--- imach/src/imach.c 2010/06/14 07:50:17 1.139 +++ imach/src/imach.c 2015/04/30 08:27:53 1.188 @@ -1,6 +1,212 @@ -/* $Id: imach.c,v 1.139 2010/06/14 07:50:17 brouard Exp $ +/* $Id: imach.c,v 1.188 2015/04/30 08:27:53 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.188 2015/04/30 08:27:53 brouard + *** empty log message *** + + Revision 1.187 2015/04/29 09:11:15 brouard + *** empty log message *** + + Revision 1.186 2015/04/23 12:01:52 brouard + Summary: V1*age is working now, version 0.98q1 + + Some codes had been disabled in order to simplify and Vn*age was + working in the optimization phase, ie, giving correct MLE parameters, + but, as usual, outputs were not correct and program core dumped. + + Revision 1.185 2015/03/11 13:26:42 brouard + Summary: Inclusion of compile and links command line for Intel Compiler + + Revision 1.184 2015/03/11 11:52:39 brouard + Summary: Back from Windows 8. Intel Compiler + + Revision 1.183 2015/03/10 20:34:32 brouard + Summary: 0.98q0, trying with directest, mnbrak fixed + + We use directest instead of original Powell test; probably no + incidence on the results, but better justifications; + We fixed Numerical Recipes mnbrak routine which was wrong and gave + wrong results. + + Revision 1.182 2015/02/12 08:19:57 brouard + Summary: Trying to keep directest which seems simpler and more general + Author: Nicolas Brouard + + Revision 1.181 2015/02/11 23:22:24 brouard + Summary: Comments on Powell added + + Author: + + Revision 1.180 2015/02/11 17:33:45 brouard + Summary: Finishing move from main to function (hpijx and prevalence_limit) + + Revision 1.179 2015/01/04 09:57:06 brouard + Summary: back to OS/X + + Revision 1.178 2015/01/04 09:35:48 brouard + *** empty log message *** + + Revision 1.177 2015/01/03 18:40:56 brouard + Summary: Still testing ilc32 on OSX + + Revision 1.176 2015/01/03 16:45:04 brouard + *** empty log message *** + + Revision 1.175 2015/01/03 16:33:42 brouard + *** empty log message *** + + Revision 1.174 2015/01/03 16:15:49 brouard + Summary: Still in cross-compilation + + Revision 1.173 2015/01/03 12:06:26 brouard + Summary: trying to detect cross-compilation + + Revision 1.172 2014/12/27 12:07:47 brouard + Summary: Back from Visual Studio and Intel, options for compiling for Windows XP + + Revision 1.171 2014/12/23 13:26:59 brouard + Summary: Back from Visual C + + Still problem with utsname.h on Windows + + Revision 1.170 2014/12/23 11:17:12 brouard + Summary: Cleaning some \%% back to %% + + The escape was mandatory for a specific compiler (which one?), but too many warnings. + + Revision 1.169 2014/12/22 23:08:31 brouard + Summary: 0.98p + + Outputs some informations on compiler used, OS etc. Testing on different platforms. + + Revision 1.168 2014/12/22 15:17:42 brouard + Summary: update + + Revision 1.167 2014/12/22 13:50:56 brouard + Summary: Testing uname and compiler version and if compiled 32 or 64 + + Testing on Linux 64 + + Revision 1.166 2014/12/22 11:40:47 brouard + *** empty log message *** + + Revision 1.165 2014/12/16 11:20:36 brouard + Summary: After compiling on Visual C + + * imach.c (Module): Merging 1.61 to 1.162 + + Revision 1.164 2014/12/16 10:52:11 brouard + Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn + + * imach.c (Module): Merging 1.61 to 1.162 + + Revision 1.163 2014/12/16 10:30:11 brouard + * imach.c (Module): Merging 1.61 to 1.162 + + Revision 1.162 2014/09/25 11:43:39 brouard + Summary: temporary backup 0.99! + + Revision 1.1 2014/09/16 11:06:58 brouard + Summary: With some code (wrong) for nlopt + + Author: + + Revision 1.161 2014/09/15 20:41:41 brouard + Summary: Problem with macro SQR on Intel compiler + + 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. @@ -357,10 +563,22 @@ 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 @@ -373,34 +591,62 @@ end */ +/* #define DEBUG */ +/* #define DEBUGBRENT */ +#define POWELL /* Instead of NLOPT */ +/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */ +/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */ - - #include #include #include #include + +#ifdef _WIN32 +#include +#include +#include +#else #include +#endif #include #include + +#if defined(__GNUC__) +#include /* Doesn't work on Windows */ +#endif + #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 + +#ifdef NLOPT +#include +typedef struct { + double (* function)(double [] ); +} myfunc_data ; +#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"*/ @@ -409,38 +655,46 @@ 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 1.139 2010/06/14 07:50:17 brouard Exp $ */ +/* $Id: imach.c,v 1.188 2015/04/30 08:27:53 brouard Exp $ */ /* $State: Exp $ */ -char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite "; -char fullversion[]="$Revision: 1.139 $ $Date: 2010/06/14 07:50:17 $"; +char version[]="Imach version 0.98q1, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015"; +char fullversion[]="$Revision: 1.188 $ $Date: 2015/04/30 08:27:53 $"; 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' */ +int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */ +/* 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 */ @@ -458,7 +712,9 @@ int **mw; /* mw[mi][i] is number of the int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ 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. */ +int countcallfunc=0; /* Count the number of calls to func */ 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 ; */ /* Used in readdata only */ @@ -500,12 +756,17 @@ 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; @@ -535,7 +796,12 @@ static double maxarg1,maxarg2; #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a)) #define rint(a) floor(a+0.5) - +/* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */ +#define mytinydouble 1.0e-16 +/* #define DEQUAL(a,b) (fabs((a)-(b)) 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 ) @@ -572,7 +845,7 @@ static int split( char *path, char *dirc the name of the file (name), its extension only (ext) and its first part of the name (finame) */ char *ss; /* pointer */ - int l1, l2; /* length counters */ + int l1=0, l2=0; /* length counters */ l1 = strlen(path ); /* length of path */ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); @@ -583,7 +856,11 @@ static int split( char *path, char *dirc printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ /* get current working directory */ /* extern char* getcwd ( char *buf , int len);*/ - if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { +#ifdef WIN32 + if (_getcwd( dirc, FILENAME_MAX ) == NULL ) { +#else + if (getcwd(dirc, FILENAME_MAX) == NULL) { +#endif return( GLOCK_ERROR_GETCWD ); } /* got dirc from getcwd*/ @@ -594,7 +871,7 @@ static int split( char *path, char *dirc if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); strcpy( name, ss ); /* save file name */ strncpy( dirc, path, l1 - l2 ); /* now the directory */ - dirc[l1-l2] = 0; /* add zero */ + dirc[l1-l2] = '\0'; /* add zero */ printf(" DIRC2 = %s \n",dirc); } /* We add a separator at the end of dirc if not exists */ @@ -646,9 +923,80 @@ char *trimbb(char *out, char *in) return s; } +/* char *substrchaine(char *out, char *in, char *chain) */ +/* { */ +/* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */ +/* char *s, *t; */ +/* t=in;s=out; */ +/* while ((*in != *chain) && (*in != '\0')){ */ +/* *out++ = *in++; */ +/* } */ + +/* /\* *in matches *chain *\/ */ +/* while ((*in++ == *chain++) && (*in != '\0')){ */ +/* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ +/* } */ +/* in--; chain--; */ +/* while ( (*in != '\0')){ */ +/* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ +/* *out++ = *in++; */ +/* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */ +/* } */ +/* *out='\0'; */ +/* out=s; */ +/* return out; */ +/* } */ +char *substrchaine(char *out, char *in, char *chain) +{ + /* Substract chain 'chain' from 'in', return and output 'out' */ + /* in="V1+V1*age+age*age+V2", chain="age*age" */ + + char *strloc; + + strcpy (out, in); + strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */ + printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); + if(strloc != NULL){ + /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */ + memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); + /* strcpy (strloc, strloc +strlen(chain));*/ + } + printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); + return out; +} + + +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="abcdef" and alocc="ghi2j". + 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' + /* 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 @@ -709,6 +1057,24 @@ int nbocc(char *s, char occ) /* } */ /* } */ +#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 ********************/ void nrerror(char error_text[]) @@ -816,7 +1182,9 @@ 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. */ } @@ -906,6 +1274,19 @@ char *subdirf3(char fileres[], char *pre return tmpout; } +char *asc_diff_time(long time_sec, char ascdiff[]) +{ + long sec_left, days, hours, minutes; + days = (time_sec) / (60*60*24); + sec_left = (time_sec) % (60*60*24); + hours = (sec_left) / (60*60) ; + sec_left = (sec_left) %(60*60); + minutes = (sec_left) /60; + sec_left = (sec_left) % (60); + sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); + return ascdiff; +} + /***************** f1dim *************************/ extern int ncom; extern double *pcom,*xicom; @@ -926,11 +1307,17 @@ double f1dim(double x) /*****************brent *************************/ double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) -{ +{ + /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is + * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates + * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of + * the minimum is returned as xmin, and the minimum function