--- imach/src/imach.c 2009/07/06 10:21:25 1.133 +++ imach/src/imach.c 2014/09/02 09:24:05 1.160 @@ -1,6 +1,122 @@ -/* $Id: imach.c,v 1.133 2009/07/06 10:21:25 brouard Exp $ +/* $Id: imach.c,v 1.160 2014/09/02 09:24:05 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.160 2014/09/02 09:24:05 brouard + *** empty log message *** + + Revision 1.159 2014/09/01 10:34:10 brouard + Summary: WIN32 + Author: Brouard + + Revision 1.158 2014/08/27 17:11:51 brouard + *** empty log message *** + + Revision 1.157 2014/08/27 16:26:55 brouard + Summary: Preparing windows Visual studio version + Author: Brouard + + In order to compile on Visual studio, time.h is now correct and time_t + and tm struct should be used. difftime should be used but sometimes I + just make the differences in raw time format (time(&now). + Trying to suppress #ifdef LINUX + Add xdg-open for __linux in order to open default browser. + + Revision 1.156 2014/08/25 20:10:10 brouard + *** empty log message *** + + Revision 1.155 2014/08/25 18:32:34 brouard + Summary: New compile, minor changes + Author: Brouard + + Revision 1.154 2014/06/20 17:32:08 brouard + Summary: Outputs now all graphs of convergence to period prevalence + + Revision 1.153 2014/06/20 16:45:46 brouard + Summary: If 3 live state, convergence to period prevalence on same graph + Author: Brouard + + Revision 1.152 2014/06/18 17:54:09 brouard + Summary: open browser, use gnuplot on same dir than imach if not found in the path + + Revision 1.151 2014/06/18 16:43:30 brouard + *** empty log message *** + + Revision 1.150 2014/06/18 16:42:35 brouard + Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) + Author: brouard + + Revision 1.149 2014/06/18 15:51:14 brouard + Summary: Some fixes in parameter files errors + Author: Nicolas Brouard + + Revision 1.148 2014/06/17 17:38:48 brouard + Summary: Nothing new + Author: Brouard + + Just a new packaging for OS/X version 0.98nS + + Revision 1.147 2014/06/16 10:33:11 brouard + *** empty log message *** + + Revision 1.146 2014/06/16 10:20:28 brouard + Summary: Merge + Author: Brouard + + Merge, before building revised version. + + Revision 1.145 2014/06/10 21:23:15 brouard + Summary: Debugging with valgrind + Author: Nicolas Brouard + + Lot of changes in order to output the results with some covariates + After the Edimburgh REVES conference 2014, it seems mandatory to + improve the code. + No more memory valgrind error but a lot has to be done in order to + continue the work of splitting the code into subroutines. + Also, decodemodel has been improved. Tricode is still not + optimal. nbcode should be improved. Documentation has been added in + the source code. + + Revision 1.143 2014/01/26 09:45:38 brouard + Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising + + * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... + (Module): Version 0.98nR Running ok, but output format still only works for three covariates. + + Revision 1.142 2014/01/26 03:57:36 brouard + Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 + + * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... + + Revision 1.141 2014/01/26 02:42:01 brouard + * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... + + Revision 1.140 2011/09/02 10:37:54 brouard + Summary: times.h is ok with mingw32 now. + + Revision 1.139 2010/06/14 07:50:17 brouard + After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. + I remember having already fixed agemin agemax which are pointers now but not cvs saved. + + Revision 1.138 2010/04/30 18:19:40 brouard + *** empty log message *** + + Revision 1.137 2010/04/29 18:11:38 brouard + (Module): Checking covariates for more complex models + than V1+V2. A lot of change to be done. Unstable. + + Revision 1.136 2010/04/26 20:30:53 brouard + (Module): merging some libgsl code. Fixing computation + of likelione (using inter/intrapolation if mle = 0) in order to + get same likelihood as if mle=1. + Some cleaning of code and comments added. + + Revision 1.135 2009/10/29 15:33:14 brouard + (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. + + Revision 1.134 2009/10/29 13:18:53 brouard + (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. + Revision 1.133 2009/07/06 10:21:25 brouard just nforces @@ -334,10 +450,22 @@ begin-prev-date,... open gnuplot file open html file - period (stable) prevalence - for age prevalim() - h Pij x - variance of p varprob + period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate + for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ****** + | 65 1 0 2 1 3 1 4 0 0.96326 0.03674 + freexexit2 possible for memory heap. + + h Pij x | pij_nom ficrestpij + # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3 + 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 + 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907 + + 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340 + 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597 + variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in () + Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix + Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix + forecasting if prevfcast==1 prevforecast call prevalence() health expectancies Variance-covariance of DFLE @@ -357,22 +485,37 @@ #include #include #include + +#ifdef _WIN32 +#include +#else #include +#endif #include #include #include #include -extern int errno; +/* extern int errno; */ +/* #ifdef LINUX */ +/* #include */ +/* #include "timeval.h" */ +/* #else */ /* #include */ +/* #endif */ + #include -#include "timeval.h" + +#ifdef GSL +#include +#include +#endif /* #include */ /* #define _(String) gettext (String) */ -#define MAXLINE 256 +#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */ #define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ @@ -381,38 +524,46 @@ extern int errno; #define GLOCK_ERROR_NOPATH -1 /* empty path */ #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ -#define MAXPARM 128 /* Maximum number of parameters for the optimization */ -#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */ +#define MAXPARM 128 /**< Maximum number of parameters for the optimization */ +#define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */ #define NINTERVMAX 8 -#define NLSTATEMAX 8 /* Maximum number of live states (for func) */ -#define NDEATHMAX 8 /* Maximum number of dead states (for func) */ -#define NCOVMAX 20 /* Maximum number of covariates */ +#define NLSTATEMAX 8 /**< Maximum number of live states (for func) */ +#define NDEATHMAX 8 /**< Maximum number of dead states (for func) */ +#define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */ +#define codtabm(h,k) 1 & (h-1) >> (k-1) ; #define MAXN 20000 -#define YEARM 12. /* Number of months per year */ +#define YEARM 12. /**< Number of months per year */ #define AGESUP 130 #define AGEBASE 40 -#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */ -#ifdef UNIX -#define DIRSEPARATOR '/' -#define CHARSEPARATOR "/" -#define ODIRSEPARATOR '\\' -#else +#define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */ +#ifdef _WIN32 #define DIRSEPARATOR '\\' #define CHARSEPARATOR "\\" #define ODIRSEPARATOR '/' +#else +#define DIRSEPARATOR '/' +#define CHARSEPARATOR "/" +#define ODIRSEPARATOR '\\' #endif -/* $Id: imach.c,v 1.133 2009/07/06 10:21:25 brouard Exp $ */ +/* $Id: imach.c,v 1.160 2014/09/02 09:24:05 brouard Exp $ */ /* $State: Exp $ */ -char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite "; -char fullversion[]="$Revision: 1.133 $ $Date: 2009/07/06 10:21:25 $"; +char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)"; +char fullversion[]="$Revision: 1.160 $ $Date: 2014/09/02 09:24:05 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ int nvar=0, nforce=0; /* Number of variables, number of forces */ -int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */ +/* 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 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 cptcov=0; /* Working variable */ int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ @@ -431,9 +582,11 @@ int **dh; /* dh[mi][i] is number of step int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between * wave mi and wave mi+1 is not an exact multiple of stepm. */ double jmean=1; /* Mean space between 2 waves */ +double **matprod2(); /* test */ double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ -FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; +/*FILE *fic ; */ /* Used in readdata only */ +FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; FILE *ficlog, *ficrespow; int globpr=0; /* Global variable for printing or not */ double fretone; /* Only one call to likelihood */ @@ -471,12 +624,17 @@ char popfile[FILENAMELENGTH]; char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ; -struct timeval start_time, end_time, curr_time, last_time, forecast_time; -struct timezone tzp; -extern int gettimeofday(); -struct tm tmg, tm, tmf, *gmtime(), *localtime(); -long time_value; -extern long time(); +/* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */ +/* struct timezone tzp; */ +/* extern int gettimeofday(); */ +struct tm tml, *gmtime(), *localtime(); + +extern time_t time(); + +struct tm start_time, end_time, curr_time, last_time, forecast_time; +time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */ +struct tm tm; + char strcurr[80], strfor[80]; char *endptr; @@ -529,12 +687,19 @@ double dateintmean=0; double *weight; int **s; /* Status */ -double *agedc, **covar, idx; -int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; +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]*cov[2]; */ +double idx; +int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ +int *Ndum; /** Freq of modality (tricode */ +int **codtab; /**< codtab=imatrix(1,100,1,10); */ +int **Tvard, *Tprod, cptcovprod, *Tvaraff; double *lsurv, *lpop, *tpop; -double ftol=FTOL; /* Tolerance for computing Max Likelihood */ -double ftolhess; /* Tolerance for computing hessian */ +double ftol=FTOL; /**< Tolerance for computing Max Likelihood */ +double ftolhess; /**< Tolerance for computing hessian */ /**************** split *************************/ static int split( char *path, char *dirc, char *name, char *ext, char *finame ) @@ -604,11 +769,11 @@ void replace_back_to_slash(char *s, char } char *trimbb(char *out, char *in) -{ /* Trim multiple blanks in line */ +{ /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */ char *s; s=out; while (*in != '\0'){ - while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){ + while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/ in++; } *out++ = *in++; @@ -617,6 +782,63 @@ char *trimbb(char *out, char *in) return s; } +char *cutl(char *blocc, char *alocc, char *in, char occ) +{ + /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' + and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') + gives blocc="abcdef2ghi" and alocc="j". + If occ is not found blocc is null and alocc is equal to in. Returns blocc + */ + char *s, *t; + t=in;s=in; + while ((*in != occ) && (*in != '\0')){ + *alocc++ = *in++; + } + if( *in == occ){ + *(alocc)='\0'; + s=++in; + } + + if (s == t) {/* occ not found */ + *(alocc-(in-s))='\0'; + in=s; + } + while ( *in != '\0'){ + *blocc++ = *in++; + } + + *blocc='\0'; + return t; +} +char *cutv(char *blocc, char *alocc, char *in, char occ) +{ + /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' + and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2') + gives blocc="abcdef2ghi" and alocc="j". + If occ is not found blocc is null and alocc is equal to in. Returns alocc + */ + char *s, *t; + t=in;s=in; + while (*in != '\0'){ + while( *in == occ){ + *blocc++ = *in++; + s=in; + } + *blocc++ = *in++; + } + if (s == t) /* occ not found */ + *(blocc-(in-s))='\0'; + else + *(blocc-(in-s)-1)='\0'; + in=s; + while ( *in != '\0'){ + *alocc++ = *in++; + } + + *alocc='\0'; + return s; +} + int nbocc(char *s, char occ) { int i,j=0; @@ -629,27 +851,45 @@ int nbocc(char *s, char occ) return j; } -void cutv(char *u,char *v, char*t, char occ) -{ - /* cuts string t into u and v where u ends before first occurence of char 'occ' - and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') - gives u="abcedf" and v="ghi2j" */ - int i,lg,j,p=0; - i=0; - for(j=0; j<=strlen(t)-1; j++) { - if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; - } +/* void cutv(char *u,char *v, char*t, char occ) */ +/* { */ +/* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */ +/* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */ +/* gives u="abcdef2ghi" and v="j" *\/ */ +/* int i,lg,j,p=0; */ +/* i=0; */ +/* lg=strlen(t); */ +/* for(j=0; j<=lg-1; j++) { */ +/* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */ +/* } */ - lg=strlen(t); - for(j=0; j=(p+1))(v[j-p-1] = t[j]); */ +/* } */ +/* } */ - for(j=0; j<= lg; j++) { - if (j>=(p+1))(v[j-p-1] = t[j]); +#ifdef _WIN32 +char * strsep(char **pp, const char *delim) +{ + char *p, *q; + + if ((p = *pp) == NULL) + return 0; + if ((q = strpbrk (p, delim)) != NULL) + { + *pp = q + 1; + *q = '\0'; } + else + *pp = 0; + return p; } +#endif /********************** nrerror ********************/ @@ -758,7 +998,9 @@ double **matrix(long nrl, long nrh, long for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; return m; - /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) + /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0]) +m[i] = address of ith row of the table. &(m[i]) is its value which is another adress +that of m[i][0]. In order to get the value p m[i][0] but it is unitialized. */ } @@ -871,7 +1113,7 @@ double brent(double ax, double bx, doubl { int iter; double a,b,d,etemp; - double fu,fv,fw,fx; + double fu=0,fv,fw,fx; double ftemp; double p,q,r,tol1,tol2,u,v,w,x,xm; double e=0.0; @@ -1032,7 +1274,7 @@ char *asc_diff_time(long time_sec, char sec_left = (sec_left) %(60*60); minutes = (sec_left) /60; sec_left = (sec_left) % (60); - sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left); + sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); return ascdiff; } @@ -1054,15 +1296,18 @@ void powell(double p[], double **xi, int xits=vector(1,n); *fret=(*func)(p); for (j=1;j<=n;j++) pt[j]=p[j]; + rcurr_time = time(NULL); for (*iter=1;;++(*iter)) { fp=(*fret); ibig=0; del=0.0; - last_time=curr_time; - (void) gettimeofday(&curr_time,&tzp); - printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout); - fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog); -/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */ + rlast_time=rcurr_time; + /* (void) gettimeofday(&curr_time,&tzp); */ + rcurr_time = time(NULL); + curr_time = *localtime(&rcurr_time); + printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); + fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); +/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */ for (i=1;i<=n;i++) { printf(" %d %.12f",i, p[i]); fprintf(ficlog," %d %.12lf",i, p[i]); @@ -1072,25 +1317,25 @@ void powell(double p[], double **xi, int fprintf(ficlog,"\n"); fprintf(ficrespow,"\n");fflush(ficrespow); if(*iter <=3){ - tm = *localtime(&curr_time.tv_sec); - strcpy(strcurr,asctime(&tm)); + tml = *localtime(&rcurr_time); + strcpy(strcurr,asctime(&tml)); /* asctime_r(&tm,strcurr); */ - forecast_time=curr_time; + rforecast_time=rcurr_time; itmp = strlen(strcurr); if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ strcurr[itmp-1]='\0'; - printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); - fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); + printf("\nConsidering the time needed for this 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){ - forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec); - tmf = *localtime(&forecast_time.tv_sec); + rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); + forecast_time = *localtime(&rforecast_time); /* asctime_r(&tmf,strfor); */ - strcpy(strfor,asctime(&tmf)); + 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(forecast_time.tv_sec-curr_time.tv_sec,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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); + 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++) { @@ -1193,7 +1438,7 @@ double **prevalim(double **prlim, int nl int i, ii,j,k; double min, max, maxmin, maxmax,sumnew=0.; - double **matprod2(); + /* double **matprod2(); */ /* test */ double **out, cov[NCOVMAX+1], **pmij(); double **newm; double agefin, delaymax=50 ; /* Max number of years to converge */ @@ -1209,21 +1454,23 @@ double **prevalim(double **prlim, int nl for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ newm=savm; /* Covariates have to be included here again */ - cov[2]=agefin; - - for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; - /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/ - } - for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; - for (k=1; k<=cptcovprod;k++) - cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; - - /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ - /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ - /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ - out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); - + cov[2]=agefin; + + for (k=1; k<=cptcovn;k++) { + cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; + /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/ + } + /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ + /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */ + /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */ + + /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/ + /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/ + /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/ + /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */ + /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */ + out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */ + savm=oldm; oldm=newm; maxmax=0.; @@ -1234,6 +1481,7 @@ double **prevalim(double **prlim, int nl sumnew=0; for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k]; prlim[i][j]= newm[i][j]/(1-sumnew); + /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/ max=FMAX(max,prlim[i][j]); min=FMIN(min,prlim[i][j]); } @@ -1250,41 +1498,56 @@ double **prevalim(double **prlim, int nl double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate ) { - double s1, s2; + /* According to parameters values stored in x and the covariate's values stored in cov, + computes the probability to be observed in state j being in state i by appying the + model to the ncovmodel covariates (including constant and age). + lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc] + and, according on how parameters are entered, the position of the coefficient xij(nc) of the + ncth covariate in the global vector x is given by the formula: + j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel + Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation, + sums on j different of i to get 1-pii/pii, deduces pii, and then all pij. + Outputs ps[i][j] the probability to be observed in j being in j according to + the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij] + */ + double s1, lnpijopii; /*double t34;*/ int i,j,j1, nc, ii, jj; for(i=1; i<= nlstate; i++){ for(j=1; ji s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */ + for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){ + /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/ + lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc]; +/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */ } - ps[i][j]=s2; + ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */ } } - /*ps[3][2]=1;*/ 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; j(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ } else if (mle==4){ /* mle=4 no inter-extrapolation */ lli=log(out[s1][s2]); /* Original formula */ - } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */ - lli=log(out[s1][s2]); /* Original formula */ + } else{ /* mle=0 back to 1 */ + lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ + /*lli=log(out[s1][s2]); */ /* Original formula */ } /* End of if */ ipmx +=1; sw += weight[i]; ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ if(globpr){ - fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ + fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ %11.6f %11.6f %11.6f ", \ num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); @@ -1926,13 +2204,13 @@ double hessii(double x[], double delta, fx=func(x); for (i=1;i<=npar;i++) p2[i]=x[i]; - for(l=0 ; l <=lmax; l++){ + for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */ l1=pow(10,l); delts=delt; for(k=1 ; k 0) { - for (z1=1; z1<=cptcoveff; z1++) - if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) - bool=0; + 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]][i]!= nbcode[Tvaraff[z1]][codtab[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, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", + bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1], + j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/ + /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/ + } } + if (bool==1){ for(m=firstpass; m<=lastpass; m++){ k2=anint[m][i]+(mint[m][i]/12.); @@ -2143,7 +2430,7 @@ void freqsummary(char fileres[], int ia /*}*/ } } - } + } /* end i */ /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ pstamp(ficresp); @@ -2151,6 +2438,9 @@ void freqsummary(char fileres[], int ia fprintf(ficresp, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); fprintf(ficresp, "**********\n#"); + fprintf(ficlog, "\n#********** Variable "); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficlog, "**********\n#"); } for(i=1; i<=nlstate;i++) fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); @@ -2227,7 +2517,7 @@ void freqsummary(char fileres[], int ia printf("Others in log...