileresu);*/ - if((ficresp=fopen(fileresp,"w"))==NULL) { - printf("Problem with prevalence resultfile: %s\n", fileresp); - fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); - exit(0); - } +void freqsummary(char fileres[], 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 */ + + int i, m, jk, j1, bool, z1,j; + int iind=0, iage=0; + int mi; /* Effective wave */ + int first; + double ***freq; /* Frequencies */ + double *meanq; + double **meanqt; + double *pp, **prop, *posprop, *pospropt; + double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0; + char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH]; + double agebegin, ageend; + + pp=vector(1,nlstate); + prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE); + posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ + pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ + /* prop=matrix(1,nlstate,iagemin,iagemax+3); */ + meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */ + meanqt=matrix(1,lastpass,1,nqtveff); + strcpy(fileresp,"P_"); + strcat(fileresp,fileresu); + /*strcat(fileresphtm,fileresu);*/ + if((ficresp=fopen(fileresp,"w"))==NULL) { + printf("Problem with prevalence resultfile: %s\n", fileresp); + 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)); - fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno)); - fflush(ficlog); - exit(70); - } - else{ - fprintf(ficresphtm,"\nIMaCh PHTM_ %s\n %s
%s \ + 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)); + fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno)); + fflush(ficlog); + exit(70); + } + else{ + fprintf(ficresphtm,"\nIMaCh PHTM_ %s\n %s
%s \
\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

\n",fileresphtm, fileresphtm); + 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

\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{ - fprintf(ficresphtmfr,"\nIMaCh PHTM_Frequency table %s\n %s
%s \ + 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{ + fprintf(ficresphtmfr,"\nIMaCh PHTM_Frequency table %s\n %s
%s \
\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); + 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); - j1=0; + freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE); + j1=0; - j=cptcoveff; - if (cptcovn<1) {j=1;ncodemax[1]=1;} + j=ncoveff; + if (cptcovn<1) {j=1;ncodemax[1]=1;} - first=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 - */ + /* 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 + */ - for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */ - 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 (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */ + 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; + dateintsum=0; + k2cpt=0; + /* For that comination of covariate j1, we count and print the frequencies */ + for (iind=1; iind<=imx; iind++) { /* For each individual iind */ + bool=1; + if (nqfveff >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]; + } + for (z1=1; z1<=ncoveff; 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 i 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*/ + } + } /* end z1 */ + } /* cptcovn > 0 */ + + if (bool==1){ /* We selected an individual iin satisfying combination j1 */ + /* 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)) { + dateintsum=dateintsum+k2; + k2cpt++; + /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ + } + /*}*/ + } /* 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) { + fprintf(ficresp, "\n#********** Variable "); + fprintf(ficresphtm, "\n

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

********** Variable "); + for (z1=1; z1<=ncoveff; 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<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); + 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 (iind=1; iind<=imx; iind++) { /* For each individual iind */ - bool=1; - if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */ - for (z1=1; z1<=cptcoveff; z1++) { - if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ - /* Tests if the value of each of the covariates of i is equal to filter j1 */ - 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*/ - } - } /* end z1 */ - } /* cptcovn > 0 */ - - if (bool==1){ - /* 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)) { - dateintsum=dateintsum+k2; - k2cpt++; - /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */ - } - /*}*/ - } /* 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 (cptcovn>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
"); - 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); - } - } - pospropt[jk] +=posprop[jk]; - } /* end loop jk */ - /* pospropt=0.; */ - for(jk=-1; jk <=nlstate+ndeath; jk++){ - for(m=-1; m <=nlstate+ndeath; m++){ - if(freq[jk][m][iage] !=0 ) { /* minimizing output */ - if(first==1){ - printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); - } - fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]); - } - if(jk!=0 && m!=0) - fprintf(ficresphtmfr," ",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++){ - if(posproptt < 1.e-5){ - fprintf(ficresphtm,"",pospropt[jk],posproptt); - }else{ - fprintf(ficresphtm,"",pospropt[jk]/posproptt,pospropt[jk],posproptt); - } - } - fprintf(ficresphtm,"\n"); - fprintf(ficresphtm,"
Age%d%d
0
Unknown
Total
%d%d%.5f%.0f%.0f%dNaNq%.0f%.0f%.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(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 */ - dateintmean=dateintsum/k2cpt; + for(jk=1; jk <=nlstate ; jk++){ + /* posprop[jk]=0; */ + for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */ + pp[jk] += freq[jk][m][iage]; + } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */ + + for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){ + pos += pp[jk]; /* pos is the total number of transitions until this age */ + posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state + from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state + from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */ + } + for(jk=1; jk <=nlstate ; jk++){ + if(pos>=1.e-5){ + if(first==1) + printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos); + }else{ + if(first==1) + printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); + } + if( iage <= iagemax){ + if(pos>=1.e-5){ + fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta); + fprintf(ficresphtm,"%d%.5f%.0f%.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta); + /*probs[iage][jk][j1]= pp[jk]/pos;*/ + /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/ + } + else{ + fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta); + fprintf(ficresphtm,"%dNaNq%.0f%.0f",iage, prop[jk][iage],pospropta); + } + } + pospropt[jk] +=posprop[jk]; + } /* end loop jk */ + /* pospropt=0.; */ + for(jk=-1; jk <=nlstate+ndeath; jk++){ + for(m=-1; m <=nlstate+ndeath; m++){ + if(freq[jk][m][iage] !=0 ) { /* minimizing output */ + if(first==1){ + printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); + } + fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]); + } + if(jk!=0 && m!=0) + fprintf(ficresphtmfr,"%.0f ",freq[jk][m][iage]); + } + } /* end loop jk */ + posproptt=0.; + for(jk=1; jk <=nlstate; jk++){ + posproptt += pospropt[jk]; + } + fprintf(ficresphtmfr,"\n "); + if(iage <= iagemax){ + fprintf(ficresp,"\n"); + fprintf(ficresphtm,"\n"); + } + if(first==1) + printf("Others in log...\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); + } + } + 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 */ + dateintmean=dateintsum/k2cpt; - fclose(ficresp); - fclose(ficresphtm); - fclose(ficresphtmfr); - free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE); - free_vector(pospropt,1,nlstate); - free_vector(posprop,1,nlstate); - free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE); - free_vector(pp,1,nlstate); - /* End of Freq */ - } + 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(pospropt,1,nlstate); + free_vector(posprop,1,nlstate); + free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE); + free_vector(pp,1,nlstate); + /* End of freqsummary */ +} /************ Prevalence ********************/ void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) @@ -4101,10 +4306,10 @@ void concatwav(int wav[], int **dh, int and mw[mi+1][i]. dh depends on stepm. */ - int i, mi, m; + int i=0, mi=0, m=0, mli=0; /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1; double sum=0., jmean=0.;*/ - int first, firstwo, firsthree, firstfour; + int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0; int j, k=0,jk, ju, jl; double sum=0.; first=0; @@ -4114,160 +4319,190 @@ void concatwav(int wav[], int **dh, int jmin=100000; jmax=-1; jmean=0.; + +/* Treating live states */ for(i=1; i<=imx; i++){ /* For simple cases and if state is death */ - mi=0; + mi=0; /* First valid wave */ + mli=0; /* Last valid wave */ m=firstpass; while(s[m][i] <= nlstate){ /* a live state */ - if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */ - mw[++mi][i]=m; - } - if(m >=lastpass){ - if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ - if(firsthree == 0){ - printf("Information! Unknown health status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m); - firsthree=1; - } - fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m); - mw[++mi][i]=m; - } - if(s[m][i]==-2){ /* Vital status is really unknown */ - nbwarn++; - if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */ - printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); - fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); - } - break; - } - break; + if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */ + mli=m-1;/* mw[++mi][i]=m-1; */ + }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */ + mw[++mi][i]=m; + mli=m; + } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */ + if(m < lastpass){ /* m < lastpass, standard case */ + m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */ } - else - m++; + else{ /* m >= lastpass, eventual special issue with warning */ +#ifdef UNKNOWNSTATUSNOTCONTRIBUTING + break; +#else + if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ + if(firsthree == 0){ + printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m); + firsthree=1; + } + fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m); + mw[++mi][i]=m; + mli=m; + } + if(s[m][i]==-2){ /* Vital status is really unknown */ + nbwarn++; + if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */ + printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); + fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m); + } + break; + } + break; +#endif + }/* End m >= lastpass */ }/* end while */ - + + /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */ /* After last pass */ +/* Treating death states */ if (s[m][i] > nlstate){ /* In a death state */ + /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */ + /* } */ mi++; /* Death is another wave */ /* if(mi==0) never been interviewed correctly before death */ - /* Only death is a correct wave */ + /* Only death is a correct wave */ mw[mi][i]=m; - }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */ + } +#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; */ - nberr++; if ((int)anint[m][i]!