value is returned as brent , the + * returned function value. + */ int iter; double a,b,d,etemp; - double fu,fv,fw,fx; - double ftemp; + double fu=0,fv,fw,fx; + double ftemp=0.; double p,q,r,tol1,tol2,u,v,w,x,xm; double e=0.0; @@ -944,7 +1331,7 @@ double brent(double ax, double bx, doubl /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/ printf(".");fflush(stdout); fprintf(ficlog,".");fflush(ficlog); -#ifdef DEBUG +#ifdef DEBUGBRENT printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol); /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */ @@ -979,19 +1366,19 @@ double brent(double ax, double bx, doubl if (fu <= fx) { if (u >= x) a=x; else b=x; SHFT(v,w,x,u) - SHFT(fv,fw,fx,fu) - } else { - if (u < x) a=u; else b=u; - if (fu <= fw || w == x) { - v=w; - w=u; - fv=fw; - fw=fu; - } else if (fu <= fv || v == x || v == w) { - v=u; - fv=fu; - } - } + SHFT(fv,fw,fx,fu) + } else { + if (u < x) a=u; else b=u; + if (fu <= fw || w == x) { + v=w; + w=u; + fv=fw; + fw=fu; + } else if (fu <= fv || v == x || v == w) { + v=u; + fv=fu; + } + } } nrerror("Too many iterations in brent"); *xmin=x; @@ -1002,46 +1389,129 @@ double brent(double ax, double bx, doubl void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, double (*func)(double)) -{ +{ /* Given a function func , and given distinct initial points ax and bx , this routine searches in +the downhill direction (defined by the function as evaluated at the initial points) and returns +new points ax , bx , cx that bracket a minimum of the function. Also returned are the function +values at the three points, fa, fb , and fc such that fa > fb and fb < fc. + */ double ulim,u,r,q, dum; double fu; - - *fa=(*func)(*ax); - *fb=(*func)(*bx); + + double scale=10.; + int iterscale=0; + + *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/ + *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */ + + + /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */ + /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */ + /* *bx = *ax - (*ax - *bx)/scale; */ + /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */ + /* } */ + if (*fb > *fa) { SHFT(dum,*ax,*bx,dum) - SHFT(dum,*fb,*fa,dum) - } + SHFT(dum,*fb,*fa,dum) + } *cx=(*bx)+GOLD*(*bx-*ax); *fc=(*func)(*cx); - while (*fb > *fc) { +#ifdef DEBUG + printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); + fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc); +#endif + while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */ r=(*bx-*ax)*(*fb-*fc); q=(*bx-*cx)*(*fb-*fa); u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ - (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); - ulim=(*bx)+GLIMIT*(*cx-*bx); - if ((*bx-u)*(u-*cx) > 0.0) { + (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */ + ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */ + if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */ fu=(*func)(u); - } else if ((*cx-u)*(u-ulim) > 0.0) { +#ifdef DEBUG + /* f(x)=A(x-u)**2+f(u) */ + double A, fparabu; + A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u); + fparabu= *fa - A*(*ax-u)*(*ax-u); + printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); + fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu); + /* And thus,it can be that fu > *fc even if fparabu < *fc */ + /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489), + (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */ + /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/ +#endif +#ifdef MNBRAKORIGINAL +#else + if (fu > *fc) { +#ifdef DEBUG + printf("mnbrak4 fu > fc \n"); + fprintf(ficlog, "mnbrak4 fu > fc\n"); +#endif + /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/ */ + /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\/ */ + dum=u; /* Shifting c and u */ + u = *cx; + *cx = dum; + dum = fu; + fu = *fc; + *fc =dum; + } else { /* end */ +#ifdef DEBUG + printf("mnbrak3 fu < fc \n"); + fprintf(ficlog, "mnbrak3 fu < fc\n"); +#endif + dum=u; /* Shifting c and u */ + u = *cx; + *cx = dum; + dum = fu; + fu = *fc; + *fc =dum; + } +#endif + } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */ +#ifdef DEBUG + printf("mnbrak2 u after c but before ulim\n"); + fprintf(ficlog, "mnbrak2 u after c but before ulim\n"); +#endif fu=(*func)(u); if (fu < *fc) { +#ifdef DEBUG + printf("mnbrak2 u after c but before ulim AND fu < fc\n"); + fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu = 0.0) { + SHFT(*fb,*fc,fu,(*func)(u)) + } + } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */ +#ifdef DEBUG + printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); + fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n"); +#endif u=ulim; fu=(*func)(u); - } else { + } else { /* u could be left to b (if r > q parabola has a maximum) */ +#ifdef DEBUG + printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); + fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n"); +#endif u=(*cx)+GOLD*(*cx-*bx); fu=(*func)(u); - } + } /* end tests */ SHFT(*ax,*bx,*cx,u) - SHFT(*fa,*fb,*fc,fu) - } + SHFT(*fa,*fb,*fc,fu) +#ifdef DEBUG + printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); + fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu); +#endif + } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */ } /*************** linmin ************************/ - +/* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and +resets p to where the function func(p) takes on a minimum along the direction xi from p , +and replaces xi by the actual vector displacement that p was moved. Also returns as fret +the value of func at the returned location p . This is actually all accomplished by calling the +routines mnbrak and brent .*/ int ncom; double *pcom,*xicom; double (*nrfunc)(double []); @@ -1056,6 +1526,8 @@ void linmin(double p[], double xi[], int int j; double xx,xmin,bx,ax; double fx,fb,fa; + + double scale=10., axs, xxs, xxss; /* Scale added for infinity */ ncom=n; pcom=vector(1,n); @@ -1065,36 +1537,59 @@ void linmin(double p[], double xi[], int pcom[j]=p[j]; xicom[j]=xi[j]; } - ax=0.0; - xx=1.0; - mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); - *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); + + axs=0.0; + xxss=1; /* 1 and using scale */ + xxs=1; + do{ + ax=0.; + xx= xxs; + mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */ + /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */ + /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */ + /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */ + /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */ + /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */ + /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/ + if (fx != fx){ + xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */ + printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); + } + }while(fx != fx); + + *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/ + /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */ + /* fmin = f(p[j] + xmin * xi[j]) */ + /* P+lambda n in that direction (lambdamin), with TOL between abscisses */ + /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */ #ifdef DEBUG printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin); #endif + printf("linmin end "); for (j=1;j<=n;j++) { - xi[j] *= xmin; - p[j] += xi[j]; + /* printf(" before xi[%d]=%12.8f", j,xi[j]); */ + xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */ + if(xxs <1.0) + printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); + p[j] += xi[j]; /* Parameters values are updated accordingly */ } + printf("\n"); + printf("Comparing last *frec(xmin)=%12.8f from Brent and frec(0.)=%12.8f \n", (*func)(p)); free_vector(xicom,1,n); free_vector(pcom,1,n); } -char *asc_diff_time(long time_sec, char ascdiff[]) -{ - long sec_left, days, hours, minutes; - days = (time_sec) / (60*60*24); - sec_left = (time_sec) % (60*60*24); - hours = (sec_left) / (60*60) ; - 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); - return ascdiff; -} /*************** powell ************************/ +/* +Minimization of a function func of n variables. Input consists of an initial starting point +p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di- +rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value +such that failure to decrease by more than this amount on one iteration signals doneness. On +output, p is set to the best point found, xi is the then-current direction set, fret is the returned +function value at p , and iter is the number of iterations taken. The routine linmin is used. + */ void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, double (*func)(double [])) { @@ -1102,6 +1597,7 @@ void powell(double p[], double **xi, int double (*func)(double [])); int i,ibig,j; double del,t,*pt,*ptt,*xit; + double directest; double fp,fptt; double *xits; int niterf, itmp; @@ -1112,15 +1608,18 @@ 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); + fp=(*fret); /* From former iteration or initial value */ 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]); @@ -1130,38 +1629,41 @@ 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)); -/* asctime_r(&tm,strcurr); */ - forecast_time=curr_time; + tml = *localtime(&rcurr_time); + strcpy(strcurr,asctime(&tml)); + rforecast_time=rcurr_time; itmp = strlen(strcurr); if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ strcurr[itmp-1]='\0'; - 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 the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); + fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time); for(niterf=10;niterf<=30;niterf+=10){ - forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec); - tmf = *localtime(&forecast_time.tv_sec); -/* asctime_r(&tmf,strfor); */ - strcpy(strfor,asctime(&tmf)); + rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); + forecast_time = *localtime(&rforecast_time); + strcpy(strfor,asctime(&forecast_time)); itmp = strlen(strfor); if(strfor[itmp-1]=='\n') strfor[itmp-1]='\0'; - printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(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++) { - for (j=1;j<=n;j++) xit[j]=xi[j][i]; + for (i=1;i<=n;i++) { /* For each direction i */ + for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */ fptt=(*fret); #ifdef DEBUG - printf("fret=%lf \n",*fret); - fprintf(ficlog,"fret=%lf \n",*fret); + printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret); + fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret); #endif - printf("%d",i);fflush(stdout); + printf("%d",i);fflush(stdout); /* print direction (parameter) i */ fprintf(ficlog,"%d",i);fflush(ficlog); - linmin(p,xit,n,fret,func); - if (fabs(fptt-(*fret)) > del) { + linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/ + /* Outputs are fret(new point p) p is updated and xit rescaled */ + if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */ + /* because that direction will be replaced unless the gain del is small */ + /* in comparison with the 'probable' gain, mu^2, with the last average direction. */ + /* Unless the n directions are conjugate some gain in the determinant may be obtained */ + /* with the new direction. */ del=fabs(fptt-(*fret)); ibig=i; } @@ -1174,14 +1676,29 @@ void powell(double p[], double **xi, int fprintf(ficlog," x(%d)=%.12e",j,xit[j]); } for(j=1;j<=n;j++) { - printf(" p=%.12e",p[j]); - fprintf(ficlog," p=%.12e",p[j]); + printf(" p(%d)=%.12e",j,p[j]); + fprintf(ficlog," p(%d)=%.12e",j,p[j]); } printf("\n"); fprintf(ficlog,"\n"); #endif - } - if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { + } /* end loop on each direction i */ + /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */ + /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */ + /* New value of last point Pn is not computed, P(n-1) */ + if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */ + /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */ + /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */ + /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */ + /* decreased of more than 3.84 */ + /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */ + /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */ + /* By adding 10 parameters more the gain should be 18.31 */ + + /* Starting the program with initial values given by a former maximization will simply change */ + /* the scales of the directions and the directions, because the are reset to canonical directions */ + /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */ + /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */ #ifdef DEBUG int k[2],l; k[0]=1; @@ -1213,20 +1730,56 @@ void powell(double p[], double **xi, int return; } if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); - for (j=1;j<=n;j++) { + for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */ ptt[j]=2.0*p[j]-pt[j]; xit[j]=p[j]-pt[j]; pt[j]=p[j]; } - fptt=(*func)(ptt); - if (fptt < fp) { - t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); - if (t < 0.0) { - linmin(p,xit,n,fret,func); + fptt=(*func)(ptt); /* f_3 */ + if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */ + /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */ + /* From x1 (P0) distance of x2 is at h and x3 is 2h */ + /* Let f"(x2) be the 2nd derivative equal everywhere. */ + /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */ + /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */ + /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */ + /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */ +#ifdef NRCORIGINAL + t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/ +#else + t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */ + t= t- del*SQR(fp-fptt); +#endif + directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */ +#ifdef DEBUG + printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); + fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest); + printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), + (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); + fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt), + (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt)); + printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t); + fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t); +#endif +#ifdef POWELLORIGINAL + if (t < 0.0) { /* Then we use it for new direction */ +#else + if (directest*t < 0.0) { /* Contradiction between both tests */ + printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del); + printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); + fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del); + fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt); + } + if (directest < 0.0) { /* Then we use it for new direction */ +#endif + linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/ for (j=1;j<=n;j++) { - xi[j][ibig]=xi[j][n]; - xi[j][n]=xit[j]; + xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */ + xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */ } + printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); + fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig); + #ifdef DEBUG printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig); @@ -1237,8 +1790,8 @@ void powell(double p[], double **xi, int printf("\n"); fprintf(ficlog,"\n"); #endif - } - } + } /* end of t negative */ + } /* end if (fptt < fp) */ } } @@ -1248,39 +1801,43 @@ double **prevalim(double **prlim, int nl { /* Computes the prevalence limit in each live state at age x by left multiplying the unit matrix by transitions matrix until convergence is reached */ - + 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 */ - + for (ii=1;ii<=nlstate+ndeath;ii++) for (j=1;j<=nlstate+ndeath;j++){ oldm[ii][j]=(ii==j ? 1.0 : 0.0); } - - cov[1]=1.; - - /* Even if hstepm = 1, at least one multiplication by the unit matrix */ + + cov[1]=1.; + + /* Even if hstepm = 1, at least one multiplication by the unit matrix */ for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){ newm=savm; /* Covariates have to be included here again */ cov[2]=agefin; - + if(nagesqr==1) + cov[3]= agefin*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]]);*/ + cov[2+nagesqr+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++) - cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; + /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ + for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2]; + for (k=1; k<=cptcovprod;k++) /* Useless */ + cov[2+nagesqr+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); + /* 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; @@ -1292,16 +1849,18 @@ 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]); } maxmin=max-min; maxmax=FMAX(maxmax,maxmin); - } + } /* j loop */ if(maxmax < ftolpl){ return prlim; } - } + } /* age loop */ + return prlim; /* should not reach here */ } /*************** transition probabilities ***************/ @@ -1323,7 +1882,7 @@ double **pmij(double **ps, double *cov, */ double s1, lnpijopii; /*double t34;*/ - int i,j,j1, nc, ii, jj; + int i,j, nc, ii, jj; for(i=1; i<= nlstate; i++){ for(j=1; jfunction)(xt); /* p xt[1]@8 is fine */ + /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */ + printf("Function = %.12lf ",fret); + for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); + printf("\n"); + free_vector(xt,1,n); + return fret; +} +#endif /*************** log-likelihood *************/ double func( double *x) @@ -1476,12 +2060,16 @@ double func( double *x) int s1, s2; double bbh, survp; long ipmx; + double agexact; /*extern weight */ /* We are differentiating ll according to initial status */ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/ /*for(i=1;ifunction = func; + printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d)); + nlopt_set_min_objective(opt, myfunc, d); + nlopt_set_xtol_rel(opt, ftol); + if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) { + printf("nlopt failed! %d\n",creturn); + } + else { + printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT); + printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf); + iter=1; /* not equal */ + } + nlopt_destroy(opt); +#endif free_matrix(xi,1,npar,1,npar); fclose(ficrespow); - printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); - fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); - fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); + printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); + fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); + fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p)); } @@ -1895,7 +2570,7 @@ void hesscov(double **matcov, double p[] { double **a,**y,*x,pd; double **hess; - int i, j,jk; + int i, j; int *indx; double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar); @@ -2008,13 +2683,13 @@ 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 khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */ - k=kmax; l=lmax*10.; + k=kmax; l=lmax*10; } else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ delts=delt; @@ -2044,7 +2719,7 @@ double hessii(double x[], double delta, double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) { int i; - int l=1, l1, lmax=20; + int l=1, lmax=20; double k1,k2,k3,k4,res,fx; double p2[MAXPARM+1]; int k; @@ -2159,7 +2834,7 @@ void pstamp(FILE *fichier) void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[]) { /* Some frequencies */ - int i, m, jk, k1,i1, j1, bool, z1,j; + int i, m, jk, j1, bool, z1,j; int first; double ***freq; /* Frequencies */ double *pp, **prop; @@ -2183,29 +2858,37 @@ void freqsummary(char fileres[], int ia first=1; - for(k1=1; k1<=j;k1++){ - for(i1=1; i1<=ncodemax[k1];i1++){ - j1++; + /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */ + /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */ + /* j1++; */ + for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); scanf("%d", i);*/ for (i=-5; i<=nlstate+ndeath; i++) for (jk=-5; jk<=nlstate+ndeath; jk++) for(m=iagemin; m <= iagemax+3; m++) freq[i][jk][m]=0; - - for (i=1; i<=nlstate; i++) - for(m=iagemin; m <= iagemax+3; m++) - prop[i][m]=0; + + for (i=1; i<=nlstate; i++) + for(m=iagemin; m <= iagemax+3; m++) + prop[i][m]=0; dateintsum=0; k2cpt=0; for (i=1; i<=imx; i++) { bool=1; - if (cptcovn>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.); @@ -2225,7 +2908,7 @@ 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); @@ -2233,6 +2916,9 @@ 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); @@ -2309,7 +2995,7 @@ void freqsummary(char fileres[], int ia printf("Others in log...