\n"); fprintf(ficlog,"\n"); } - } + /*}*/ } dateintmean=dateintsum/k2cpt; @@ -2252,6 +2542,7 @@ void prevalence(double ***probs, double double pos,posprop; double y2; /* in fractional years */ int iagemin, iagemax; + int first; /** to stop verbosity which is redirected to log file */ iagemin= (int) agemin; iagemax= (int) agemax; @@ -2260,12 +2551,13 @@ void prevalence(double ***probs, double /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ j1=0; - j=cptcoveff; + /*j=cptcoveff;*/ if (cptcovn<1) {j=1;ncodemax[1]=1;} - for(k1=1; k1<=j;k1++){ - for(i1=1; i1<=ncodemax[k1];i1++){ - j1++; + first=1; + for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ + /*for(i1=1; i1<=ncodemax[k1];i1++){ + j1++;*/ for (i=1; i<=nlstate; i++) for(m=iagemin; m <= iagemax+3; m++) @@ -2295,22 +2587,25 @@ void prevalence(double ***probs, double } } for(i=iagemin; i <= iagemax+3; i++){ - for(jk=1,posprop=0; jk <=nlstate ; jk++) { posprop += prop[jk][i]; } - + for(jk=1; jk <=nlstate ; jk++){ if( i <= iagemax){ if(posprop>=1.e-5){ probs[i][jk][j1]= prop[jk][i]/posprop; - } else - printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]); + } else{ + if(first==1){ + first=0; + printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]); + } + } } }/* end jk */ }/* end i */ - } /* end i1 */ - } /* end k1 */ + /*} *//* end i1 */ + } /* end j1 */ /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ /*free_vector(pp,1,nlstate);*/ @@ -2430,7 +2725,7 @@ void concatwav(int wav[], int **dh, int dh[mi][i]=jk; bh[mi][i]=0; }else{ /* We want a negative bias in order to only have interpolation ie - * at the price of an extra matrix product in likelihood */ + * to avoid the price of an extra matrix product in likelihood */ dh[mi][i]=jk+1; bh[mi][i]=ju; } @@ -2456,44 +2751,84 @@ void concatwav(int wav[], int **dh, int } jmean=sum/k; printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean); - fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean); + fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean); } /*********** Tricode ****************************/ -void tricode(int *Tvar, int **nbcode, int imx) +void tricode(int *Tvar, int **nbcode, int imx, int *Ndum) { - - /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */ + /**< 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[j]][1]= + */ + + int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; + int modmaxcovj=0; /* Modality max of covariates j */ + int cptcode=0; /* Modality max of covariates j */ + int modmincovj=0; /* Modality min of covariates j */ + - int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; - int cptcode=0; cptcoveff=0; - for (k=0; k 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);*/ - if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate (should be 0 or 1 now) - Tvar[j]. If V=sex and male is 0 and - female is 1, then cptcode=1.*/ - } - - for (i=0; i<=cptcode; i++) { /* i=-1 ?*/ - if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j - th covariate. In fact - ncodemax[j]=2 - (dichotom. variables only) but - it can be more */ + /* 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.*/ + } + printf(" 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=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */ + printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]); + if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */ + ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */ + } + /* 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 */ } /* Ndum[-1] number of undefined modalities */ - ij=1; - for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */ - for (k=0; k<= maxncov; k++) { /* k=-1 ?*/ + /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ + /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */ + /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125; + modmincovj=3; modmaxcovj = 7; + There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3; + which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy + variables V1_1 and V1_2. + nbcode[Tvar[j]][ij]=k; + nbcode[Tvar[j]][1]=0; + nbcode[Tvar[j]][2]=1; + nbcode[Tvar[j]][3]=2; + */ + ij=1; /* ij is similar to i but can jumps over null modalities */ + for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */ + for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */ + /*recode from 0 */ if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */ nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode. k is a modality. If we have model=V1+V1*sex @@ -2501,29 +2836,34 @@ void tricode(int *Tvar, int **nbcode, in ij++; } if (ij > ncodemax[j]) break; - } - } - } - - for (k=0; k< maxncov; k++) Ndum[k]=0; - - for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and 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]++; - } + } /* end of loop on */ + } /* end of loop on modality */ + } /* 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 (i=1; i<=ncovmodel-2; i++) { /* -2, cste and 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]++; + } ij=1; - for (i=1; i<= maxncov; i++) { + 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)){ - Tvaraff[ij]=i; /*For printing */ + /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/ + Tvaraff[ij]=i; /*For printing (unclear) */ ij++; - } + }else + Tvaraff[ij]=0; } ij--; - cptcoveff=ij; /*Number of simple covariates*/ + cptcoveff=ij; /*Number of total covariates*/ + } + /*********** Health Expectancies ****************/ void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) @@ -3119,15 +3459,15 @@ void varevsij(char optionfilefiname[], d free_vector(gmp,nlstate+1,nlstate+ndeath); free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath); free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/ - fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65"); + fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */ /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */ /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */ - fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev)); - fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev)); - fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev)); + fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev)); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev)); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev)); fprintf(fichtm,"\n
File (multiple files are possible if covariates are present): %s\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev)); fprintf(fichtm,"\n
Probability is computed over estepm=%d months.

\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); /* fprintf(fichtm,"\n
Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year

\n", stepm,YEARM,digitp,digit); @@ -3237,20 +3577,19 @@ void varprob(char optionfilefiname[], do int i, j=0, i1, k1, l1, t, tj; int k2, l2, j1, z1; int k=0,l, cptcode; - int first=1, first1; + int first=1, first1, first2; double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp; double **dnewm,**doldm; double *xp; double *gp, *gm; double **gradg, **trgradg; double **mu; - double age,agelim, cov[NCOVMAX]; + double age,agelim, cov[NCOVMAX+1]; double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */ int theta; char fileresprob[FILENAMELENGTH]; char fileresprobcov[FILENAMELENGTH]; char fileresprobcor[FILENAMELENGTH]; - double ***varpij; strcpy(fileresprob,"prob"); @@ -3323,12 +3662,13 @@ standard deviations wide on each axis. < To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
\n"); cov[1]=1; - tj=cptcoveff; + /* tj=cptcoveff; */ + tj = (int) pow(2,cptcoveff); if (cptcovn<1) {tj=1;ncodemax[1]=1;} j1=0; - for(t=1; t<=tj;t++){ - for(i1=1; i1<=ncodemax[t];i1++){ - j1++; + for(j1=1; j1<=tj;j1++){ + /*for(i1=1; i1<=ncodemax[t];i1++){ */ + /*j1++;*/ if (cptcovn>0) { fprintf(ficresprob, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); @@ -3351,19 +3691,24 @@ To be simple, these graphs help to under fprintf(ficresprobcor, "**********\n#"); } + gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); + trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); + gp=vector(1,(nlstate)*(nlstate+ndeath)); + gm=vector(1,(nlstate)*(nlstate+ndeath)); for (age=bage; age<=fage; age ++){ cov[2]=age; for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; + cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4 + * 1 1 1 1 1 + * 2 2 1 1 1 + * 3 1 2 1 1 + */ + /* nbcode[1][1]=0 nbcode[1][2]=1;*/ } for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; for (k=1; k<=cptcovprod;k++) cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; - gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath)); - trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); - gp=vector(1,(nlstate)*(nlstate+ndeath)); - gm=vector(1,(nlstate)*(nlstate+ndeath)); for(theta=1; theta <=npar; theta++){ for(i=1; i<=npar; i++) @@ -3401,10 +3746,6 @@ To be simple, these graphs help to under matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); - free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); - free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); pmij(pmmij,cov,ncovmodel,x,nlstate); @@ -3438,17 +3779,22 @@ To be simple, these graphs help to under i=0; for (k=1; k<=(nlstate);k++){ for (l=1; l<=(nlstate+ndeath);l++){ - i=i++; + i++; fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l); fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l); for (j=1; j<=i;j++){ + /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */ fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]); fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age])); } } }/* end of loop for state */ } /* end of loop for age */ - + free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + /* Confidence intervalle of pij */ /* fprintf(ficgp,"\nunset parametric;unset label"); @@ -3461,7 +3807,7 @@ To be simple, these graphs help to under */ /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ - first1=1; + first1=1;first2=2; for (k2=1; k2<=(nlstate);k2++){ for (l2=1; l2<=(nlstate+ndeath);l2++){ if(l2==k2) continue; @@ -3482,6 +3828,16 @@ To be simple, these graphs help to under /* Computing eigen value of matrix of covariance */ lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.; + if ((lc2 <0) || (lc1 <0) ){ + if(first2==1){ + first1=0; + printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor); + } + fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog); + /* lc1=fabs(lc1); */ /* If we want to have them positive */ + /* lc2=fabs(lc2); */ + } + /* Eigen vectors */ v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12)); /*v21=sqrt(1.-v11*v11); *//* error */ @@ -3501,7 +3857,7 @@ To be simple, these graphs help to under first=0; fprintf(ficgp,"\nset parametric;unset label"); fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); - fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(ficgp,"\nset ter png small size 320, 240"); fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\ :\ %s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,\ @@ -3532,7 +3888,7 @@ To be simple, these graphs help to under } /* k12 */ } /*l1 */ }/* k1 */ - } /* loop covariates */ + /* } /* loop covariates */ } free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); @@ -3578,7 +3934,7 @@ void printinghtml(char fileres[], char t fprintf(fichtm," \n
  • Graphs

    • "); - m=cptcoveff; + m=pow(2,cptcoveff); if (cptcovn < 1) {m=1;ncodemax[1]=1;} jj1=0; @@ -3592,20 +3948,20 @@ fprintf(fichtm," \n

    • Graphs fprintf(fichtm," ************\n
      "); } /* Pij */ - fprintf(fichtm,"
      - Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png
      \ -",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); + fprintf(fichtm,"
      - Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d_1.png
      \ +",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); /* Quasi-incidences */ fprintf(fichtm,"
      - Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\ - before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png
      \ -",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); + before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d_2.png
      \ +",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); /* Period (stable) prevalence in each health state */ - for(cpt=1; cpt- Period (stable) prevalence in each health state : %s%d%d.png
      \ -",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); + for(cpt=1; cpt<=nlstate;cpt++){ + fprintf(fichtm,"
      - Convergence from each state (1 to %d) to period (stable) prevalence in state %d %s%d_%d.png
      \ +",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); } for(cpt=1; cpt<=nlstate;cpt++) { - fprintf(fichtm,"\n
      - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : %s%d%d.png
      \ -",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); + fprintf(fichtm,"\n
      - Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : %s%d%d.png
      \ +",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); } } /* end i1 */ }/* End k1 */ @@ -3652,7 +4008,7 @@ fprintf(fichtm," \n
      • Graphs fflush(fichtm); fprintf(fichtm,"
        • Graphs

          • "); - m=cptcoveff; + m=pow(2,cptcoveff); if (cptcovn < 1) {m=1;ncodemax[1]=1;} jj1=0; @@ -3667,8 +4023,8 @@ fprintf(fichtm," \n

          • Graphs } for(cpt=1; cpt<=nlstate;cpt++) { fprintf(fichtm,"
            - Observed (cross-sectional) and period (incidence based) \ -prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png
            \ -",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); +prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png
            \ +",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); } fprintf(fichtm,"\n
            - Total life expectancy by age and \ health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \ @@ -3701,38 +4057,38 @@ void printinggnuplot(char fileres[], cha strcpy(dirfileres,optionfilefiname); strcpy(optfileres,"vpl"); /* 1eme*/ + fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n"); for (cpt=1; cpt<= nlstate ; cpt ++) { - for (k1=1; k1<= m ; k1 ++) { - fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); - fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1); + for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */ + fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1); + fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1); fprintf(ficgp,"set xlabel \"Age\" \n\ set ylabel \"Probability\" \n\ -set ter png small\n\ -set size 0.65,0.65\n\ +set ter png small size 320, 240\n\ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"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 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); + fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"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 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); + fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); } - fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); + fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1)); } } /*2 eme*/ - + fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n"); for (k1=1; k1<= m ; k1 ++) { fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1); - fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage); + fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage); for (i=1; i<= nlstate+1 ; i ++) { k=2*i; @@ -3748,14 +4104,14 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); } - fprintf(ficgp,"\" t\"\" w l 0,"); + fprintf(ficgp,"\" t\"\" w l lt 0,"); fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); for (j=1; j<= nlstate+1 ; j ++) { if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); } - if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); - else fprintf(ficgp,"\" t\"\" w l 0,"); + if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); + else fprintf(ficgp,"\" t\"\" w l lt 0,"); } } @@ -3766,8 +4122,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* k=2+nlstate*(2*cpt-2); */ k=2+(nlstate+1)*(cpt-1); fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); - fprintf(ficgp,"set ter png small\n\ -set size 0.65,0.65\n\ + fprintf(ficgp,"set ter png small size 320, 240\n\ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); @@ -3787,28 +4142,29 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u } /* CV preval stable (period) */ - for (k1=1; k1<= m ; k1 ++) { - for (cpt=1; cpt<=nlstate ; cpt ++) { + for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */ + for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */ k=3; - fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); + fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt); + fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1); fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\ -set ter png small\nset size 0.65,0.65\n\ +set ter png small size 320, 240\n\ unset log y\n\ -plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1); - - for (i=1; i< nlstate ; i ++) - fprintf(ficgp,"+$%d",k+i+1); - fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1); - - l=3+(nlstate+ndeath)*cpt; - fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1); - for (i=1; i< nlstate ; i ++) { - l=3+(nlstate+ndeath)*cpt; - fprintf(ficgp,"+$%d",l+i+1); - } - fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1); - } - } +plot [%.f:%.f] ", ageminpar, agemaxpar); + for (i=1; i<= nlstate ; i ++){ + if(i==1) + fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij")); + else + fprintf(ficgp,", '' "); + l=(nlstate+ndeath)*(i-1)+1; + fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); + for (j=1; j<= (nlstate-1) ; j ++) + fprintf(ficgp,"+$%d",k+l+j); + fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt); + } /* nlstate */ + fprintf(ficgp,"\n"); + } /* end cpt state*/ + } /* end covariate */ /* proba elementaires */ for(i=1,jk=1; i <=nlstate; i++){ @@ -3822,15 +4178,15 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 } } } - + /*goto avoid;*/ for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ for(jk=1; jk <=m; jk++) { - fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); + fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); if (ng==2) fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); else fprintf(ficgp,"\nset title \"Probability\"\n"); - fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); + fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); i=1; for(k2=1; k2<=nlstate; k2++) { k3=i; @@ -3840,13 +4196,13 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); else fprintf(ficgp," exp(p%d+p%d*x",i,i+1); - ij=1; + ij=1;/* To be checked else nbcode[0][0] wrong */ for(j=3; j <=ncovmodel; j++) { - if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { - fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); - ij++; - } - else + /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */ + /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */ + /* ij++; */ + /* } */ + /* else */ fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); } fprintf(ficgp,")/(1"); @@ -3855,11 +4211,11 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); ij=1; for(j=3; j <=ncovmodel; j++){ - if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { - fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); - ij++; - } - else + /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */ + /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */ + /* ij++; */ + /* } */ + /* else */ fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]); } fprintf(ficgp,")"); @@ -3872,6 +4228,7 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 } /* end k2 */ } /* end jk */ } /* end ng */ + avoid: fflush(ficgp); } /* end gnuplot */ @@ -4373,6 +4730,47 @@ double gompertz(double x[]) return -2*L*num/sump; } +#ifdef GSL +/******************* Gompertz_f Likelihood ******************************/ +double gompertz_f(const gsl_vector *v, void *params) +{ + double A,B,LL=0.0,sump=0.,num=0.; + double *x= (double *) v->data; + int i,n=0; /* n is the size of the sample */ + + for (i=0;i<=imx-1 ; i++) { + sump=sump+weight[i]; + /* sump=sump+1;*/ + num=num+1; + } + + + /* for (i=0; i<=imx; i++) + if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ + printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]); + for (i=1;i<=imx ; i++) + { + if (cens[i] == 1 && wav[i]>1) + A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))); + + if (cens[i] == 0 && wav[i]>1) + A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp))) + +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM); + + /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ + if (wav[i] > 1 ) { /* ??? */ + LL=LL+A*weight[i]; + /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/ + } + } + + /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/ + printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump); + + return -2*LL*num/sump; +} +#endif + /******************* Printing html file ***********/ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ @@ -4414,112 +4812,573 @@ void printinggnuplotmort(char fileres[], strcpy(optfileres,"vpl"); fprintf(ficgp,"set out \"graphmort.png\"\n "); fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); - fprintf(ficgp, "set ter png small\n set log y\n"); - fprintf(ficgp, "set size 0.65,0.65\n"); + fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); + /* fprintf(ficgp, "set size 0.65,0.65\n"); */ fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp); } - - - - -/***********************************************/ -/**************** Main Program *****************/ -/***********************************************/ - -int main(int argc, char *argv[]) +int readdata(char datafile[], int firstobs, int lastobs, int *imax) { - int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); - int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; - int linei, month, year,iout; - int jj, ll, li, lj, lk, imk; - int numlinepar=0; /* Current linenumber of parameter file */ - int itimes; - int NDIM=2; - int vpopbased=0; - char ca[32], cb[32], cc[32]; + /*-------- data file ----------*/ + FILE *fic; char dummy[]=" "; - /* FILE *fichtm; *//* Html File */ - /* FILE *ficgp;*/ /*Gnuplot File */ - struct stat info; - double agedeb, agefin,hf; - double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; - - double fret; - double **xi,tmp,delta; - - double dum; /* Dummy variable */ - double ***p3mat; - double ***mobaverage; - int *indx; - char line[MAXLINE], linepar[MAXLINE]; - char linetmp[MAXLINE]; - char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; - char pathr[MAXLINE], pathimach[MAXLINE]; - char **bp, *tok, *val; /* pathtot */ - int firstobs=1, lastobs=10; - int sdeb, sfin; /* Status at beginning and end */ - int c, h , cpt,l; - int ju,jl, mi; - int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; - int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; - int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ - int mobilav=0,popforecast=0; - int hstepm, nhstepm; - int agemortsup; - float sumlpop=0.; - double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; - double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; - - double