= 9999) { /* date of last interview is known */ - if(firstwo==0){ - printf("Error! Death for individual %ld line=%d occurred %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 ); - firstwo=1; - } - fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %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 ); + 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++; + if(firstfiv==0){ + printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing 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], s[m][i], i,m ); + firstfiv=1; + }else{ + fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m ); + } + }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 ); + 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 ); + } }else{ /* end date of interview is known */ - /* 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 ); - firstfour=1; - } - fprintf(ficlog,"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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); + /* 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 ); + firstfour=1; + } + fprintf(ficlog,"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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m ); } - } - wav[i]=mi; + } /* end if date of death is known */ +#endif + wav[i]=mi; /* mi should be the last effective wave (or mli) */ + /* wav[i]=mw[mi][i]; */ if(mi==0){ nbwarn++; if(first==0){ - printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); - first=1; + printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); + first=1; } if(first==1){ - fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); + fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); } } /* end mi==0 */ } /* End individuals */ /* wav and mw are no more changed */ - + for(i=1; i<=imx; i++){ for(mi=1; mi nlstate) { /* A death */ - 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 */ - else if(j<0){ - nberr++; - printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); - j=1; /* Temporary Dangerous patch */ - printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); - fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); - fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); - } - k=k+1; - if (j >= jmax){ - jmax=j; - ijmax=i; - } - if (j <= jmin){ - jmin=j; - ijmin=i; - } - sum=sum+j; - /*if (j<0) printf("j=%d num=%d \n",j,i);*/ - /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ - } - } - else{ - j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); + if (s[mw[mi+1][i]][i] > nlstate) { /* A death */ + 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 */ + else if(j<0){ + nberr++; + printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + j=1; /* Temporary Dangerous patch */ + printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); + fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); + } + k=k+1; + if (j >= jmax){ + jmax=j; + ijmax=i; + } + if (j <= jmin){ + jmin=j; + ijmin=i; + } + sum=sum+j; + /*if (j<0) printf("j=%d num=%d \n",j,i);*/ + /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ + } + } + else{ + j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */ - - k=k+1; - if (j >= jmax) { - jmax=j; - ijmax=i; - } - else if (j <= jmin){ - jmin=j; - ijmin=i; - } - /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ - /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ - if(j<0){ - nberr++; - printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); - fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); - } - sum=sum+j; - } - jk= j/stepm; - jl= j -jk*stepm; - ju= j -(jk+1)*stepm; - if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ - if(jl==0){ - dh[mi][i]=jk; - bh[mi][i]=0; - }else{ /* We want a negative bias in order to only have interpolation ie - * to avoid the price of an extra matrix product in likelihood */ - dh[mi][i]=jk+1; - bh[mi][i]=ju; - } - }else{ - if(jl <= -ju){ - dh[mi][i]=jk; - bh[mi][i]=jl; /* bias is positive if real duration - * is higher than the multiple of stepm and negative otherwise. - */ - } - else{ - dh[mi][i]=jk+1; - bh[mi][i]=ju; - } - if(dh[mi][i]==0){ - dh[mi][i]=1; /* At least one step */ - bh[mi][i]=ju; /* At least one step */ - /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/ - } - } /* end if mle */ + + k=k+1; + if (j >= jmax) { + jmax=j; + ijmax=i; + } + else if (j <= jmin){ + jmin=j; + ijmin=i; + } + /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ + /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ + if(j<0){ + nberr++; + printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); + } + sum=sum+j; + } + jk= j/stepm; + jl= j -jk*stepm; + ju= j -(jk+1)*stepm; + if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */ + if(jl==0){ + dh[mi][i]=jk; + bh[mi][i]=0; + }else{ /* We want a negative bias in order to only have interpolation ie + * to avoid the price of an extra matrix product in likelihood */ + dh[mi][i]=jk+1; + bh[mi][i]=ju; + } + }else{ + if(jl <= -ju){ + dh[mi][i]=jk; + bh[mi][i]=jl; /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + } + else{ + dh[mi][i]=jk+1; + bh[mi][i]=ju; + } + if(dh[mi][i]==0){ + dh[mi][i]=1; /* At least one step */ + bh[mi][i]=ju; /* At least one step */ + /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/ + } + } /* end if mle */ } } /* end wave */ } @@ -4282,8 +4517,8 @@ void concatwav(int wav[], int **dh, int /**< 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 2 (V2) - * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually); + * 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; @@ -4293,58 +4528,66 @@ void concatwav(int wav[], int **dh, int /* cptcoveff=0; */ - *cptcov=0; + /* *cptcov=0; */ for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */ - /* Loop on covariates without age and products */ - for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */ + /* 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 (j=1; j<=cptcovsnq; j++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */ for (k=-1; k < maxncov; k++) Ndum[k]=0; 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[j]][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 is 1, then modmaxcovj=1.*/ + modality of this covariate Vj*/ + switch(Typevar[j]) { + case 1: /* A real fixed dummy covariate */ + ij=(int)(covar[Tvar[j]][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.*/ + break; + case 2: + break; + + } } /* end for loop on individuals i */ printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj); fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], 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 (i=0; i<=cptcode; i++) {*/ for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */ printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]); if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */ - if( k != -1){ - ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th - covariate for which somebody answered excluding - undefined. Usually 2: 0 and 1. */ - } - ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th - covariate for which somebody answered including - undefined. Usually 3: -1, 0 and 1. */ + if( k != -1){ + ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th + covariate for which somebody answered excluding + undefined. Usually 2: 0 and 1. */ + } + ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th + covariate for which somebody answered including + undefined. Usually 3: -1, 0 and 1. */ } /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for - historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */ + * 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; @@ -4360,14 +4603,14 @@ void concatwav(int wav[], int **dh, int */ 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[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/ - cptcode = ij; /* New max modality for covar j */ + if (Ndum[i] == 0) { /* If nobody responded to this modality k */ + break; + } + ij++; + nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/ + cptcode = ij; /* New max modality for covar j */ } /* end of loop on modality i=-1 to 1 or more */ - + /* 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 */ @@ -4383,29 +4626,33 @@ void concatwav(int wav[], int **dh, int /* } /\* 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; + for (k=-1; k< maxncov; k++) Ndum[k]=0; 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 might be -1 if status was unknown */ - Ndum[ij]++; /* Might be supersed V1 + V1*age */ - } - - 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) */ - /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ - if((Ndum[i]!=0) && (i<=ncovcol)){ - ij++; - /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ - Tvaraff[ij]=i; /*For printing (unclear) */ - }else{ - /* Tvaraff[ij]=0; */ - } - } - /* ij--; */ - /* cptcoveff=ij; /\*Number of total covariates*\/ */ - *cptcov=ij; /*Number of total covariates*/ - + /* 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 might be -1 if status was unknown */ + Ndum[ij]++; /* Might be supersed V1 + V1*age */ + } /* 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) */ + /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/ + if((Ndum[i]!=0) && (i<=ncovcol)){ + /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ + Tvaraff[++ij]=i; /*For printing (unclear) */ + }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*/ } @@ -5256,7 +5503,7 @@ To be simple, these graphs help to under tj = (int) pow(2,cptcoveff); if (cptcovn<1) {tj=1;ncodemax[1]=1;} j1=0; - for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates */ + for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/ if (cptcovn>0) { fprintf(ficresprob, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); @@ -5670,7 +5917,7 @@ See page 'Matrix of variance-covariance jj1++; if (cptcovn > 0) { fprintf(fichtm,"