\n"); fprintf(ficlog,"\n"); } - } + /*}*/ } dateintmean=dateintsum/k2cpt; @@ -2328,12 +3014,13 @@ void prevalence(double ***probs, double We still use firstpass and lastpass as another selection. */ - int i, m, jk, k1, i1, j1, bool, z1,j; - double ***freq; /* Frequencies */ - double *pp, **prop; - double pos,posprop; + int i, m, jk, j1, bool, z1,j; + + double **prop; + double 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; @@ -2342,12 +3029,13 @@ 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++) @@ -2377,22 +3065,25 @@ 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);*/ @@ -2417,7 +3108,7 @@ void concatwav(int wav[], int **dh, int int j, k=0,jk, ju, jl; double sum=0.; first=0; - jmin=1e+5; + jmin=100000; jmax=-1; jmean=0.; for(i=1; i<=imx; i++){ @@ -2538,49 +3229,86 @@ 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) { - /* 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 */ + /**< 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 Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; + int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX; int modmaxcovj=0; /* Modality max of covariates j */ + int cptcode=0; /* Modality max of covariates j */ + int modmincovj=0; /* Modality min of covariates j */ + + cptcoveff=0; - 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 > modmaxcovj) modmaxcovj=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 coded 0 and female is 1, then modmaxcovj=1.*/ - } + } /* end for loop on individuals */ + 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<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */ - if( Ndum[i] != 0 ) - ncodemax[j]++; - /* Number of modalities of the j th covariate. In fact - ncodemax[j]=2 (dichotom. variables only) but it could be more for - historical reasons */ + /*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 ie V%d with value %d: %d\n", j, Tvar[j], i, 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 */ /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */ - ij=1; - for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */ - for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */ + /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. + If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; + modmincovj=3; modmaxcovj = 7; + There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; + which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; + defining two dummy variables: variables V1_1 and V1_2. + nbcode[Tvar[j]][ij]=k; + nbcode[Tvar[j]][1]=0; + nbcode[Tvar[j]][2]=1; + nbcode[Tvar[j]][3]=2; + */ + 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. + nbcode[Tvar[j]][ij]=k; /* stores the modality k in an array nbcode. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ ij++; @@ -2590,32 +3318,37 @@ void tricode(int *Tvar, int **nbcode, in } /* 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=0; k< maxncov; k++) Ndum[k]=0; + 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]++; - } + for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ + /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ + ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ + Ndum[ij]++; /* Might be supersed V1 + V1*age */ + } ij=1; - for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */ + 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[] ) { /* Health expectancies, no variances */ - int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2; + int i, j, nhstepm, hstepm, h, nstepm; int nhstepma, nstepma; /* Decreasing with age */ double age, agelim, hf; double ***p3mat; @@ -2934,10 +3667,13 @@ void varevsij(char optionfilefiname[], d /* Variance of health expectancies */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ /* double **newm;*/ + /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/ + + int movingaverage(); double **dnewm,**doldm; double **dnewmp,**doldmp; int i, j, nhstepm, hstepm, h, nstepm ; - int k, cptcode; + int k; double *xp; double **gp, **gm; /* for var eij */ double ***gradg, ***trgradg; /*for var eij */ @@ -3204,15 +3940,15 @@ 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); @@ -3237,10 +3973,9 @@ void varprevlim(char fileres[], double * { /* Variance of prevalence limit */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ - double **newm; + double **dnewm,**doldm; int i, j, nhstepm, hstepm; - int k, cptcode; double *xp; double *gp, *gm; double **gradg, **trgradg; @@ -3319,23 +4054,22 @@ void varprevlim(char fileres[], double * /************ Variance of one-step probabilities ******************/ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[]) { - int i, j=0, i1, k1, l1, t, tj; + int i, j=0, k1, l1, tj; int k2, l2, j1, z1; - int k=0,l, cptcode; - int first=1, first1; + int k=0, l; + 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, 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"); @@ -3408,12 +4142,13 @@ 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]]); @@ -3436,19 +4171,27 @@ 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; + if(nagesqr==1) + cov[3]= age*age; for (k=1; k<=cptcovn;k++) { - cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]]; + cov[2+nagesqr+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<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[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]]]; + cov[2+nagesqr+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++) @@ -3486,10 +4229,6 @@ 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); @@ -3523,17 +4262,22 @@ 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"); @@ -3546,7 +4290,7 @@ 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; @@ -3568,10 +4312,13 @@ To be simple, these graphs help to under 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) ){ - printf("Error: 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. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor); - fprintf(ficlog,"Error: 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", lc1, lc2, v1, v2, cv12);fflush(ficlog); - lc1=fabs(lc1); - lc2=fabs(lc2); + 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 */ @@ -3593,7 +4340,7 @@ 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,\ @@ -3624,7 +4371,7 @@ 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); @@ -3670,7 +4417,7 @@ 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; @@ -3684,20 +4431,20 @@ 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 to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s%d_%d.png
      \ +", cpt, cpt, nlstate, 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 */ @@ -3744,7 +4491,7 @@ 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; @@ -3759,8 +4506,8 @@ 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) \ @@ -3778,7 +4525,7 @@ true period expectancies (those weighted void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){ char dirfileres[132],optfileres[132]; - int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; + int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0; int ng=0; /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */ /* printf("Problem with file %s",optionfilegnuplot); */ @@ -3793,61 +4540,61 @@ 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\ -plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1); +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)"); + 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)"); + 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*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); for (i=1; i<= nlstate ; i ++) { - if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); + if (i==cpt) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%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; - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%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 (j==i) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); } if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,"); else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); + 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 (j==i) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); } - fprintf(ficgp,"\" t\"\" w l 0,"); - fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1); + fprintf(ficgp,"\" t\"\" w l lt 0,"); + fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1); for (j=1; j<= nlstate+1 ; j ++) { - if (j==i) fprintf(ficgp," \%%lf (\%%lf)"); - else fprintf(ficgp," \%%*lf (\%%*lf)"); + if (j==i) fprintf(ficgp," %%lf (%%lf)"); + else fprintf(ficgp," %%*lf (%%*lf)"); } - if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0"); - else fprintf(ficgp,"\" t\"\" w l 0,"); + if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0"); + else fprintf(ficgp,"\" t\"\" w l lt 0,"); } } @@ -3858,8 +4605,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u /* k=2+nlstate*(2*cpt-2); */ k=2+(nlstate+1)*(cpt-1); fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1); - fprintf(ficgp,"set