bage, fage, age, agelim, agebase; - double ftolpl=FTOL; - double **prlim; - double *severity; - double ***param; /* Matrix of parameters */ - double *p; - double **matcov; /* Matrix of covariance */ - double ***delti3; /* Scale */ - double *delti; /* Scale */ - double ***eij, ***vareij; - double **varpl; /* Variances of prevalence limits by age */ - double *epj, vepp; - double kk1, kk2; - double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; - double **ximort; - char *alph[]={"a","a","b","c","d","e"}, str[4]; - int *dcwave; - - char z[1]="c", occ; - - char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; - char *strt, strtend[80]; + int i, j, n; + int linei, month, year,iout; + char line[MAXLINE], linetmp[MAXLINE]; + char stra[80], strb[80]; char *stratrunc; int lstra; - long total_usecs; - -/* setlocale (LC_ALL, ""); */ -/* bindtextdomain (PACKAGE, LOCALEDIR); */ -/* textdomain (PACKAGE); */ -/* setlocale (LC_CTYPE, ""); */ -/* setlocale (LC_MESSAGES, ""); */ + + if((fic=fopen(datafile,"r"))==NULL) { + printf("Problem while opening datafile: %s\n", datafile);return 1; + fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1; + } + + i=1; + linei=0; + while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { + linei=linei+1; + for(j=strlen(line); j>=0;j--){ /* Untabifies line */ + if(line[j] == '\t') + line[j] = ' '; + } + for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ + ; + }; + line[j+1]=0; /* Trims blanks at end of line */ + if(line[0]=='#'){ + fprintf(ficlog,"Comment line\n%s\n",line); + printf("Comment line\n%s\n",line); + continue; + } + trimbb(linetmp,line); /* Trims multiple blanks in line */ + for (j=0; line[j]!='\0';j++){ + line[j]=linetmp[j]; + } + + + for (j=maxwav;j>=1;j--){ + cutv(stra, strb, line, ' '); + if(strb[0]=='.') { /* Missing status */ + 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 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; + + strcpy(line,stra); + cutv(stra, strb,line,' '); + if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + } + else if(iout=sscanf(strb,"%s.",dummy) != 0){ + month=99; + year=9999; + }else{ + printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j); + fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog); + return 1; + } + anint[j][i]= (double) year; + mint[j][i]= (double)month; + strcpy(line,stra); + } /* ENd Waves */ + + cutv(stra, strb,line,' '); + if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + } + else if(iout=sscanf(strb,"%s.",dummy) != 0){ + month=99; + 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; + } + andc[i]=(double) year; + moisdc[i]=(double) month; + strcpy(line,stra); + + cutv(stra, strb,line,' '); + if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + } + else if(iout=sscanf(strb,"%s.", dummy) != 0){ + month=99; + year=9999; + }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; + } + 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; + + } + annais[i]=(double)(year); + moisnais[i]=(double)(month); + strcpy(line,stra); + + cutv(stra, strb,line,' '); + errno=0; + dval=strtod(strb,&endptr); + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); + fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); + fflush(ficlog); + return 1; + } + weight[i]=dval; + strcpy(line,stra); + + for (j=ncovcol;j>=1;j--){ + cutv(stra, strb,line,' '); + if(strb[0]=='.') { /* Missing status */ + lval=-1; + }else{ + errno=0; + lval=strtol(strb,&endptr,10); + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line); + fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);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; + } + covar[j][i]=(double)(lval); + 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); + } + else + num[i]=atol(stra); + /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ + printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ + + 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); + + + +} +void removespace(char *str) { + char *p1 = str, *p2 = str; + do + while (*p2 == ' ') + p2++; + 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 + * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 + * - cptcovn or number of covariates k of the models excluding age*products =6 + * - 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 i1, j1, k1, k2; + char modelsav[80]; + char stra[80], strb[80], strc[80], strd[80],stre[80]; + + /*removespace(model);*/ + if (strlen(model) >1){ /* If there is at least 1 covariate */ + j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; + j=nbocc(model,'+'); /**< j=Number of '+' */ + j1=nbocc(model,'*'); /**< j1=Number of '*' */ + cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */ + cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 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 */ + strcpy(modelsav,model); + if (strstr(model,"AGE") !=0){ + printf("Error. AGE must be in lower case 'age' model=%s ",model); + fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog); + return 1; + } + if (strstr(model,"v") !=0){ + printf("Error. 'v' must be in upper case 'V' model=%s ",model); + fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); + return 1; + } + + /* Design + * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight + * < ncovcol=8 > + * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + * 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 + * 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 + * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11 + * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product + * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8 + * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2]; + * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted + * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 + * < ncovcol=8 > + * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2 + * k= 1 2 3 4 5 6 7 8 9 10 11 12 + * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8 + * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} + * p Tprod[1]@2={ 6, 5} + *p Tvard[1][1]@4= {7, 8, 5, 6} + * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8 + * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + *How to reorganize? + * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age + * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6} + * {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 */ + /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */ + /* k=3 V4 Tvar[k=3]= 4 (from V4) */ + /* k=2 V1 Tvar[k=2]= 1 (from V1) */ + /* k=1 Tvar[1]=2 (from V2) */ + /* k=5 Tvar[5] */ + /* for (k=1; k<=cptcovn;k++) { */ + /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */ + /* } */ + /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+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 */ + Tvar[k]=0; + cptcovage=0; + for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */ + cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' + modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ + /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ + /*scanf("%d",i);*/ + if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */ + cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ + if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */ + /* covar is not filled and then is empty */ + 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 */ + cptcovage++; /* Sums the number of covariates which include age as a product */ + Tage[cptcovage]=k; /* Tage[1] = 4 */ + /*printf("stre=%s ", stre);*/ + } else if (strcmp(strd,"age")==0) { /* or age*Vn */ + cptcovprod--; + cutl(stre,strb,strc,'V'); + Tvar[k]=atoi(stre); + cptcovage++; + Tage[cptcovage]=k; + } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/ + /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */ + 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 + because this model-covariate is a construction we invent a new column + ncovcol + 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 */ + 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) */ + 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 */ + covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; + } + } /* End age is not in the model */ + } /* End if model includes a product */ + else { /* no more sum */ + /*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++; + Tvar[k]=atoi(strd); + } + 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);*/ + } /* end of loop + */ + } /* end model */ + + /*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);*/ + + + return (0); /* with covar[new additional covariate if product] and Tage if age */ + endread: + printf("Exiting decodemodel: "); + return (1); +} + +calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) +{ + int i, m; + + for (i=1; i<=imx; i++) { + for(m=2; (m<= maxwav); m++) { + if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ + anint[m][i]=9999; + s[m][i]=-1; + } + if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ + *nberr++; + printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); + fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); + s[m][i]=-1; + } + if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ + *nberr++; + printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); + fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); + s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ + } + } + } + + for (i=1; i<=imx; i++) { + agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); + for(m=firstpass; (m<= lastpass); m++){ + if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ + if (s[m][i] >= nlstate+1) { + if(agedc[i]>0) + if((int)moisdc[i]!=99 && (int)andc[i]!=9999) + agev[m][i]=agedc[i]; + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + else { + if ((int)andc[i]!=9999){ + nbwarn++; + printf("Warning negative age at death: %ld line:%d\n",num[i],i); + fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); + agev[m][i]=-1; + } + } + } + else if(s[m][i] !=9){ /* Standard case, age in fractional + years but with the precision of a month */ + agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); + if((int)mint[m][i]==99 || (int)anint[m][i]==9999) + agev[m][i]=1; + else if(agev[m][i] < *agemin){ + *agemin=agev[m][i]; + printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin); + } + else if(agev[m][i] >*agemax){ + *agemax=agev[m][i]; + /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/ + } + /*agev[m][i]=anint[m][i]-annais[i];*/ + /* agev[m][i] = age[i]+2*m;*/ + } + else { /* =9 */ + agev[m][i]=1; + s[m][i]=-1; + } + } + else /*= 0 Unknown */ + agev[m][i]=1; + } + + } + for (i=1; i<=imx; i++) { + for(m=firstpass; (m<=lastpass); m++){ + if (s[m][i] > (nlstate+ndeath)) { + *nberr++; + printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); + fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); + return 1; + } + } + } + + /*for (i=1; i<=imx; i++){ + for (m=firstpass; (m1) cptcovn=nbocc(model,'+')+1; - /* where is ncovprod ?