************ Results for covariates"); - for (cpt=1; cpt<=cptcoveff;cpt++) + for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */ fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); fprintf(fichtm," ************\n
"); @@ -5697,15 +5944,15 @@ true period expectancies (those weighted } /******************* Gnuplot file **************/ - void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){ +void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){ char dirfileres[132],optfileres[132]; - char gplotcondition[132]; + char gplotcondition[132]; int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; int lv=0, vlv=0, kl=0; int ng=0; int vpopbased; - int ioffset; /* variable offset for columns */ + int ioffset; /* variable offset for columns */ /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ /* printf("Problem with file %s",optionfilegnuplot); */ @@ -5714,158 +5961,162 @@ true period expectancies (those weighted /*#ifdef windows */ fprintf(ficgp,"cd \"%s\" \n",pathc); - /*#endif */ + /*#endif */ m=pow(2,cptcoveff); /* Contribution to likelihood */ /* Plot the probability implied in the likelihood */ - fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); - fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";"); - /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */ - fprintf(ficgp,"\nset ter pngcairo size 640, 480"); + fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n"); + fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";"); + /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */ + fprintf(ficgp,"\nset ter pngcairo size 640, 480"); /* nice for mle=4 plot by number of matrix products. replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */ /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */ - /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */ - fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); - fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); - fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); - fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); - for (i=1; i<= nlstate ; i ++) { - fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i); - fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk)); - fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1); - for (j=2; j<= nlstate+ndeath ; j ++) { - fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j); - } - fprintf(ficgp,";\nset out; unset ylabel;\n"); - } - /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */ - /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */ - /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */ - fprintf(ficgp,"\nset out;unset log\n"); - /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */ + /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */ + fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_")); + fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk)); + fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_")); + fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk)); + for (i=1; i<= nlstate ; i ++) { + fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i); + fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk)); + fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1); + for (j=2; j<= nlstate+ndeath ; j ++) { + fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j); + } + fprintf(ficgp,";\nset out; unset ylabel;\n"); + } + /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */ + /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */ + /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */ + fprintf(ficgp,"\nset out;unset log\n"); + /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */ strcpy(dirfileres,optionfilefiname); strcpy(optfileres,"vpl"); - /* 1eme*/ + /* 1eme*/ for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */ for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */ /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files "); for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */ - lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ - /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ - /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ - /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ - vlv= nbcode[Tvaraff[k]][lv]; /* 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 */ - fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; /* 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 */ + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); } fprintf(ficgp,"\n#\n"); - if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); - continue; - } + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1); - fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1); - fprintf(ficgp,"set xlabel \"Age\" \n\ + 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); - 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); - 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*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); - for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); - else fprintf(ficgp," %%*lf (%%*lf)"); - } - fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); - 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 */ - kl=0; - for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ - lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ - /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ - /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ - /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ - vlv= nbcode[Tvaraff[k]][lv]; - kl++; - /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ - /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ - /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ - /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ - if(k==cptcoveff){ - fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ - 6+(cpt-1), cpt ); - }else{ - fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); - kl++; - } - } /* end covariate */ - } - fprintf(ficgp,"\nset out \n"); + 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); + 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*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1); + for (i=1; i<= nlstate ; i ++) { + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); + 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:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */ + fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */ + if(cptcoveff ==0){ + fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt ); + }else{ + kl=0; + for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */ + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + kl++; + /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */ + /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ + /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ + /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/ + if(k==cptcoveff){ + fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \ + 6+(cpt-1), cpt ); + }else{ + fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]); + kl++; + } + } /* end covariate */ + } /* end if no covariate */ + } /* end if backcast */ + fprintf(ficgp,"\nset out \n"); } /* k1 */ } /* cpt */ /*2 eme*/ for (k1=1; k1<= m ; k1 ++) { - fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files "); - 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 */ - /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ - /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ - vlv= nbcode[Tvaraff[k]][lv]; - fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); - } - fprintf(ficgp,"\n#\n"); - if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",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 */ + 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 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + } + fprintf(ficgp,"\n#\n"); + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } - fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1); - 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); - else - fprintf(ficgp,"\nreplot "); - for (i=1; i<= nlstate+1 ; i ++) { - k=2*i; - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased); - 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); - 