ter png small\n\ -set size 0.65,0.65\n\ + fprintf(ficgp,"set ter png small size 320, 240\n\ plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt); /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1); for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) "); @@ -3879,80 +4625,113 @@ 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 */ + fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n"); for(i=1,jk=1; i <=nlstate; i++){ + fprintf(ficgp,"# initial state %d\n",i); for(k=1; k <=(nlstate+ndeath); k++){ if (k != i) { + fprintf(ficgp,"# current state %d\n",k); for(j=1; j <=ncovmodel; j++){ - fprintf(ficgp,"p%d=%f ",jk,p[jk]); + fprintf(ficgp,"p%d=%f; ",jk,p[jk]); jk++; - fprintf(ficgp,"\n"); } + fprintf(ficgp,"\n"); } } } + fprintf(ficgp,"##############\n#\n"); + /*goto avoid;*/ + fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n"); + fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); + fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); + fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); + fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n"); + fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); + fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); + fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); + fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n"); + fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n"); + fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n"); + fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n"); + fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n"); + fprintf(ficgp,"#\n"); for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/ + fprintf(ficgp,"# ng=%d\n",ng); + fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m); for(jk=1; jk <=m; jk++) { - fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); + fprintf(ficgp,"# jk=%d\n",jk); + 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; for(k=1; k<=(nlstate+ndeath); k++) { if (k != k2){ if(ng==2) - fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); + if(nagesqr==0) + fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr); else - fprintf(ficgp," exp(p%d+p%d*x",i,i+1); - ij=1; - 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++; + if(nagesqr==0) + fprintf(ficgp," exp(p%d+p%d*x",i,i+1); + else /* nagesqr =1 */ + fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr); + ij=1;/* To be checked else nbcode[0][0] wrong */ + for(j=3; j <=ncovmodel-nagesqr; j++) { + if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */ + fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-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,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]); } fprintf(ficgp,")/(1"); - for(k1=1; k1 <=nlstate; k1++){ - fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); + for(k1=1; k1 <=nlstate; k1++){ + if(nagesqr==0) + fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1); + else /* nagesqr =1 */ + fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr); + ij=1; - for(j=3; j <=ncovmodel; j++){ + for(j=3; j <=ncovmodel-nagesqr; 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]]]); + fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,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,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]); } fprintf(ficgp,")"); } @@ -3964,6 +4743,7 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 } /* end k2 */ } /* end jk */ } /* end ng */ + /* avoid: */ fflush(ficgp); } /* end gnuplot */ @@ -4011,14 +4791,13 @@ int movingaverage(double ***probs, doubl /************** Forecasting ******************/ -prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ +void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ /* proj1, year, month, day of starting projection agemin, agemax range of age dateprev1 dateprev2 range of dates during which prevalence is computed anproj2 year of en of projection (same day and month as proj1). */ - int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1; - int *popage; + int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; double agec; /* generic age */ double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; double *popeffectif,*popcount; @@ -4135,7 +4914,7 @@ prevforecast(char fileres[], double anpr } /************** Forecasting *****not tested NB*************/ -populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ +void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; int *popage; @@ -4312,8 +5091,8 @@ void prwizard(int ncovmodel, int nlstate /* Wizard to print covariance matrix template */ - char ca[32], cb[32], cc[32]; - int i,j, k, l, li, lj, lk, ll, jj, npar, itimes; + char ca[32], cb[32]; + int i,j, k, li, lj, lk, ll, jj, npar, itimes; int numlinepar; printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); @@ -4534,7 +5313,7 @@ fprintf(fichtm,"

            • Life table=1;j--){ @@ -4604,8 +5381,8 @@ int readdata(char datafile[], int firsto 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); + 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; } } @@ -4613,14 +5390,14 @@ int readdata(char datafile[], int firsto strcpy(line,stra); cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - else if(iout=sscanf(strb,"%s.") != 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 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); + 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; @@ -4629,14 +5406,14 @@ int readdata(char datafile[], int firsto } /* ENd Waves */ cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - else if(iout=sscanf(strb,"%s.",dummy) != 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); + 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; @@ -4644,19 +5421,19 @@ int readdata(char datafile[], int firsto strcpy(line,stra); cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){ } - else if(iout=sscanf(strb,"%s.") != 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 birth (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 birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog); + 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 %ld 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 %ld 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); + 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; } @@ -4668,8 +5445,8 @@ int readdata(char datafile[], int firsto 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); + 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; } @@ -4684,13 +5461,13 @@ int readdata(char datafile[], int firsto 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); + 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 '%d' at line number %ld for individual %d, '%s'\n \ + 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 \ @@ -4699,7 +5476,7 @@ int readdata(char datafile[], int firsto 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 \ + 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 \ @@ -4731,7 +5508,7 @@ int readdata(char datafile[], int firsto fclose(fic); return (0); - endread: + /* endread: */ printf("Exiting readdata: "); fclose(fic); return (1); @@ -4739,97 +5516,195 @@ int readdata(char datafile[], int firsto } - -int decodemodel ( char model[], int lastobs) +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+age*age + * - nagesqr = 1 if age*age in the model, otherwise 0. + * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age + * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age + * - cptcovage number of covariates with age*products =2 + * - cptcovs number of simple covariates + * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10 + * which is a new column after the 9 (ncovcol) variables. + * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual + * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage + * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6. + * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 . + */ { - int i, j, k; - int i1, j1, k1, k2; + int i, j, k, ks; + int j1, k1, k2; char modelsav[80]; - char stra[80], strb[80], strc[80], strd[80],stre[80]; + char stra[80], strb[80], strc[80], strd[80],stre[80]; + char *strpt; + /*removespace(model);*/ 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*age+V3 =>(2 plus signs) + 1=3 - but the covariates which are product must be computed and stored. */ - cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */ - - strcpy(modelsav,model); + j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0; 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); + printf("Error. AGE must be in lower case 'age' model=1+age+%s ",model); + fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s ",model);fflush(ficlog); return 1; } - - /* 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]; */ - for(k=cptcovn; k>=1;k--){ - cutv(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 */ - cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=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'); /* stre="V3" */ - Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=2 ; 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--; - cutv(strb,stre,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 */ - cutv(strb,stre,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 */ - cutv(strb,strc,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*/ - Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */ - Tvar[cptcovn+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovn=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 */ - covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i]; - } - k1++; - k2=k2+2; - } /* 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);*/ - cutv(strd,strc,strb,'V'); - Tvar[k]=atoi(strc); - } - 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 */ + 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; + } + strcpy(modelsav,model); + if ((strpt=strstr(model,"age*age")) !