*/ - ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/ + covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */ + 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 + */ + if (strlen(model)>1) + ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/ + else + ncovmodel=2; nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ npar= nforce*ncovmodel; /* Number of parameters like aij*/ @@ -4693,13 +5561,13 @@ int main(int argc, char *argv[]) matcov=matrix(1,npar,1,npar); } else{ - /* Read guess parameters */ + /* Read guessed parameters */ /* Reads comments: lines beginning with '#' */ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; - puts(line); + fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); } @@ -4742,6 +5610,7 @@ run imach with mle=-1 to get a correct t } fflush(ficlog); + /* Reads scales values */ p=param[1][1]; /* Reads comments: lines beginning with '#' */ @@ -4749,7 +5618,7 @@ run imach with mle=-1 to get a correct t ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; - puts(line); + fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); } @@ -4768,462 +5637,162 @@ run imach with mle=-1 to get a correct t for(k=1; k<=ncovmodel;k++){ fscanf(ficpar,"%le",&delti3[i][j][k]); printf(" %le",delti3[i][j][k]); - fprintf(ficparo," %le",delti3[i][j][k]); - fprintf(ficlog," %le",delti3[i][j][k]); - } - fscanf(ficpar,"\n"); - numlinepar++; - printf("\n"); - fprintf(ficparo,"\n"); - fprintf(ficlog,"\n"); - } - } - fflush(ficlog); - - delti=delti3[1][1]; - - - /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ - - /* Reads comments: lines beginning with '#' */ - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - numlinepar++; - puts(line); - fputs(line,ficparo); - fputs(line,ficlog); - } - ungetc(c,ficpar); - - matcov=matrix(1,npar,1,npar); - for(i=1; i <=npar; i++) - for(j=1; j <=npar; j++) matcov[i][j]=0.; - - for(i=1; i <=npar; i++){ - fscanf(ficpar,"%s",&str); - if(mle==1) - printf("%s",str); - fprintf(ficlog,"%s",str); - fprintf(ficparo,"%s",str); - 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,"\n"); - numlinepar++; - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficparo,"\n"); - } - for(i=1; i <=npar; i++) - for(j=i+1;j<=npar;j++) - matcov[i][j]=matcov[j][i]; - - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - - fflush(ficlog); - - /*-------- Rewriting parameter file ----------*/ - strcpy(rfileres,"r"); /* "Rparameterfile */ - strcat(rfileres,optionfilefiname); /* Parameter file first name*/ - strcat(rfileres,"."); /* */ - strcat(rfileres,optionfilext); /* Other files have txt extension */ - if((ficres =fopen(rfileres,"w"))==NULL) { - printf("Problem writing new parameter file: %s\n", fileres);goto end; - fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; - } - fprintf(ficres,"#%s\n",version); - } /* End of mle != -3 */ - - /*-------- data file ----------*/ - if((fic=fopen(datafile,"r"))==NULL) { - printf("Problem while opening datafile: %s\n", datafile);goto end; - fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end; - } - - n= lastobs; - severity = vector(1,maxwav); - outcome=imatrix(1,maxwav+1,1,n); - num=lvector(1,n); - moisnais=vector(1,n); - annais=vector(1,n); - moisdc=vector(1,n); - andc=vector(1,n); - agedc=vector(1,n); - cod=ivector(1,n); - weight=vector(1,n); - for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ - mint=matrix(1,maxwav,1,n); - anint=matrix(1,maxwav,1,n); - s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ - tab=ivector(1,NCOVMAX); - ncodemax=ivector(1,8); - - i=1; - linei=0; - while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { - linei=linei+1; - for(j=strlen(line); j>=0;j--){ /* Untabifies line */ - if(line[j] == '\t') - line[j] = ' '; - } - for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ - ; - }; - line[j+1]=0; /* Trims blanks at end of line */ - if(line[0]=='#'){ - fprintf(ficlog,"Comment line\n%s\n",line); - printf("Comment line\n%s\n",line); - continue; - } - trimbb(linetmp,line); /* Trims multiple blanks in line */ - for (j=0; line[j]!='\0';j++){ - line[j]=linetmp[j]; - } - - - for (j=maxwav;j>=1;j--){ - cutv(stra, strb,line,' '); - if(strb[0]=='.') { /* Missing status */ - 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 %ld 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 %ld 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); - goto end; - } - } - s[j][i]=lval; - - strcpy(line,stra); - cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ - } - else if(iout=sscanf(strb,"%s.") != 0){ - month=99; - year=9999; - }else{ - printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j); - fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog); - goto end; - } - anint[j][i]= (double) year; - mint[j][i]= (double)month; - strcpy(line,stra); - } /* ENd Waves */ - - cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ - } - else if(iout=sscanf(strb,"%s.",dummy) != 0){ - month=99; - year=9999; - }else{ - printf("Error reading data around '%s' at line number %ld 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 %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); - goto end; - } - andc[i]=(double) year; - moisdc[i]=(double) month; - strcpy(line,stra); - - cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ - } - else if(iout=sscanf(strb,"%s.") != 0){ - month=99; - year=9999; - }else{ - printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j); - fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);fflush(ficlog); - goto end; - } - annais[i]=(double)(year); - moisnais[i]=(double)(month); - strcpy(line,stra); - - cutv(stra, strb,line,' '); - errno=0; - dval=strtod(strb,&endptr); - if( strb[0]=='\0' || (*endptr != '\0')){ - printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); - fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); - fflush(ficlog); - goto end; - } - weight[i]=dval; - strcpy(line,stra); - - for (j=ncovcol;j>=1;j--){ - cutv(stra, strb,line,' '); - if(strb[0]=='.') { /* Missing status */ - lval=-1; - }else{ - errno=0; - lval=strtol(strb,&endptr,10); - if( strb[0]=='\0' || (*endptr != '\0')){ - printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line); - fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog); - goto end; - } - } - if(lval <-1 || lval >1){ - printf("Error reading data around '%d' at line number %ld 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 '%d' at line number %ld 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); - goto end; - } - covar[j][i]=(double)(lval); - 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); - } - else - num[i]=atol(stra); - /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ - printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ - - i=i+1; - } /* End loop reading data */ - fclose(fic); - /* printf("ii=%d", ij); - scanf("%d",i);*/ - imx=i-1; /* Number of individuals */ - - /* for (i=1; i<=imx; i++){ - if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3; - if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3; - if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3; - }*/ - /* for (i=1; i<=imx; i++){ - if (s[4][i]==9) s[4][i]=-1; - printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ - - /* for (i=1; i<=imx; i++) */ - - /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08; - else weight[i]=1;*/ - - /* Calculation of the number of parameters from char model */ - Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ - Tprod=ivector(1,15); - Tvaraff=ivector(1,15); - Tvard=imatrix(1,15,1,2); - Tage=ivector(1,15); - - if (strlen(model) >1){ /* If there is at least 1 covariate */ - j=0, j1=0, k1=1, k2=1; - j=nbocc(model,'+'); /* j=Number of '+' */ - j1=nbocc(model,'*'); /* j1=Number of '*' */ - cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */ - cptcovprod=j1; /*Number of products V1*V2 =1 */ - - strcpy(modelsav,model); - if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){ - printf("Error. Non available option model=%s ",model); - fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog); - goto end; - } - - /* 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 */ - for(i=(j+1); i>=1;i--){ - cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' - modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 - stra=V2 - */ - if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ - /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ - /*scanf("%d",i);*/ - if (strchr(strb,'*')) { /* Model includes a product V1+V3*age+V2 strb=V3*age*/ - cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */ - if (strcmp(strc,"age")==0) { /* Vn*age */ - cptcovprod--; - cutv(strb,stre,strd,'V'); - Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */ - cptcovage++; /* Sums the number of covariates including age as a product */ - Tage[cptcovage]=i; /* Tage[1] =2 */ - /*printf("stre=%s ", stre);*/ - } - else if (strcmp(strd,"age")==0) { /* or age*Vn */ - cptcovprod--; - cutv(strb,stre,strc,'V'); - Tvar[i]=atoi(stre); - cptcovage++; - Tage[cptcovage]=i; - } - else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/ - cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/ - Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar. - If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */ - cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */ - Tprod[k1]=i; /* Tprod[1] */ - Tvard[k1][1]=atoi(strc); /* m*/ - Tvard[k1][2]=atoi(stre); /* n */ - Tvar[cptcovn+k2]=Tvard[k1][1]; - Tvar[cptcovn+k2+1]=Tvard[k1][2]; - for (k=1; k<=lastobs;k++) - covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k]; - k1++; - k2=k2+2; + fprintf(ficparo," %le",delti3[i][j][k]); + fprintf(ficlog," %le",delti3[i][j][k]); } + fscanf(ficpar,"\n"); + numlinepar++; + printf("\n"); + fprintf(ficparo,"\n"); + fprintf(ficlog,"\n"); } - else { /* no more sum */ - /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/ - /* scanf("%d",i);*/ - cutv(strd,strc,strb,'V'); - Tvar[i]=atoi(strc); - } - strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ - /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav); - scanf("%d",i);*/ - } /* end of loop + */ - } /* end model */ - - /*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); + } + fflush(ficlog); - scanf("%d ",i);*/ + /* Reads covariance matrix */ + delti=delti3[1][1]; - /* if(mle==1){*/ - if (weightopt != 1) { /* Maximisation without weights*/ - for(i=1;i<=n;i++) weight[i]=1.0; - } - /*-calculation of age at interview from date of interview and age at death -*/ - agev=matrix(1,maxwav,1,imx); - for (i=1; i<=imx; i++) { - for(m=2; (m<= maxwav); m++) { - if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){ - anint[m][i]=9999; - s[m][i]=-1; - } - if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){ - nberr++; - printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); - fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i); - s[m][i]=-1; - } - if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ - nberr++; - printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); - fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); - s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */ - } + /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ + + /* Reads comments: lines beginning with '#' */ + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + numlinepar++; + fputs(line,stdout); + fputs(line,ficparo); + fputs(line,ficlog); } - } - - for (i=1; i<=imx; i++) { - agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); - for(m=firstpass; (m<= lastpass); m++){ - if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ - if (s[m][i] >= nlstate+1) { - if(agedc[i]>0) - if((int)moisdc[i]!