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); - for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," %%lf (%%lf)"); - else fprintf(ficgp," %%*lf (%%*lf)"); - } - if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); - 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 \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1); + 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); + else + fprintf(ficgp,"\nreplot "); + for (i=1; i<= nlstate+1 ; i ++) { + k=2*i; + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased); + 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); + 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+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased); + for (j=1; j<= nlstate+1 ; j ++) { + if (j==i) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); + } + if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); + else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n"); + } /* state */ + } /* vpopbased */ + fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */ } /* k1 */ @@ -5875,18 +6126,18 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u for (cpt=1; cpt<= nlstate ; cpt ++) { fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ - lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ - /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ - /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ - /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ - vlv= nbcode[Tvaraff[k]][lv]; - fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ + /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); } fprintf(ficgp,"\n#\n"); - if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); - continue; - } + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } /* k=2+nlstate*(2*cpt-2); */ k=2+(nlstate+1)*(cpt-1); @@ -5894,41 +6145,41 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u fprintf(ficgp,"set ter svg size 640, 480\n\ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt); /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); - for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); - fprintf(ficgp,"\" t \"e%d1\" w l",cpt); - fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); - for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); - fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); + fprintf(ficgp,"\" t \"e%d1\" w l",cpt); + fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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); */ 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(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/ + 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(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); } } - /* 4eme */ + /* 4eme */ /* Survival functions (period) from state i in state j by initial state i */ for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ - lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ - /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */ - /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ - /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ - vlv= nbcode[Tvaraff[k]][lv]; - fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); + 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 */ + /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + vlv= nbcode[Tvaraff[k]][lv]; + fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); } fprintf(ficgp,"\n#\n"); - if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); - continue; - } + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ @@ -5937,16 +6188,16 @@ unset log y\n plot [%.f:%.f] ", ageminpar, agemaxpar); k=3; for (i=1; i<= nlstate ; i ++){ - if(i==1){ - fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); - }else{ - fprintf(ficgp,", '' "); - } - l=(nlstate+ndeath)*(i-1)+1; - fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); - for (j=2; j<= nlstate+ndeath ; j ++) - fprintf(ficgp,"+$%d",k+l+j-1); - fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt); + if(i==1){ + fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_")); + }else{ + fprintf(ficgp,", '' "); + } + l=(nlstate+ndeath)*(i-1)+1; + fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); + for (j=2; j<= nlstate+ndeath ; j ++) + fprintf(ficgp,"+$%d",k+l+j-1); + fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt); } /* nlstate */ fprintf(ficgp,"\nset out\n"); } /* end cpt state*/ @@ -5956,7 +6207,7 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) /* Survival functions (period) from state i in state j by final state j */ for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */ 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); 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 */ @@ -5967,10 +6218,10 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); } fprintf(ficgp,"\n#\n"); - if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); - continue; - } + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\ @@ -6006,7 +6257,7 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) /* CV preval stable (period) for each covariate */ for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ - + fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt); for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */ @@ -6017,15 +6268,15 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); } fprintf(ficgp,"\n#\n"); - if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); - continue; - } - + if(invalidvarcomb[k1]){ + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; + } + fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ -set ter svg size 640, 480\n\ -unset log y\n\ +set ter svg size 640, 480\n \ +unset log y\n \ plot [%.f:%.f] ", ageminpar, agemaxpar); k=3; /* Offset */ for (i=1; i<= nlstate ; i ++){ @@ -6042,8 +6293,8 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) fprintf(ficgp,"\nset out\n"); } /* end cpt state*/ } /* end covariate */ - - + + /* 7eme */ if(backcast == 1){ /* CV back preval stable (period) for each covariate */ @@ -6054,14 +6305,14 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) 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 */ /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */ - /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ + /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */ vlv= nbcode[Tvaraff[k]][lv]; fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); } fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); - continue; + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; } fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1); @@ -6090,7 +6341,7 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) } /* end covariate */ } /* End if backcast */ - /* 8eme */ + /* 8eme */ if(prevfcast==1){ /* Projection from cross-sectional to stable (period) for each covariate */ @@ -6107,15 +6358,15 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) } fprintf(ficgp,"\n#\n"); if(invalidvarcomb[k1]){ - fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); - continue; + fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); + continue; } 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,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\ -set ter svg size 640, 480\n \ -unset log y\n \ +set ter svg size 640, 480\n \ +unset log y\n \ plot [%.f:%.f] ", ageminpar, agemaxpar); for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */ /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ @@ -6145,8 +6396,8 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) ioffset=4; /* Age is in 4 */ }else{ ioffset=6; /* Age is in 6 */ - /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ - /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ + /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/ + /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */ } fprintf(ficgp," u %d:(",ioffset); kl=0; @@ -6172,34 +6423,34 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt ); }else{ - fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ - ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt ); + fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ + ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt ); } } /* end if covariate */ } /* nlstate */ fprintf(ficgp,"\nset out\n"); - } /* end cpt state*/ - } /* end covariate */ - } /* End if prevfcast */ + } /* end cpt state*/ + } /* end covariate */ + } /* End if prevfcast */ - /* proba elementaires */ - fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); + /* proba elementaires */ + fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); for(i=1,jk=1; i <=nlstate; i++){ fprintf(ficgp,"# initial state %d\n",i); for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { - fprintf(ficgp,"# current state %d\n",k); - for(j=1; j <=ncovmodel; j++){ - fprintf(ficgp,"p%d=%f; ",jk,p[jk]); - jk++; - } - fprintf(ficgp,"\n"); + fprintf(ficgp,"# current state %d\n",k); + for(j=1; j <=ncovmodel; j++){ + fprintf(ficgp,"p%d=%f; ",jk,p[jk]); + jk++; + } + fprintf(ficgp,"\n"); } } - } + } fprintf(ficgp,"##############\n#\n"); - + /*goto avoid;*/ fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n"); fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); @@ -6215,113 +6466,113 @@ plot [%.f:%.f] ", ageminpar, agemaxpar) fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); fprintf(ficgp,"#\n"); - for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/ - fprintf(ficgp,"# ng=%d\n",ng); - fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); - for(jk=1; jk <=m; jk++) { - fprintf(ficgp,"# jk=%d\n",jk); - fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng); - 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 */ - fprintf(ficgp,"\nunset log y"); - }else if (ng==2){ - fprintf(ficgp,"\nset ylabel \"Probability\"\n"); - fprintf(ficgp,"\nset log y"); - }else if (ng==3){ - fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); - fprintf(ficgp,"\nset log y"); - }else - fprintf(ficgp,"\nunset title "); - fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar); - i=1; - for(k2=1; k2<=nlstate; k2++) { - k3=i; - for(k=1; k<=(nlstate+ndeath); k++) { - if (k != k2){ - switch( ng) { - case 1: - if(nagesqr==0) - fprintf(ficgp," p%d+p%d*x",i,i+1); - else /* nagesqr =1 */ - fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); - break; - case 2: /* ng=2 */ - if(nagesqr==0) - fprintf(ficgp," exp(p%d+p%d*x",i,i+1); - else /* nagesqr =1 */ - fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); - break; - case 3: - if(nagesqr==0) - fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); - else /* nagesqr =1 */ - fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); - break; - } - ij=1;/* To be checked else nbcode[0][0] wrong */ - for(j=3; j <=ncovmodel-nagesqr; j++) { - /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ - if(ij <=cptcovage) { /* Bug valgrind */ - if((j-2)==Tage[ij]) { /* Bug valgrind */ - fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); - /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ - ij++; - } - } - else - fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); - } - }else{ - i=i-ncovmodel; - if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */ - fprintf(ficgp," (1."); - } + for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/ + fprintf(ficgp,"# ng=%d\n",ng); + fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); + for(jk=1; jk <=m; jk++) { + fprintf(ficgp,"# jk=%d\n",jk); + fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng); + 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 */ + fprintf(ficgp,"\nunset log y"); + }else if (ng==2){ + fprintf(ficgp,"\nset ylabel \"Probability\"\n"); + fprintf(ficgp,"\nset log y"); + }else if (ng==3){ + fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); + fprintf(ficgp,"\nset log y"); + }else + fprintf(ficgp,"\nunset title "); + fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar); + i=1; + for(k2=1; k2<=nlstate; k2++) { + k3=i; + for(k=1; k<=(nlstate+ndeath); k++) { + if (k != k2){ + switch( ng) { + case 1: + if(nagesqr==0) + fprintf(ficgp," p%d+p%d*x",i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); + break; + case 2: /* ng=2 */ + if(nagesqr==0) + fprintf(ficgp," exp(p%d+p%d*x",i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); + break; + case 3: + if(nagesqr==0) + fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); + break; + } + ij=1;/* To be checked else nbcode[0][0] wrong */ + for(j=3; j <=ncovmodel-nagesqr; j++) { + /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ + if(ij <=cptcovage) { /* Bug valgrind */ + if((j-2)==Tage[ij]) { /* Bug valgrind */ + fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ + ij++; + } + } + else + fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */ + } + }else{ + i=i-ncovmodel; + if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */ + fprintf(ficgp," (1."); + } - if(ng != 1){ - fprintf(ficgp,")/(1"); + if(ng != 1){ + fprintf(ficgp,")/(1"); - for(k1=1; k1 <=nlstate; k1++){ - if(nagesqr==0) - fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); - else /* nagesqr =1 */ - fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); + for(k1=1; k1 <=nlstate; k1++){ + if(nagesqr==0) + fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); + else /* nagesqr =1 */ + fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); - ij=1; - for(j=3; j <=ncovmodel-nagesqr; j++){ - if(ij <=cptcovage) { /* Bug valgrind */ - if((j-2)==Tage[ij]) { /* Bug valgrind */ - fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); - /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ - ij++; - } - } - else - fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); - } - fprintf(ficgp,")"); - } - fprintf(ficgp,")"); - if(ng ==2) - fprintf(ficgp," t \"p%d%d\" ", k2,k); - else /* ng= 3 */ - fprintf(ficgp," t \"i%d%d\" ", k2,k); - }else{ /* end ng <> 1 */ - if( k !=k2) /* logit p11 is hard to draw */ - fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k); - } - if ((k+k2)!= (nlstate*2+ndeath) && ng != 1) - fprintf(ficgp,","); - if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath)) - fprintf(ficgp,","); - i=i+ncovmodel; - } /* end k */ - } /* end k2 */ - fprintf(ficgp,"\n set out\n"); - } /* end jk */ - } /* end ng */ - /* avoid: */ - fflush(ficgp); + ij=1; + for(j=3; j <=ncovmodel-nagesqr; j++){ + if(ij <=cptcovage) { /* Bug valgrind */ + if((j-2)==Tage[ij]) { /* Bug valgrind */ + fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); + /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ + ij++; + } + } + else + fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */ + } + fprintf(ficgp,")"); + } + fprintf(ficgp,")"); + if(ng ==2) + fprintf(ficgp," t \"p%d%d\" ", k2,k); + else /* ng= 3 */ + fprintf(ficgp," t \"i%d%d\" ", k2,k); + }else{ /* end ng <> 1 */ + if( k !=k2) /* logit p11 is hard to draw */ + fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k); + } + if ((k+k2)!= (nlstate*2+ndeath) && ng != 1) + fprintf(ficgp,","); + if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath)) + fprintf(ficgp,","); + i=i+ncovmodel; + } /* end k */ + } /* end k2 */ + fprintf(ficgp,"\n set out\n"); + } /* end jk */ + } /* end ng */ + /* avoid: */ + fflush(ficgp); } /* end gnuplot */ @@ -7156,12 +7407,13 @@ int readdata(char datafile[], int firsto /*-------- data file ----------*/ FILE *fic; char dummy[]=" "; - int i=0, j=0, n=0; + int i=0, j=0, n=0, iv=0; + int lstra; int linei, month, year,iout; char line[MAXLINE], linetmp[MAXLINE]; char stra[MAXLINE], strb[MAXLINE]; char *stratrunc; - int lstra; + if((fic=fopen(datafile,"r"))==NULL) { @@ -7188,24 +7440,94 @@ int readdata(char datafile[], int firsto } trimbb(linetmp,line); /* Trims multiple blanks in line */ strcpy(line, linetmp); - - + + /* Loops on waves */ for (j=maxwav;j>=1;j--){ + for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + cotqvar[j][iv][i]=-1; /* 0.0/0.0 */ + if(isalpha(strb[1])) { /* .m or .d Really Missing value */ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog); + return 1; + } + }else{ + errno=0; + /* what_kind_of_number(strb); */ + dval=strtod(strb,&endptr); + /* if( strb[0]=='\0' || (*endptr != '\0')){ */ + /* if(strb != endptr && *endptr == '\0') */ + /* dval=dlval; */ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog); + return 1; + } + cotqvar[j][iv][i]=dval; + } + strcpy(line,stra); + }/* end loop ntqv */ + + for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + }else{ + errno=0; + lval=strtol(strb,&endptr,10); + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog); + return 1; + } + } + if(lval <-1 || lval >1){ + printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j); + fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j);fflush(ficlog); + return 1; + } + cotvar[j][iv][i]=(double)(lval); + strcpy(line,stra); + }/* end loop ntv */ + + /* Statuses at wave */ cutv(stra, strb, line, ' '); - if(strb[0]=='.') { /* Missing status */ + if(strb[0]=='.') { /* Missing value */ lval=-1; }else{ errno=0; lval=strtol(strb,&endptr,10); - /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ if( strb[0]=='\0' || (*endptr != '\0')){ printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav); fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog); return 1; } } + s[j][i]=lval; + /* Date of Interview */ strcpy(line,stra); cutv(stra, strb,line,' '); if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ @@ -7221,8 +7543,9 @@ int readdata(char datafile[], int firsto anint[j][i]= (double) year; mint[j][i]= (double)month; strcpy(line,stra); - } /* ENd Waves */ + } /* End loop on waves */ + /* Date of death */ cutv(stra, strb,line,' '); if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } @@ -7231,13 +7554,14 @@ int readdata(char datafile[], int firsto year=9999; }else{ printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line); - fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); - return 1; + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); + return 1; } andc[i]=(double) year; moisdc[i]=(double) month; strcpy(line,stra); + /* Date of birth */ cutv(stra, strb,line,' '); if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } @@ -7247,18 +7571,19 @@ int readdata(char datafile[], int firsto }else{ printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line); fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); - return 1; + return 1; } if (year==9999) { printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line); fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog); - return 1; - + return 1; + } annais[i]=(double)(year); moisnais[i]=(double)(month); strcpy(line,stra); + /* Sample weight */ cutv(stra, strb,line,' '); errno=0; dval=strtod(strb,&endptr); @@ -7271,9 +7596,32 @@ int readdata(char datafile[], int firsto weight[i]=dval; strcpy(line,stra); + for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing value */ + lval=-1; + }else{ + errno=0; + /* what_kind_of_number(strb); */ + dval=strtod(strb,&endptr); + /* if(strb != endptr && *endptr == '\0') */ + /* dval=dlval; */ + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog); + return 1; + } + coqvar[iv][i]=dval; + covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ + } + strcpy(line,stra); + }/* end loop nqv */ + + /* Covariate values */ for (j=ncovcol;j>=1;j--){ cutv(stra, strb,line,' '); - if(strb[0]=='.') { /* Missing status */ + if(strb[0]=='.') { /* Missing covariate value */ lval=-1; }else{ errno=0; @@ -7288,20 +7636,20 @@ int readdata(char datafile[], int firsto printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ - For example, for multinomial values like 1, 2 and 3,\n \ - build V1=0 V2=0 for the reference value (1),\n \ - V1=1 V2=0 for (2) \n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ - output of IMaCh is often meaningless.