=0){ + printf(" strpt=%s, model=%s\n",strpt, model); + if(strpt != model){ + printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ + corresponding column of parameters.\n",model); + fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \ + 'model=1+age+age*age+V1' or 'model=1+age+age*age+V1+V1*age', please swap as well as \n \ + corresponding column of parameters.\n",model); fflush(ficlog); + return 1; + } + + nagesqr=1; + if (strstr(model,"+age*age") !=0) + substrchaine(modelsav, model, "+age*age"); + else if (strstr(model,"age*age+") !=0) + substrchaine(modelsav, model, "age*age+"); + else + substrchaine(modelsav, model, "age*age"); + }else + nagesqr=0; + if (strlen(modelsav) >1){ + j=nbocc(modelsav,'+'); /**< j=Number of '+' */ + j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */ + cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */ + cptcovt= j+1; /* Number of total covariates in the model, not including + * cst, age and age*age + * V1+V1*age+ V3 + V3*V4+age*age=> 4*/ + /* including age products which are counted in cptcovage. + * but the covariates which are products must be treated + * separately: ncovn=4- 2=2 (V1+V3). */ + cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */ + cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */ + + + /* Design + * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight + * < ncovcol=8 > + * 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]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */ + /* + * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */ + for(k=cptcovt; k>=1;k--) /**< Number of covariates */ + 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; V1+V1*age Tvar[2]=1 */ + cptcovage++; /* Sums the number of covariates which include age as a product */ + Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */ + /*printf("stre=%s ", stre);*/ + } 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 + on total covariates */ + } /* end if strlen(modelsave == 0) age*age might exist */ + } /* end if strlen(model == 0) */ /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ @@ -4842,12 +5717,12 @@ int decodemodel ( char model[], int last return (0); /* with covar[new additional covariate if product] and Tage if age */ - endread: + /*endread:*/ printf("Exiting decodemodel: "); return (1); } -calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) +int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn ) { int i, m; @@ -4858,13 +5733,13 @@ calandcheckages(int imx, int maxwav, dou 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); + *nberr = *nberr + 1; + printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); + 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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr); s[m][i]=-1; } if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){ - *nberr++; + (*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 */ @@ -4877,11 +5752,11 @@ calandcheckages(int imx, int maxwav, dou 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) + 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 { + }else { if ((int)andc[i]!=9999){ nbwarn++; printf("Warning negative age at death: %ld line:%d\n",num[i],i); @@ -4889,6 +5764,7 @@ calandcheckages(int imx, int maxwav, dou agev[m][i]=-1; } } + } /* agedc > 0 */ } else if(s[m][i] !=9){ /* Standard case, age in fractional years but with the precision of a month */ @@ -4901,7 +5777,7 @@ calandcheckages(int imx, int maxwav, dou } 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); + /* 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;*/ @@ -4919,7 +5795,7 @@ calandcheckages(int imx, int maxwav, dou for (i=1; i<=imx; i++) { for(m=firstpass; (m<=lastpass); m++){ if (s[m][i] > (nlstate+ndeath)) { - *nberr++; + (*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; @@ -4939,11 +5815,346 @@ calandcheckages(int imx, int maxwav, dou fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); return (0); - endread: + /* endread:*/ printf("Exiting calandcheckages: "); return (1); } +#if defined(_MSC_VER) +/*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ +/*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/ +//#include "stdafx.h" +//#include +//#include +//#include +//#include +typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL); + +LPFN_ISWOW64PROCESS fnIsWow64Process; + +BOOL IsWow64() +{ + BOOL bIsWow64 = FALSE; + + //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS) + // (HANDLE, PBOOL); + + //LPFN_ISWOW64PROCESS fnIsWow64Process; + + HMODULE module = GetModuleHandle(_T("kernel32")); + const char funcName[] = "IsWow64Process"; + fnIsWow64Process = (LPFN_ISWOW64PROCESS) + GetProcAddress(module, funcName); + + if (NULL != fnIsWow64Process) + { + if (!fnIsWow64Process(GetCurrentProcess(), + &bIsWow64)) + //throw std::exception("Unknown error"); + printf("Unknown error\n"); + } + return bIsWow64 != FALSE; +} +#endif + +void syscompilerinfo() + { + /* #include "syscompilerinfo.h"*/ + /* command line Intel compiler 32bit windows, XP compatible:*/ + /* /GS /W3 /Gy + /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D + "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D + "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo + /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" + */ + /* 64 bits */ + /* + /GS /W3 /Gy + /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG" + /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope + /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir + "x64\Release\" /Fp"x64\Release\IMaCh.pch" */ + /* Optimization are useless and O3 is slower than O2 */ + /* + /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" + /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo + /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel + /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" + */ + /* Link is */ /* /OUT:"visual studio + 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT + /PDB:"visual studio + 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE + "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib" + "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib" + "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib" + /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO + /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker' + uiAccess='false'" + /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF + /NOLOGO /TLBID:1 + */ +#if defined __INTEL_COMPILER +#if defined(__GNUC__) + struct utsname sysInfo; /* For Intel on Linux and OS/X */ +#endif +#elif defined(__GNUC__) +#ifndef __APPLE__ +#include /* Only on gnu */ +#endif + struct utsname sysInfo; + int cross = CROSS; + if (cross){ + printf("Cross-"); + fprintf(ficlog, "Cross-"); + } +#endif + +#include + + printf("Compiled with:");fprintf(ficlog,"Compiled with:"); +#if defined(__clang__) + printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ +#endif +#if defined(__ICC) || defined(__INTEL_COMPILER) + printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */ +#endif +#if defined(__GNUC__) || defined(__GNUG__) + printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */ +#endif +#if defined(__HP_cc) || defined(__HP_aCC) + printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */ +#endif +#if defined(__IBMC__) || defined(__IBMCPP__) + printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */ +#endif +#if defined(_MSC_VER) + printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */ +#endif +#if defined(__PGI) + printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */ +#endif +#if defined(__SUNPRO_C) || defined(__SUNPRO_CC) + printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */ +#endif + printf(" for ");fprintf(ficlog," for "); + +// http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros +#ifdef _WIN32 // note the underscore: without it, it's not msdn official! + // Windows (x64 and x86) + printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) "); +#elif __unix__ // all unices, not all compilers + // Unix + printf("Unix ");fprintf(ficlog,"Unix "); +#elif __linux__ + // linux + printf("linux ");fprintf(ficlog,"linux "); +#elif __APPLE__ + // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though.. + printf("Mac OS ");fprintf(ficlog,"Mac OS "); +#endif + +/* __MINGW32__ */ +/* __CYGWIN__ */ +/* __MINGW64__ */ +// http://msdn.microsoft.com/en-us/library/b0084kay.aspx +/* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */ +/* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */ +/* _WIN64 // Defined for applications for Win64. */ +/* _M_X64 // Defined for compilations that target x64 processors. */ +/* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */ + +#if UINTPTR_MAX == 0xffffffff + printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */ +#elif UINTPTR_MAX == 0xffffffffffffffff + printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */ +#else + printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */ +#endif + +#if defined(__GNUC__) +# if defined(__GNUC_PATCHLEVEL__) +# define __GNUC_VERSION__ (__GNUC__ * 10000 \ + + __GNUC_MINOR__ * 100 \ + + __GNUC_PATCHLEVEL__) +# else +# define __GNUC_VERSION__ (__GNUC__ * 10000 \ + + __GNUC_MINOR__ * 100) +# endif + printf(" using GNU C version %d.