=99 && (int)andc[i]!=9999) - agev[m][i]=agedc[i]; - /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ - else { - if ((int)andc[i]!=9999){ - nbwarn++; - printf("Warning negative age at death: %ld line:%d\n",num[i],i); - fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i); - agev[m][i]=-1; - } - } - } - else if(s[m][i] !=9){ /* Standard case, age in fractional - years but with the precision of a month */ - agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); - if((int)mint[m][i]==99 || (int)anint[m][i]==9999) - agev[m][i]=1; - else if(agev[m][i] agemax){ - agemax=agev[m][i]; - /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ - } - /*agev[m][i]=anint[m][i]-annais[i];*/ - /* agev[m][i] = age[i]+2*m;*/ - } - else { /* =9 */ - agev[m][i]=1; - s[m][i]=-1; + ungetc(c,ficpar); + + matcov=matrix(1,npar,1,npar); + for(i=1; i <=npar; i++) + for(j=1; j <=npar; j++) matcov[i][j]=0.; + + for(i=1; i <=npar; i++){ + fscanf(ficpar,"%s",str); + if(mle==1) + printf("%s",str); + fprintf(ficlog,"%s",str); + fprintf(ficparo,"%s",str); + 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]); } - else /*= 0 Unknown */ - agev[m][i]=1; + fscanf(ficpar,"\n"); + numlinepar++; + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficparo,"\n"); } + for(i=1; i <=npar; i++) + for(j=i+1;j<=npar;j++) + matcov[i][j]=matcov[j][i]; - } - for (i=1; i<=imx; i++) { - for(m=firstpass; (m<=lastpass); m++){ - if (s[m][i] > (nlstate+ndeath)) { - nberr++; - printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); - fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); - goto end; - } + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + + fflush(ficlog); + + /*-------- Rewriting parameter file ----------*/ + strcpy(rfileres,"r"); /* "Rparameterfile */ + strcat(rfileres,optionfilefiname); /* Parameter file first name*/ + strcat(rfileres,"."); /* */ + strcat(rfileres,optionfilext); /* Other files have txt extension */ + if((ficres =fopen(rfileres,"w"))==NULL) { + printf("Problem writing new parameter file: %s\n", fileres);goto end; + fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; } - } + fprintf(ficres,"#%s\n",version); + } /* End of mle != -3 */ - /*for (i=1; i<=imx; i++){ - for (m=firstpass; (m16 */ + + /* Reads data from file datafile */ + if (readdata(datafile, firstobs, lastobs, &imx)==1) + goto end; + + /* Calculation of the number of parameters from char model */ + /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 + k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4 + k=3 V4 Tvar[k=3]= 4 (from V4) + k=2 V1 Tvar[k=2]= 1 (from V1) + k=1 Tvar[1]=2 (from V2) + */ + Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */ + /* 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. + */ + /* 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 + If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 + Tvar[3=V1*V4]=4+1 etc */ + Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */ + /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 + if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) + */ + Tvaraff=ivector(1,NCOVMAX); /* Unclear */ + Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm + * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. + * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ + Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age + 4 covariates (3 plus signs) + Tage[1=V3*age]= 4; Tage[2=age*V4] = 3 + */ + + if(decodemodel(model, lastobs) == 1) + goto end; + if((double)(lastobs-imx)/(double)imx > 1.10){ + nbwarn++; + printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); + fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx); + } + /* if(mle==1){*/ + if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/ + for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */ + } + + /*-calculation of age at interview from date of interview and age at death -*/ + agev=matrix(1,maxwav,1,imx); + + if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1) + goto end; - printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); - fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); agegomp=(int)agemin; - free_vector(severity,1,maxwav); - free_imatrix(outcome,1,maxwav+1,1,n); free_vector(moisnais,1,n); free_vector(annais,1,n); /* free_matrix(mint,1,maxwav,1,n); free_matrix(anint,1,maxwav,1,n);*/ free_vector(moisdc,1,n); free_vector(andc,1,n); - - + /* */ + wav=ivector(1,imx); dh=imatrix(1,lastpass-firstpass+1,1,imx); bh=imatrix(1,lastpass-firstpass+1,1,imx); @@ -5231,25 +5800,55 @@ run imach with mle=-1 to get a correct t /* Concatenates waves */ concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); - + /* */ + /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); ncodemax[1]=1; - if (cptcovn > 0) tricode(Tvar,nbcode,imx); - - codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of - the estimations*/ + Ndum =ivector(-1,NCOVMAX); + if (ncovmodel > 2) + tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ + + codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */ + /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/ h=0; + + + /*if (cptcovn > 0) */ + + m=pow(2,cptcoveff); for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */ - for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ - for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */ - for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ + for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ + for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/ + for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ h++; if (h>m) - h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j; + h=1; + /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 + * h 1 2 3 4 + *______________________________ + * 1 i=1 1 i=1 1 i=1 1 i=1 1 + * 2 2 1 1 1 + * 3 i=2 1 2 1 1 + * 4 2 2 1 1 + * 5 i=3 1 i=2 1 2 1 + * 6 2 1 2 1 + * 7 i=4 1 2 2 1 + * 8 2 2 2 1 + * 9 i=5 1 i=3 1 i=2 1 1 + * 10 2 1 1 1 + * 11 i=6 1 2 1 1 + * 12 2 2 1 1 + * 13 i=7 1 i=4 1 2 1 + * 14 2 1 2 1 + * 15 i=8 1 2 2 1 + * 16 2 2 2 1 + */ + codtab[h][k]=j; + /*codtab[h][Tvar[k]]=j;*/ printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); } } @@ -5264,6 +5863,10 @@ run imach with mle=-1 to get a correct t printf("\n"); } scanf("%d",i);*/ + + free_ivector(Ndum,-1,NCOVMAX); + + /*------------ gnuplot -------------*/ strcpy(optionfilegnuplot,optionfilefiname); @@ -5277,7 +5880,8 @@ run imach with mle=-1 to get a correct t else{ fprintf(ficgp,"\n# %s\n", version); fprintf(ficgp,"# %s\n", optionfilegnuplot); - fprintf(ficgp,"set missing 'NaNq'\n"); + //fprintf(ficgp,"set missing 'NaNq'\n"); + fprintf(ficgp,"set datafile missing 'NaNq'\n"); } /* fclose(ficgp);*/ /*--------- index.htm --------*/ @@ -5347,7 +5951,8 @@ Interval (in months) between two waves: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ if (mle==-3){ - ximort=matrix(1,NDIM,1,NDIM); + ximort=matrix(1,NDIM,1,NDIM); +/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ cens=ivector(1,n); ageexmed=vector(1,n); agecens=vector(1,n); @@ -5385,25 +5990,110 @@ Interval (in months) between two waves: ximort[i][j]=(i == j ? 1.0 : 0.0); } - p[1]=0.0268; p[NDIM]=0.083; + /*p[1]=0.0268; p[NDIM]=0.083;*/ /*printf("%lf %lf", p[1], p[2]);*/ +#ifdef GSL + printf("GSL optimization\n"); fprintf(ficlog,"Powell\n"); +#elsedef printf("Powell\n"); fprintf(ficlog,"Powell\n"); +#endif strcpy(filerespow,"pow-mort"); strcat(filerespow,fileres); if((ficrespow=fopen(filerespow,"w"))==NULL) { printf("Problem with resultfile: %s\n", filerespow); fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); } +#ifdef GSL + fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); +#elsedef fprintf(ficrespow,"# Powell\n# iter -2*LL"); +#endif /* for (i=1;i<=nlstate;i++) for(j=1;j<=nlstate+ndeath;j++) if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); */ fprintf(ficrespow,"\n"); +#ifdef GSL + /* gsl starts here */ + T = gsl_multimin_fminimizer_nmsimplex; + gsl_multimin_fminimizer *sfm = NULL; + gsl_vector *ss, *x; + gsl_multimin_function minex_func; + + /* Initial vertex size vector */ + ss = gsl_vector_alloc (NDIM); + + if (ss == NULL){ + GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0); + } + /* Set all step sizes to 1 */ + gsl_vector_set_all (ss, 0.001); + + /* Starting point */ + + x = gsl_vector_alloc (NDIM); + + if (x == NULL){ + gsl_vector_free(ss); + GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0); + } + + /* Initialize method and iterate */ + /* p[1]=0.0268; p[NDIM]=0.083; */ +/* gsl_vector_set(x, 0, 0.0268); */ +/* gsl_vector_set(x, 1, 0.083); */ + gsl_vector_set(x, 0, p[1]); + gsl_vector_set(x, 1, p[2]); + + minex_func.f = &gompertz_f; + minex_func.n = NDIM; + minex_func.params = (void *)&p; /* ??? */ + + sfm = gsl_multimin_fminimizer_alloc (T, NDIM); + gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss); + + printf("Iterations beginning .....\n\n"); + printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n"); + + iteri=0; + while (rval == GSL_CONTINUE){ + iteri++; + status = gsl_multimin_fminimizer_iterate(sfm); + + if (status) printf("error: %s\n", gsl_strerror (status)); + fflush(0); + + if (status) + break; + + rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6); + ssval = gsl_multimin_fminimizer_size (sfm); + + if (rval == GSL_SUCCESS) + printf ("converged to a local maximum at\n"); + + printf("%5d ", iteri); + for (it = 0; it < NDIM; it++){ + printf ("%10.5f ", gsl_vector_get (sfm->x, it)); + } + printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval); + } + + printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n"); - powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); + gsl_vector_free(x); /* initial values */ + gsl_vector_free(ss); /* inital step size */ + for (it=0; itx,it); + fprintf(ficrespow," %.12lf", p[it]); + } + gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */ +#endif +#ifdef POWELL + powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); +#endif fclose(ficrespow); hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); @@ -5464,6 +6154,12 @@ Interval (in months) between two waves: free_vector(lsurv,1,AGESUP); free_vector(lpop,1,AGESUP); free_vector(tpop,1,AGESUP); +#ifdef GSL + free_ivector(cens,1,n); + free_vector(agecens,1,n); + free_ivector(dcwave,1,n); + free_matrix(ximort,1,NDIM,1,NDIM); +#endif } /* Endof if mle==-3 */ else{ /* For mle >=1 */ @@ -5624,7 +6320,7 @@ Interval (in months) between two waves: while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); - puts(line); + fputs(line,stdout); fputs(line,ficparo); } ungetc(c,ficpar); @@ -5644,7 +6340,7 @@ Interval (in months) between two waves: while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); - puts(line); + fputs(line,stdout); fputs(line,ficparo); } ungetc(c,ficpar); @@ -5658,7 +6354,7 @@ Interval (in months) between two waves: while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); - puts(line); + fputs(line,stdout); fputs(line,ficparo); } ungetc(c,ficpar); @@ -5674,7 +6370,7 @@ Interval (in months) between two waves: while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); - puts(line); + fputs(line,stdout); fputs(line,ficparo); } ungetc(c,ficpar); @@ -5688,8 +6384,8 @@ Interval (in months) between two waves: - /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/ - /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ + /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */ + /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); @@ -5714,117 +6410,21 @@ Interval (in months) between two waves: /*--------------- Prevalence limit (period or stable prevalence) --------------*/ - - strcpy(filerespl,"pl"); - strcat(filerespl,fileres); - if((ficrespl=fopen(filerespl,"w"))==NULL) { - printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end; - fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end; - } - printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl); - fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl); - pstamp(ficrespl); - fprintf(ficrespl,"# Period (stable) prevalence \n"); - fprintf(ficrespl,"#Age "); - for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); - fprintf(ficrespl,"\n"); - - prlim=matrix(1,nlstate,1,nlstate); - - agebase=ageminpar; - agelim=agemaxpar; - ftolpl=1.e-10; - i1=cptcoveff; - if (cptcovn < 1){i1=1;} - - for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; - /* to clean */ - printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode); - fprintf(ficrespl,"\n#******"); - printf("\n#******"); - fprintf(ficlog,"\n#******"); - for(j=1;j<=cptcoveff;j++) { - fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - } - fprintf(ficrespl,"******\n"); - printf("******\n"); - fprintf(ficlog,"******\n"); - - for (age=agebase; age<=agelim; age++){ - prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); - fprintf(ficrespl,"%.0f ",age ); - for(j=1;j<=cptcoveff;j++) - fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - for(i=1; i<=nlstate;i++) - fprintf(ficrespl," %.5f", prlim[i][i]); - fprintf(ficrespl,"\n"); - } - } - } +#include "prevlim.h" /* Use ficrespl, ficlog */ fclose(ficrespl); - /*------------- h Pij x at various ages ------------*/ - - strcpy(filerespij,"pij"); strcat(filerespij,fileres); - if((ficrespij=fopen(filerespij,"w"))==NULL) { - printf("Problem with Pij resultfile: %s\n", filerespij);goto end; - fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end; - } - printf("Computing pij: result on file '%s' \n", filerespij); - fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij); - - stepsize=(int) (stepm+YEARM-1)/YEARM; - /*if (stepm<=24) stepsize=2;*/ - - agelim=AGESUP; - hstepm=stepsize*YEARM; /* Every year of age */ - hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ - - /* 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 "); - for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; - fprintf(ficrespij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficrespij,"******\n"); - - for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ - nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ - - /* nhstepm=nhstepm*YEARM; aff par mois*/ +#ifdef FREEEXIT2 +#include "freeexit2.h" +#endif - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate+ndeath;j++) - fprintf(ficrespij," %1d-%1d",i,j); - fprintf(ficrespij,"\n"); - for (h=0; h<=nhstepm; h++){ - fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate+ndeath;j++) - fprintf(ficrespij," %.5f", p3mat[i][j][h]); - fprintf(ficrespij,"\n"); - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - fprintf(ficrespij,"\n"); - } - } - } + /*------------- h Pij x at various ages ------------*/ +#include "hpijx.h" + fclose(ficrespij); + /*-------------- Variance of one-step probabilities---*/ + k=1; varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); - fclose(ficrespij); probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); for(i=1;i<=AGESUP;i++) @@ -5873,9 +6473,10 @@ Interval (in months) between two waves: } printf("Computing Health Expectancies: result on file '%s' \n", filerese); fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese); - for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; + /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ + + for (k=1; k <= (int) pow(2,cptcoveff); k++){ fprintf(ficreseij,"\n#****** "); for(j=1;j<=cptcoveff;j++) { fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); @@ -5887,7 +6488,7 @@ Interval (in months) between two waves: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); - } + /*}*/ } fclose(ficreseij); @@ -5932,10 +6533,11 @@ Interval (in months) between two waves: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); - for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; - fprintf(ficrest,"\n#****** "); + /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ + + for (k=1; k <= (int) pow(2,cptcoveff); k++){ + fprintf(ficrest,"\n#****** "); for(j=1;j<=cptcoveff;j++) fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); fprintf(ficrest,"******\n"); @@ -5957,12 +6559,18 @@ Interval (in months) between two waves: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); + /* + */ + /* goto endfree; */ vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); pstamp(ficrest); + + for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/ - oldm=oldms;savm=savms; - varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); + oldm=oldms;savm=savms; /* Segmentation fault */ + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); + fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are "); if(vpopbased==1) fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav); else @@ -6006,10 +6614,10 @@ Interval (in months) between two waves: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); free_vector(epj,1,nlstate+1); - } + /*}*/ } free_vector(weight,1,n); - free_imatrix(Tvard,1,15,1,2); + free_imatrix(Tvard,1,NCOVMAX,1,2); free_imatrix(s,1,maxwav+1,1,n); free_matrix(anint,1,maxwav,1,n); free_matrix(mint,1,maxwav,1,n); @@ -6031,10 +6639,11 @@ Interval (in months) between two waves: } printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl); - for(cptcov=1,k=0;cptcov<=i1;cptcov++){ - for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; - fprintf(ficresvpl,"\n#****** "); + /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/ + + for (k=1; k <= (int) pow(2,cptcoveff); k++){ + fprintf(ficresvpl,"\n#****** "); for(j=1;j<=cptcoveff;j++) fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); fprintf(ficresvpl,"******\n"); @@ -6043,7 +6652,7 @@ Interval (in months) between two waves: oldm=oldms;savm=savms; varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart); free_matrix(varpl,1,nlstate,(int) bage, (int)fage); - } + /*}*/ } fclose(ficresvpl); @@ -6051,10 +6660,9 @@ Interval (in months) between two waves: /*---------- End : free ----------------*/ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); - } /* mle==-3 arrives here for freeing */ endfree: - free_matrix(prlim,1,nlstate,1,nlstate); + free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); @@ -6066,11 +6674,11 @@ Interval (in months) between two waves: free_matrix(agev,1,maxwav,1,imx); free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); - free_ivector(ncodemax,1,8); - free_ivector(Tvar,1,15); - free_ivector(Tprod,1,15); - free_ivector(Tvaraff,1,15); - free_ivector(Tage,1,15); + free_ivector(ncodemax,1,NCOVMAX); + free_ivector(Tvar,1,NCOVMAX); + free_ivector(Tprod,1,NCOVMAX); + free_ivector(Tvaraff,1,NCOVMAX); + free_ivector(Tage,1,NCOVMAX); free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); free_imatrix(codtab,1,100,1,10); @@ -6087,17 +6695,18 @@ Interval (in months) between two waves: } printf("See log file on %s\n",filelog); /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */ - (void) gettimeofday(&end_time,&tzp); - tm = *localtime(&end_time.tv_sec); - tmg = *gmtime(&end_time.tv_sec); - strcpy(strtend,asctime(&tm)); + /*(void) gettimeofday(&end_time,&tzp);*/ + rend_time = time(NULL); + end_time = *localtime(&rend_time); + /* tml = *localtime(&end_time.tm_sec); */ + strcpy(strtend,asctime(&end_time)); printf("Local time at start %s\nLocal time at end %s",strstart, strtend); fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); - printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); + printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); - printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec); - fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); - fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec); + printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); + fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout)); + fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time)); /* printf("Total time was %d uSec.\n", total_usecs);*/ /* if(fileappend(fichtm,optionfilehtm)){ */ fprintf(fichtm,"
            Local time at start %s
            Local time at end %s
            \n",strstart, strtend); @@ -6116,19 +6725,19 @@ Interval (in months) between two waves: printf("Current directory %s!\n",pathcd); /*strcat(plotcmd,CHARSEPARATOR);*/ sprintf(plotcmd,"gnuplot"); -#ifndef UNIX +#ifdef _WIN32 sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); #endif if(!stat(plotcmd,&info)){ - printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); + printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); if(!stat(getenv("GNUPLOTBIN"),&info)){ - printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); + printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout); }else strcpy(pplotcmd,plotcmd); -#ifdef UNIX +#ifdef __unix strcpy(plotcmd,GNUPLOTPROGRAM); if(!stat(plotcmd,&info)){ - printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); + printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout); }else strcpy(pplotcmd,plotcmd); #endif @@ -6136,20 +6745,31 @@ Interval (in months) between two waves: strcpy(pplotcmd,plotcmd); sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); - printf("Starting graphs with: %s\n",plotcmd);fflush(stdout); + printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); if((outcmd=system(plotcmd)) != 0){ - printf("\n Problem with gnuplot\n"); + printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd); + printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); + sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); + if((outcmd=system(plotcmd)) != 0) + printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); } - printf(" Wait..."); + printf(" Successful, please wait..."); while (z[0] != 'q') { /* chdir(path); */ - printf("\nType e to edit output files, g to graph again and q for exiting: "); + printf("\nType e to edit results with your browser, g to graph again and q for exit: "); scanf("%s",z); /* if (z[0] == 'c') system("./imach"); */ if (z[0] == 'e') { - printf("Starting browser with: %s",optionfilehtm);fflush(stdout); - system(optionfilehtm); +#ifdef __APPLE__ + sprintf(pplotcmd, "open %s", optionfilehtm); +#elif __linux + sprintf(pplotcmd, "xdg-open %s", optionfilehtm); +#else + sprintf(pplotcmd, "%s", optionfilehtm); +#endif + printf("Starting browser with: %s",pplotcmd);fflush(stdout); + system(pplotcmd); } else if (z[0] == 'g') system(plotcmd); else if (z[0] == 'q') exit(0); @@ -6160,6 +6780,3 @@ Interval (in months) between two waves: scanf("%s",z); } } - - -