\n \ + output of IMaCh is often meaningless.\n \ Exiting.\n",lval,linei, i,line,j); fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ - For example, for multinomial values like 1, 2 and 3,\n \ - build V1=0 V2=0 for the reference value (1),\n \ - V1=1 V2=0 for (2) \n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ - output of IMaCh is often meaningless.\n \ + output of IMaCh is often meaningless.\n \ Exiting.\n",lval,linei, i,line,j);fflush(ficlog); return 1; } @@ -7309,7 +7657,7 @@ int readdata(char datafile[], int firsto strcpy(line,stra); } lstra=strlen(stra); - + if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ stratrunc = &(stra[lstra-9]); num[i]=atol(stratrunc); @@ -7321,19 +7669,17 @@ int readdata(char datafile[], int firsto i=i+1; } /* End loop reading data */ - + *imax=i-1; /* Number of individuals */ fclose(fic); - + return (0); /* endread: */ - printf("Exiting readdata: "); - fclose(fic); - return (1); - - - + printf("Exiting readdata: "); + fclose(fic); + return (1); } + void removespace(char *str) { char *p1 = str, *p2 = str; do @@ -7342,20 +7688,21 @@ void removespace(char *str) { while (*p1++ == *p2++); } -int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns: - * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age - * - nagesqr = 1 if age*age in the model, otherwise 0. - * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age - * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age - * - cptcovage number of covariates with age*products =2 - * - cptcovs number of simple covariates - * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10 - * which is a new column after the 9 (ncovcol) variables. - * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual - * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage - * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. - * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . - */ +int decodemodel ( char model[], int lastobs) + /**< This routine decode the model and returns: + * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age + * - nagesqr = 1 if age*age in the model, otherwise 0. + * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age + * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age + * - cptcovage number of covariates with age*products =2 + * - cptcovs number of simple covariates + * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10 + * which is a new column after the 9 (ncovcol) variables. + * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual + * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage + * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. + * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . + */ { int i, j, k, ks; int j1, k1, k2; @@ -7380,15 +7727,14 @@ int decodemodel ( char model[], int last if ((strpt=strstr(model,"age*age")) !=0){ printf(" strpt=%s, model=%s\n",strpt, model); if(strpt != model){ - printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ corresponding column of parameters.\n",model); - fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \ corresponding column of parameters.\n",model); fflush(ficlog); - return 1; - } - + return 1; + } nagesqr=1; if (strstr(model,"+age*age") !=0) substrchaine(modelsav, model, "+age*age"); @@ -7401,17 +7747,17 @@ int decodemodel ( char model[], int last if (strlen(modelsav) >1){ j=nbocc(modelsav,'+'); /**< j=Number of '+' */ j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ - cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */ + cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */ cptcovt= j+1; /* Number of total covariates in the model, not including - * cst, age and age*age - * V1+V1*age+ V3 + V3*V4+age*age=> 4*/ - /* including age products which are counted in cptcovage. - * but the covariates which are products must be treated - * separately: ncovn=4- 2=2 (V1+V3). */ + * cst, age and age*age + * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/ + /* including age products which are counted in cptcovage. + * but the covariates which are products must be treated + * separately: ncovn=4- 2=2 (V1+V3). */ cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ - - + + /* Design * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight * < ncovcol=8 > @@ -7419,8 +7765,8 @@ int decodemodel ( char model[], int last * k= 1 2 3 4 5 6 7 8 * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8 * covar[k,i], value of kth covariate if not including age for individual i: - * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8) - * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8 + * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8) + * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8 * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and * Tage[++cptcovage]=k * if products, new covar are created after ncovcol with k1 @@ -7445,7 +7791,7 @@ int decodemodel ( char model[], int last * {2, 1, 4, 8, 5, 6, 3, 7} * Struct [] */ - + /* This loop fills the array Tvar from the string 'model'.*/ /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */ /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */ @@ -7460,7 +7806,7 @@ int decodemodel ( char model[], int last /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */ /* * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ - for(k=cptcovt; k>=1;k--) /**< Number of covariates */ + for(k=cptcovt; k>=1;k--) /**< Number of covariates not including constant and age, neither age*age*/ Tvar[k]=0; cptcovage=0; for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ @@ -7476,6 +7822,7 @@ int decodemodel ( char model[], int last cptcovprod--; cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */ Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */ + Typevar[k]=1; /* 1 for age product */ cptcovage++; /* Sums the number of covariates which include age as a product */ Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ /*printf("stre=%s ", stre);*/ @@ -7483,6 +7830,7 @@ int decodemodel ( char model[], int last cptcovprod--; cutl(stre,strb,strc,'V'); Tvar[k]=atoi(stre); + Typevar[k]=1; /* 1 for age product */ cptcovage++; Tage[cptcovage]=k; } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ @@ -7490,18 +7838,21 @@ int decodemodel ( char model[], int last cptcovn++; cptcovprodnoage++;k1++; cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ - Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but + Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but because this model-covariate is a construction we invent a new column - ncovcol + k1 + which is after existing variables ncovcol+nqv+ntv+nqtv + k1 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2 Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */ + Typevar[k]=2; /* 2 for double fixed dummy covariates */ cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */ Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */ Tvard[k1][1] =atoi(strc); /* m 1 for V1*/ Tvard[k1][2] =atoi(stre); /* n 4 for V4*/ - k2=k2+2; - Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */ - Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */ + k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */ + /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */ + /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */ + /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */ + /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */ for (i=1; i<=lastobs;i++){ /* Computes the new covariate which is a product of covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */ @@ -7513,31 +7864,141 @@ int decodemodel ( char model[], int last /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ /* scanf("%d",i);*/ cutl(strd,strc,strb,'V'); - ks++; /**< Number of simple covariates */ - cptcovn++; + ks++; /**< Number of simple covariates*/ + cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */ Tvar[k]=atoi(strd); + Typevar[k]=0; /* 0 for simple covariates */ } strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ - /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); - scanf("%d",i);*/ + /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); + scanf("%d",i);*/ } /* end of loop + on total covariates */ } /* end if strlen(modelsave == 0) age*age might exist */ } /* end if strlen(model == 0) */ /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ - + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); - printf("cptcovprod=%d ", cptcovprod); - fprintf(ficlog,"cptcovprod=%d ", cptcovprod); - - scanf("%d ",i);*/ - + printf("cptcovprod=%d ", cptcovprod); + fprintf(ficlog,"cptcovprod=%d ", cptcovprod); + scanf("%d ",i);*/ + + +/* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind + of variable (dummy vs quantitative, fixed vs time varying) is behind */ +/* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying + model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place + k = 1 2 3 4 5 6 7 8 9 + Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5 + Typevar[k]= 0 0 0 2 1 0 2 1 1 + Fixed[Tvar[k]]1 1 1 1 2 0 1 2 3 + Dummy[Tvar[k]]1 0 0 0 2 1 1 2 3 +*/ +/* Dispatching between quantitative and time varying covariates */ + /* If Tvar[k] >ncovcol it is a product */ + /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */ + /* Computing effective variables, ie used by the model, that is from the cptcovt variables */ + for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */ + if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */ + Fixed[Tvar[k]]= 