\n", __GNUC_VERSION__); + fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__); + + if (uname(&sysInfo) != -1) { + printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); + fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine); + } + else + perror("uname() error"); + //#ifndef __INTEL_COMPILER +#if !defined (__INTEL_COMPILER) && !defined(__APPLE__) + printf("GNU libc version: %s\n", gnu_get_libc_version()); + fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); +#endif +#endif + + // void main() + // { +#if defined(_MSC_VER) + if (IsWow64()){ + printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); + fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n"); + } + else{ + printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n"); + fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n"); + } + // printf("\nPress Enter to continue..."); + // getchar(); + // } + +#endif + + + } + +int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){ + /*--------------- Prevalence limit (period or stable prevalence) --------------*/ + int i, j, k, i1 ; + double ftolpl = 1.e-10; + double age, agebase, agelim; + + strcpy(filerespl,"pl"); + strcat(filerespl,fileres); + if((ficrespl=fopen(filerespl,"w"))==NULL) { + printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; + fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1; + } + 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);*/ /* back in main */ + + agebase=ageminpar; + agelim=agemaxpar; + + i1=pow(2,cptcoveff); + if (cptcovn < 1){i1=1;} + + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ + /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */ + //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ + k=k+1; + /* to clean */ + //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]); + 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"); + + fprintf(ficrespl,"#Age "); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + } + for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); + fprintf(ficrespl,"\n"); + + for (age=agebase; age<=agelim; age++){ + /* for (age=agebase; age<=agebase; 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"); + } /* Age */ + /* was end of cptcod */ + } /* cptcov */ + return 0; +} + +int hPijx(double *p, int bage, int fage){ + /*------------- h Pij x at various ages ------------*/ + + int stepsize; + int agelim; + int hstepm; + int nhstepm; + int h, i, i1, j, k; + + double agedeb; + double ***p3mat; + + strcpy(filerespij,"pij"); strcat(filerespij,fileres); + if((ficrespij=fopen(filerespij,"w"))==NULL) { + printf("Problem with Pij resultfile: %s\n", filerespij); return 1; + fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1; + } + 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 "); + i1= pow(2,cptcoveff); + /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */ + /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */ + /* k=k+1; */ + for (k=1; k <= (int) pow(2,cptcoveff); k++){ + 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*/ + + 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++){ + /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/ + 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"); + } + /*}*/ + } + return 0; +} + /***********************************************/ /**************** Main Program *****************/ @@ -4959,38 +6170,35 @@ int main(int argc, char *argv[]) double ssval; #endif 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 i,j, k, n=MAXN,iter=0,m,size=100, cptcod; + + int jj, ll, li, lj, lk; int numlinepar=0; /* Current linenumber of parameter file */ int itimes; int NDIM=2; int vpopbased=0; - char ca[32], cb[32], cc[32]; + char ca[32], cb[32]; /* FILE *fichtm; *//* Html File */ /* FILE *ficgp;*/ /*Gnuplot File */ struct stat info; - double agedeb, agefin,hf; + double agedeb; 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 line[MAXLINE]; char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; char pathr[MAXLINE], pathimach[MAXLINE]; - char **bp, *tok, *val; /* pathtot */ + char *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, jk,aa,bb, stepsize, ij; - int jnais,jdc,jint4,jint1,jint2,jint3,*tab; + int c, h , cpt; + int jl; + int i1, j1, jk, stepsize; + int *tab; int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ int mobilav=0,popforecast=0; int hstepm, nhstepm; @@ -4999,7 +6207,7 @@ int main(int argc, char *argv[]) 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 bage=0, fage=110, age, agelim, agebase; double ftolpl=FTOL; double **prlim; double ***param; /* Matrix of parameters */ @@ -5010,19 +6218,18 @@ int main(int argc, char *argv[]) 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]; + char *alph[]={"a","a","b","c","d","e"}, str[4]="1234"; int *dcwave; - char z[1]="c", occ; + char z[1]="c"; /*char *strt;*/ char strtend[80]; - long total_usecs; - + /* setlocale (LC_ALL, ""); */ /* bindtextdomain (PACKAGE, LOCALEDIR); */ /* textdomain (PACKAGE); */ @@ -5030,19 +6237,21 @@ int main(int argc, char *argv[]) /* setlocale (LC_MESSAGES, ""); */ /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - (void) gettimeofday(&start_time,&tzp); + rstart_time = time(NULL); + /* (void) gettimeofday(&start_time,&tzp);*/ + start_time = *localtime(&rstart_time); curr_time=start_time; - tm = *localtime(&start_time.tv_sec); - tmg = *gmtime(&start_time.tv_sec); - strcpy(strstart,asctime(&tm)); + /*tml = *localtime(&start_time.tm_sec);*/ + /* strcpy(strstart,asctime(&tml)); */ + strcpy(strstart,asctime(&start_time)); /* printf("Localtime (at start)=%s",strstart); */ -/* tp.tv_sec = tp.tv_sec +86400; */ -/* tm = *localtime(&start_time.tv_sec); */ +/* tp.tm_sec = tp.tm_sec +86400; */ +/* tm = *localtime(&start_time.tm_sec); */ /* tmg.tm_year=tmg.tm_year +dsign*dyear; */ /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */ /* tmg.tm_hour=tmg.tm_hour + 1; */ -/* tp.tv_sec = mktime(&tmg); */ +/* tp.tm_sec = mktime(&tmg); */ /* strt=asctime(&tmg); */ /* printf("Time(after) =%s",strstart); */ /* (void) time (&time_value); @@ -5054,7 +6263,11 @@ int main(int argc, char *argv[]) nberr=0; /* Number of errors and warnings */ nbwarn=0; +#ifdef WIN32 + _getcwd(pathcd, size); +#else getcwd(pathcd, size); +#endif printf("\n%s\n%s",version,fullversion); if(argc <=1){ @@ -5063,6 +6276,9 @@ int main(int argc, char *argv[]) i=strlen(pathr); if(pathr[i-1]=='\n') pathr[i-1]='\0'; + i=strlen(pathr); + if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */ + pathr[i-1]='\0'; for (tok = pathr; tok != NULL; ){ printf("Pathr |%s|\n",pathr); while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); @@ -5087,13 +6303,18 @@ int main(int argc, char *argv[]) /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ split(pathtot,path,optionfile,optionfilext,optionfilefiname); printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); +#ifdef WIN32 + _chdir(path); /* Can be a relative path */ + if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ +#else chdir(path); /* Can be a relative path */ - if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ - printf("Current directory %s!\n",pathcd); + if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */ +#endif + printf("Current directory %s!\n",pathcd); strcpy(command,"mkdir "); strcat(command,optionfilefiname); if((outcmd=system(command)) != 0){ - printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd); + printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd); /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */ /* fclose(ficlog); */ /* exit(1); */ @@ -5104,7 +6325,7 @@ int main(int argc, char *argv[]) /*-------- arguments in the command line --------*/ - /* Log file */ + /* Main Log file */ strcat(filelog, optionfilefiname); strcat(filelog,".log"); /* */ if((ficlog=fopen(filelog,"w"))==NULL) { @@ -5118,26 +6339,29 @@ int main(int argc, char *argv[]) path=%s \n\ optionfile=%s\n\ optionfilext=%s\n\ - optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); + optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); + + syscompilerinfo(); printf("Local time (at start):%s",strstart); fprintf(ficlog,"Local time (at start): %s",strstart); fflush(ficlog); /* (void) gettimeofday(&curr_time,&tzp); */ -/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */ +/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */ /* */ strcpy(fileres,"r"); strcat(fileres, optionfilefiname); strcat(fileres,".txt"); /* Other files have txt extension */ - /*---------arguments file --------*/ + /* Main ---------arguments file --------*/ if((ficpar=fopen(optionfile,"r"))==NULL) { - printf("Problem with optionfile %s\n",optionfile); - fprintf(ficlog,"Problem with optionfile %s\n",optionfile); + printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); + fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno)); fflush(ficlog); - goto end; + /* goto end; */ + exit(70); } @@ -5157,39 +6381,50 @@ int main(int argc, char *argv[]) ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; - puts(line); + fputs(line,stdout); fputs(line,ficparo); fputs(line,ficlog); } ungetc(c,ficpar); - fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); + fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); numlinepar++; - printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); - fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); - fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); + printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); + if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */ + model[strlen(model)-1]='\0'; + fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); + fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); fflush(ficlog); + if(model[0]=='#'|| model[0]== '\0'){ + printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \ + 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \ + 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \ + if(mle != -1){ + printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n"); + exit(1); + } + } while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; - puts(line); + fputs(line, stdout); + //puts(line); fputs(line,ficparo); fputs(line,ficlog); } ungetc(c,ficpar); - covar=matrix(0,NCOVMAX,1,n); + 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) - cptcovn=nbocc(model,'+')+1; - /* ncovprod */ - ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/ - nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ + 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,age*age makes 3*/ + else + ncovmodel=2; /* Constant and age */ nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */ npar= nforce*ncovmodel; /* Number of parameters like aij*/ if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){ @@ -5212,7 +6447,7 @@ int main(int argc, char *argv[]) goto end; exit(0); } - else if(mle==-3) { + else if(mle==-3) { /* Main Wizard */ prwizard(ncovmodel, nlstate, ndeath, model, ficparo); printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso); @@ -5220,13 +6455,13 @@ 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); } @@ -5269,6 +6504,7 @@ run imach with mle=-1 to get a correct t } fflush(ficlog); + /* Reads scales values */ p=param[1][1]; /* Reads comments: lines beginning with '#' */ @@ -5276,7 +6512,7 @@ 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); } @@ -5285,7 +6521,7 @@ run imach with mle=-1 to get a correct t for(i=1; i <=nlstate; i++){ for(j=1; j <=nlstate+ndeath-1; j++){ fscanf(ficpar,"%1d%1d",&i1,&j1); - if ((i1-i)*(j1-j)!