0; + Dummy[Tvar[k]]= 0; + ncoveff++; + }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ + Fixed[Tvar[k]]= 0; + Dummy[Tvar[k]]= 1; + nqfveff++; /* Only simple fixed quantitative variable */ + }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 0; + ntveff++; /* Only simple time varying dummy variable */ + }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){ + if( Typevar[k]==0){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + nqtveff++;/* Only simple time varying quantitative variable */ + } + }else if (Typevar[k] == 2) { + for(k1=1; k1 <= cptcovprodnoage; k1++){ + if(Tvard[k1][1] <=ncovcol){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 0; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[Tvar[k]]= 0; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 0; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + } + }else if(Tvard[k1][1] <=ncovcol+nqv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[Tvar[k]]= 0; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[Tvar[k]]= 0; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + } + }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 0; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + } + }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ + if(Tvard[k1][2] <=ncovcol){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ + Fixed[Tvar[k]]= 1; + Dummy[Tvar[k]]= 1; + } + }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 */ + }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]); + } + printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[Tvar[k]],Dummy[Tvar[k]]); + fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[Tvar[k]],Dummy[Tvar[k]]); + } + printf("Model=%s\n\ +Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\ +Fixed[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product \n\ +Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model); + printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn); + fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn); return (0); /* with covar[new additional covariate if product] and Tage if age */ /*endread:*/ - printf("Exiting decodemodel: "); - return (1); + printf("Exiting decodemodel: "); + return (1); } int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) @@ -7872,7 +8333,7 @@ int prevalence_limit(double *p, double * agebase=ageminpar; agelim=agemaxpar; - i1=pow(2,cptcoveff); + i1=pow(2,ncoveff); if (cptcovn < 1){i1=1;} for(k=1; k<=i1;k++){ @@ -7885,7 +8346,7 @@ int prevalence_limit(double *p, double * fprintf(ficrespl,"#******"); printf("#******"); fprintf(ficlog,"#******"); - for(j=1;j<=cptcoveff;j++) { + for(j=1;j<=nqfveff;j++) { fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); @@ -7901,7 +8362,7 @@ int prevalence_limit(double *p, double * } fprintf(ficrespl,"#Age "); - for(j=1;j<=cptcoveff;j++) { + for(j=1;j<=nqfveff;j++) { fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); } for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i); @@ -7911,7 +8372,7 @@ int prevalence_limit(double *p, double * /* for (age=agebase; age<=agebase; age++){ */ prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k); fprintf(ficrespl,"%.0f ",age ); - for(j=1;j<=cptcoveff;j++) + for(j=1;j<=nqfveff;j++) fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); tot=0.; for(i=1; i<=nlstate;i++){ @@ -7959,7 +8420,7 @@ int back_prevalence_limit(double *p, dou agelim=agemaxpar; - i1=pow(2,cptcoveff); + i1=pow(2,nqfveff); if (cptcovn < 1){i1=1;} for(k=1; k<=i1;k++){ @@ -7972,7 +8433,7 @@ int back_prevalence_limit(double *p, dou fprintf(ficresplb,"#******"); printf("#******"); fprintf(ficlog,"#******"); - for(j=1;j<=cptcoveff;j++) { + for(j=1;j<=nqfveff;j++) { fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); @@ -7988,7 +8449,7 @@ int back_prevalence_limit(double *p, dou } fprintf(ficresplb,"#Age "); - for(j=1;j<=cptcoveff;j++) { + for(j=1;j<=nqfveff;j++) { fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); } for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i); @@ -8010,7 +8471,7 @@ int back_prevalence_limit(double *p, dou bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k); } fprintf(ficresplb,"%.0f ",age ); - for(j=1;j<=cptcoveff;j++) + for(j=1;j<=nqfveff;j++) fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); tot=0.; for(i=1; i<=nlstate;i++){ @@ -8058,13 +8519,13 @@ int hPijx(double *p, int bage, int fage) /* hstepm=1; aff par mois*/ pstamp(ficrespij); fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); - i1= pow(2,cptcoveff); + i1= pow(2,nqfveff); /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ /* k=k+1; */ - for (k=1; k <= (int) pow(2,cptcoveff); k++){ + for (k=1; k <= (int) pow(2,nqfveff); k++){ fprintf(ficrespij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) + for(j=1;j<=nqfveff;j++) fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficrespij,"******\n"); @@ -8130,13 +8591,13 @@ 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 "); - i1= pow(2,cptcoveff); + i1= pow(2,nqfveff); /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ /* k=k+1; */ - for (k=1; k <= (int) pow(2,cptcoveff); k++){ + for (k=1; k <= (int) pow(2,nqfveff); k++){ fprintf(ficrespijb,"\n#****** "); - for(j=1;j<=cptcoveff;j++) + for(j=1;j<=nqfveff;j++) fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficrespijb,"******\n"); if(invalidvarcomb[k]){ @@ -8457,13 +8918,13 @@ int main(int argc, char *argv[]) }else break; } - if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \ - &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){ - if (num_filled != 8) { - printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); + if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \ + &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){ + if (num_filled != 11) { + printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n"); printf("but line=%s\n",line); } - printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt); + printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt); } /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ @@ -8501,8 +8962,8 @@ int main(int argc, char *argv[]) /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */ /* numlinepar=numlinepar+3; /\* In general *\/ */ /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */ - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); - fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); + fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); fflush(ficlog); /* if(model[0]=='#'|| model[0]== '\0'){ */ if(model[0]=='#'){ @@ -8531,6 +8992,9 @@ int main(int argc, char *argv[]) covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ + coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */ + cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< Time varying covariate */ + cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5 v1+v2*age+v2*v3 makes cptcovn = 3 @@ -8680,28 +9144,28 @@ run imach with mle=-1 to get a correct t /* Scans npar lines */ for(i=1; i <=npar; i++){ - count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk); + count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk); if(count != 3){ - printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ + printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); - fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ + fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\ This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model); - exit(1); + exit(1); }else{ - if(mle==1) - printf("%1d%1d%1d",i1,j1,jk); - } - fprintf(ficlog,"%1d%1d%1d",i1,j1,jk); - fprintf(ficparo,"%1d%1d%1d",i1,j1,jk); + if(mle==1) + printf("%1d%1d%d",i1,j1,jk); + } + fprintf(ficlog,"%1d%1d%d",i1,j1,jk); + fprintf(ficparo,"%1d%1d%d",i1,j1,jk); for(j=1; j <=i; j++){ - fscanf(ficpar," %le",&matcov[i][j]); - if(mle==1){ - printf(" %.5le",matcov[i][j]); - } - fprintf(ficlog," %.5le",matcov[i][j]); - fprintf(ficparo," %.5le",matcov[i][j]); + fscanf(ficpar," %le",&matcov[i][j]); + if(mle==1){ + printf(" %.5le",matcov[i][j]); + } + fprintf(ficlog," %.5le",matcov[i][j]); + fprintf(ficparo," %.5le",matcov[i][j]); } fscanf(ficpar,"\n"); numlinepar++; @@ -8713,7 +9177,7 @@ Please run with mle=-1 to get a correct /* End of read covariance matrix npar lines */ for(i=1; i <=npar; i++) for(j=i+1;j<=npar;j++) - matcov[i][j]=matcov[j][i]; + matcov[i][j]=matcov[j][i]; if(mle==1) printf("\n"); @@ -8773,6 +9237,9 @@ Please run with mle=-1 to get a correct k=1 Tvar[1]=2 (from V2) */ Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ + Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */ + Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */ + Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */ /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, Tvar[4=age*V3] is 3 and 'age' is recorded in Tage. @@ -8798,7 +9265,7 @@ Please run with mle=-1 to get a correct /* Main decodemodel */ - if(decodemodel(model, lastobs) == 1) + if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/ goto end; if((double)(lastobs-imx)/(double)imx > 1.10){ @@ -8853,7 +9320,7 @@ Please run with mle=-1 to get a correct nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); ncodemax[1]=1; Ndum =ivector(-1,NCOVMAX); - cptcoveff=0; + cptcoveff=0; if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */ tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ } @@ -9026,7 +9493,7 @@ Title=%s
Datafile=%s Firstpass=%d La 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, \ - firstpass, lastpass, stepm, weightopt, model); + firstpass, lastpass, stepm, weightopt, model); fprintf(fichtm,"\n"); fprintf(fichtm,"
Total number of observations=%d
\n\ @@ -9055,37 +9522,37 @@ Interval (in months) between two waves: ageexmed=vector(1,n); agecens=vector(1,n); dcwave=ivector(1,n); - + for (i=1; i<=imx; i++){ dcwave[i]=-1; for (m=firstpass; m<=lastpass; m++) - if (s[m][i]>nlstate) { - dcwave[i]=m; - /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ - break; - } + if (s[m][i]>nlstate) { + dcwave[i]=m; + /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ + break; + } } - + for (i=1; i<=imx; i++) { if (wav[i]>0){ - ageexmed[i]=agev[mw[1][i]][i]; - j=wav[i]; - agecens[i]=1.; - - if (ageexmed[i]> 1 && wav[i] > 0){ - agecens[i]=agev[mw[j][i]][i]; - cens[i]= 1; - }else if (ageexmed[i]< 1) - cens[i]= -1; - if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) - cens[i]=0 ; + ageexmed[i]=agev[mw[1][i]][i]; + j=wav[i]; + agecens[i]=1.; + + if (ageexmed[i]> 1 && wav[i] > 0){ + agecens[i]=agev[mw[j][i]][i]; + cens[i]= 1; + }else if (ageexmed[i]< 1) + cens[i]= -1; + if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) + cens[i]=0 ; } else cens[i]=-1; } for (i=1;i<=NDIM;i++) { for (j=1;j<=NDIM;j++) - ximort[i][j]=(i == j ? 1.0 : 0.0); + ximort[i][j]=(i == j ? 1.0 : 0.0); } /*p[1]=0.0268; p[NDIM]=0.083;*/ @@ -9300,7 +9767,7 @@ Please run with mle=-1 to get a correct printf("\n"); /*--------- results files --------------*/ - fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); @@ -9308,20 +9775,20 @@ Please run with mle=-1 to get a correct fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\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); - 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 (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(mle != 0){ @@ -9331,42 +9798,42 @@ Please run with mle=-1 to get a correct printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n"); 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(j=1; j <=ncovmodel; j++){ - printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); - fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - } - } + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) { + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + for(j=1; j <=ncovmodel; j++){ + printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); + fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk])); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + } + } } } /* end of hesscov and Wald tests */ - + /* */ fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); printf("# Scales (for hessian or gradient estimation)\n"); fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); for(i=1,jk=1; i <=nlstate; i++){ for(j=1; j <=nlstate+ndeath; j++){ - if (j!=i) { - fprintf(ficres,"%1d%1d",i,j); - printf("%1d%1d",i,j); - fprintf(ficlog,"%1d%1d",i,j); - for(k=1; k<=ncovmodel;k++){ - printf(" %.5e",delti[jk]); - fprintf(ficlog," %.5e",delti[jk]); - fprintf(ficres," %.5e",delti[jk]); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - } + if (j!=i) { + fprintf(ficres,"%1d%1d",i,j); + printf("%1d%1d",i,j); + fprintf(ficlog,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + printf(" %.5e",delti[jk]); + fprintf(ficlog," %.5e",delti[jk]); + fprintf(ficres," %.5e",delti[jk]); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficres,"\n"); + } } } @@ -9390,83 +9857,83 @@ Please run with mle=-1 to get a correct for(itimes=1;itimes<=2;itimes++){ jj=0; for(i=1; i <=nlstate; i++){ - for(j=1; j <=nlstate+ndeath; j++){ - if(j==i) continue; - for(k=1; k<=ncovmodel;k++){ - jj++; - ca[0]= k+'a'-1;ca[1]='\0'; - if(itimes==1){ - if(mle>=1) - printf("#%1d%1d%d",i,j,k); - fprintf(ficlog,"#%1d%1d%d",i,j,k); - fprintf(ficres,"#%1d%1d%d",i,j,k); - }else{ - if(mle>=1) - printf("%1d%1d%d",i,j,k); - fprintf(ficlog,"%1d%1d%d",i,j,k); - fprintf(ficres,"%1d%1d%d",i,j,k); - } - ll=0; - for(li=1;li <=nlstate; li++){ - for(lj=1;lj <=nlstate+ndeath; lj++){ - if(lj==li) continue; - for(lk=1;lk<=ncovmodel;lk++){ - ll++; - if(ll<=jj){ - cb[0]= lk +'a'-1;cb[1]='\0'; - if(ll=1) - printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); - fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); - fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); - }else{ - if(mle>=1) - printf(" %.5e",matcov[jj][ll]); - fprintf(ficlog," %.5e",matcov[jj][ll]); - fprintf(ficres," %.5e",matcov[jj][ll]); - } - }else{ - if(itimes==1){ - if(mle>=1) - printf(" Var(%s%1d%1d)",ca,i,j); - fprintf(ficlog," Var(%s%1d%1d)",ca,i,j); - fprintf(ficres," Var(%s%1d%1d)",ca,i,j); - }else{ - if(mle>=1) - printf(" %.7e",matcov[jj][ll]); - fprintf(ficlog," %.7e",matcov[jj][ll]); - fprintf(ficres," %.7e",matcov[jj][ll]); - } - } - } - } /* end lk */ - } /* end lj */ - } /* end li */ - if(mle>=1) - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - numlinepar++; - } /* end k*/ - } /*end j */ + for(j=1; j <=nlstate+ndeath; j++){ + if(j==i) continue; + for(k=1; k<=ncovmodel;k++){ + jj++; + ca[0]= k+'a'-1;ca[1]='\0'; + if(itimes==1){ + if(mle>=1) + printf("#%1d%1d%d",i,j,k); + fprintf(ficlog,"#%1d%1d%d",i,j,k); + fprintf(ficres,"#%1d%1d%d",i,j,k); + }else{ + if(mle>=1) + printf("%1d%1d%d",i,j,k); + fprintf(ficlog,"%1d%1d%d",i,j,k); + fprintf(ficres,"%1d%1d%d",i,j,k); + } + ll=0; + for(li=1;li <=nlstate; li++){ + for(lj=1;lj <=nlstate+ndeath; lj++){ + if(lj==li) continue; + for(lk=1;lk<=ncovmodel;lk++){ + ll++; + if(ll<=jj){ + cb[0]= lk +'a'-1;cb[1]='\0'; + if(ll=1) + printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); + fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); + fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj); + }else{ + if(mle>=1) + printf(" %.5e",matcov[jj][ll]); + fprintf(ficlog," %.5e",matcov[jj][ll]); + fprintf(ficres," %.5e",matcov[jj][ll]); + } + }else{ + if(itimes==1){ + if(mle>=1) + printf(" Var(%s%1d%1d)",ca,i,j); + fprintf(ficlog," Var(%s%1d%1d)",ca,i,j); + fprintf(ficres," Var(%s%1d%1d)",ca,i,j); + }else{ + if(mle>=1) + printf(" %.7e",matcov[jj][ll]); + fprintf(ficlog," %.7e",matcov[jj][ll]); + fprintf(ficres," %.7e",matcov[jj][ll]); + } + } + } + } /* end lk */ + } /* end lj */ + } /* end li */ + if(mle>=1) + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficres,"\n"); + numlinepar++; + } /* end k*/ + } /*end j */ } /* end i */ } /* end itimes */ fflush(ficlog); fflush(ficres); - while(fgets(line, MAXLINE, ficpar)) { - /* If line starts with a # it is a comment */ - if (line[0] == '#') { - numlinepar++; - fputs(line,stdout); - fputs(line,ficparo); - fputs(line,ficlog); - continue; - }else - break; - } - + while(fgets(line, MAXLINE, ficpar)) { + /* If line starts with a # it is a comment */ + if (line[0] == '#') { + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); + continue; + }else + break; + } + /* while((c=getc(ficpar))=='#' && c!= EOF){ */ /* ungetc(c,ficpar); */ /* fgets(line, MAXLINE, ficpar); */ @@ -9477,17 +9944,17 @@ Please run with mle=-1 to get a correct estepm=0; if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){ - - if (num_filled != 6) { - printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line); - fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line); - goto end; - } - printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl); - } - /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ - /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ - + + if (num_filled != 6) { + printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line); + fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line); + goto end; + } + printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl); + } + /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */ + /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */ + /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */ if (estepm==0 || estepm < stepm) estepm=stepm; if (fage <= 2) { @@ -9555,9 +10022,9 @@ Please run with mle=-1 to get a correct ungetc(c,ficpar); fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj); - fprintf(ficparo,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); - fprintf(ficlog,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); - fprintf(ficres,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); + fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); /* day and month of proj2 are not used but only year anproj2.*/ @@ -9576,11 +10043,11 @@ 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, \ - jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); + model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \ + jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2); - /*------------ free_vector -------------*/ - /* chdir(path); */ + /*------------ free_vector -------------*/ + /* chdir(path); */ /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */ /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */ @@ -9617,8 +10084,8 @@ Please run with mle=-1 to get a correct probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax); for(i=1;i<=AGESUP;i++) for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */ - for(k=1;k<=ncovcombmax;k++) - probs[i][j][k]=0.; + for(k=1;k<=ncovcombmax;k++) + probs[i][j][k]=0.; prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); if (mobilav!=0 ||mobilavproj !=0 ) { mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); @@ -9905,6 +10372,9 @@ Please run with mle=-1 to get a correct free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); + free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n); + free_ma3x(cotvar,1,maxwav,1,ntv,1,n); + free_matrix(coqvar,1,maxwav,1,n); free_matrix(covar,0,NCOVMAX,1,n); free_matrix(matcov,1,npar,1,npar); free_matrix(hess,1,npar,1,npar); @@ -9915,6 +10385,9 @@ Please run with mle=-1 to get a correct free_ivector(ncodemax,1,NCOVMAX); free_ivector(ncodemaxwundef,1,NCOVMAX); + free_ivector(Dummy,-1,NCOVMAX); + free_ivector(Fixed,-1,NCOVMAX); + free_ivector(Typevar,-1,NCOVMAX); free_ivector(Tvar,1,NCOVMAX); free_ivector(Tprod,1,NCOVMAX); free_ivector(Tvaraff,1,NCOVMAX);