=0){ + if ( (i1-i) * (j1-j) != 0){ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1); exit(1); } @@ -5307,6 +6543,7 @@ run imach with mle=-1 to get a correct t } fflush(ficlog); + /* Reads covariance matrix */ delti=delti3[1][1]; @@ -5317,7 +6554,7 @@ 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); } @@ -5328,7 +6565,7 @@ run imach with mle=-1 to get a correct t for(j=1; j <=npar; j++) matcov[i][j]=0.; for(i=1; i <=npar; i++){ - fscanf(ficpar,"%s",&str); + fscanf(ficpar,"%s",str); if(mle==1) printf("%s",str); fprintf(ficlog,"%s",str); @@ -5370,7 +6607,8 @@ run imach with mle=-1 to get a correct t fprintf(ficres,"#%s\n",version); } /* End of mle != -3 */ - + /* Main data + */ n= lastobs; num=lvector(1,n); moisnais=vector(1,n); @@ -5385,7 +6623,7 @@ run imach with mle=-1 to get a correct t 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); /* hard coded ? */ + ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */ /* Reads data from file datafile */ if (readdata(datafile, firstobs, lastobs, &imx)==1) @@ -5408,17 +6646,22 @@ run imach with mle=-1 to get a correct t ncovcol + k1 If already ncovcol=4 and model=V2+V1+V1*V4+age*V3 Tvar[3=V1*V4]=4+1 etc */ - Tprod=ivector(1,15); + 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(1,15); - Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */ - Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age + 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 */ +/* Main decodemodel */ + + if(decodemodel(model, lastobs) == 1) goto end; @@ -5446,8 +6689,8 @@ run imach with mle=-1 to get a correct t 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); @@ -5455,28 +6698,62 @@ 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-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */ + tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */ + /* Nbcode gives the value of the lth modality of jth covariate, in + V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/ + /* 1 to ncodemax[j] is the maximum value of this jth covariate */ + + 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]);*/ + /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ 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) { + if (h>m) h=1; - codtab[h][k]=j; - codtab[h][Tvar[k]]=j; - } + /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1 + * For k=4 covariates, h goes from 1 to 2**k + * codtabm(h,k)= 1 & (h-1) >> (k-1) ; + * h\k 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[12][3]=1; */ + /*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]]); } } @@ -5491,8 +6768,12 @@ run imach with mle=-1 to get a correct t printf("\n"); } scanf("%d",i);*/ + + free_ivector(Ndum,-1,NCOVMAX); + + - /*------------ gnuplot -------------*/ + /* Initialisation of ----------- gnuplot -------------*/ strcpy(optionfilegnuplot,optionfilefiname); if(mle==-3) strcat(optionfilegnuplot,"-mort"); @@ -5504,10 +6785,13 @@ 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 --------*/ + + + /* Initialisation of --------- index.htm --------*/ strcpy(optionfilehtm,optionfilefiname); /* Main html file */ if(mle==-3) @@ -5549,7 +6833,12 @@ Title=%s
              Datafile=%s Firstpass=%d La strcpy(pathr,path); strcat(pathr,optionfilefiname); +#ifdef WIN32 + _chdir(optionfilefiname); /* Move to directory named optionfile */ +#else chdir(optionfilefiname); /* Move to directory named optionfile */ +#endif + /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ @@ -5572,10 +6861,10 @@ Interval (in months) between two waves: p=param[1][1]; /* *(*(*(param +1)+1)+0) */ globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ - + /* For mortality only */ if (mle==-3){ ximort=matrix(1,NDIM,1,NDIM); -/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ + /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */ cens=ivector(1,n); ageexmed=vector(1,n); agecens=vector(1,n); @@ -5613,13 +6902,13 @@ 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 +#else printf("Powell\n"); fprintf(ficlog,"Powell\n"); #endif strcpy(filerespow,"pow-mort"); @@ -5630,7 +6919,7 @@ Interval (in months) between two waves: } #ifdef GSL fprintf(ficrespow,"# GSL optimization\n# iter -2*LL"); -#elsedef +#else fprintf(ficrespow,"# Powell\n# iter -2*LL"); #endif /* for (i=1;i<=nlstate;i++) @@ -5665,8 +6954,8 @@ Interval (in months) between two waves: /* 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, 0.0268); */ + /* gsl_vector_set(x, 1, 0.083); */ gsl_vector_set(x, 0, p[1]); gsl_vector_set(x, 1, p[2]); @@ -5783,27 +7072,28 @@ Interval (in months) between two waves: free_ivector(dcwave,1,n); free_matrix(ximort,1,NDIM,1,NDIM); #endif - } /* Endof if mle==-3 */ - + } /* Endof if mle==-3 mortality only */ + /* Standard maximisation */ else{ /* For mle >=1 */ globpr=0;/* debug */ + /* Computes likelihood for initial parameters */ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); for (k=1; k<=npar;k++) printf(" %d %8.5f",k,p[k]); printf("\n"); - globpr=1; /* to print the contributions */ + globpr=1; /* again, to print the contributions */ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw); for (k=1; k<=npar;k++) printf(" %d %8.5f",k,p[k]); printf("\n"); - if(mle>=1){ /* Could be 1 or 2 */ + if(mle>=1){ /* Could be 1 or 2, Real Maximisation */ mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); } /*--------- results files --------------*/ - fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); @@ -5943,7 +7233,7 @@ 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); @@ -5959,11 +7249,12 @@ Interval (in months) between two waves: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - + + /* Other stuffs, more or less useful */ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); - puts(line); + fputs(line,stdout); fputs(line,ficparo); } ungetc(c,ficpar); @@ -5977,7 +7268,7 @@ 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); @@ -5993,7 +7284,7 @@ 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); @@ -6007,8 +7298,8 @@ 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); @@ -6032,118 +7323,28 @@ Interval (in months) between two waves: fclose(ficres); - /*--------------- 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); + /* Other results (useful)*/ - 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"); - } - } - } + /*--------------- Prevalence limit (period or stable prevalence) --------------*/ + /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */ + prlim=matrix(1,nlstate,1,nlstate); + prevalence_limit(p, prlim, ageminpar, agemaxpar); 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"*/ + hPijx(p, bage, fage); + 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++) @@ -6164,7 +7365,8 @@ Interval (in months) between two waves: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */ /* } */ } - + + /* ------ Other prevalence ratios------------ */ /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ @@ -6192,9 +7394,10 @@ 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]]); @@ -6206,7 +7409,7 @@ 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); @@ -6251,10 +7454,11 @@ 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"); @@ -6276,12 +7480,19 @@ 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 */ + cptcod= 0; /* To be deleted */ + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */ + 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 @@ -6325,10 +7536,10 @@ 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); @@ -6350,10 +7561,11 @@ 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"); @@ -6362,7 +7574,7 @@ 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); @@ -6370,10 +7582,9 @@ 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); + /* endfree:*/ + 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); @@ -6385,11 +7596,11 @@ 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); @@ -6406,17 +7617,18 @@ 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); @@ -6429,25 +7641,31 @@ Interval (in months) between two waves: printf("Before Current directory %s!\n",pathcd); +#ifdef WIN32 + if (_chdir(pathcd) != 0) + printf("Can't move to directory %s!\n",path); + if(_getcwd(pathcd,MAXLINE) > 0) +#else if(chdir(pathcd) != 0) - printf("Can't move to directory %s!\n",path); - if(getcwd(pathcd,MAXLINE) > 0) + printf("Can't move to directory %s!\n", path); + if (getcwd(pathcd, MAXLINE) > 0) +#endif 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 @@ -6455,20 +7673,31 @@ 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); @@ -6479,6 +7708,3 @@ Interval (in months) between two waves: scanf("%s",z); } } - - -