--- imach/src/imach.c 2004/05/16 15:05:56 1.98 +++ imach/src/imach.c 2006/03/20 09:45:41 1.122 @@ -1,6 +1,111 @@ -/* $Id: imach.c,v 1.98 2004/05/16 15:05:56 brouard Exp $ +/* $Id: imach.c,v 1.122 2006/03/20 09:45:41 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.122 2006/03/20 09:45:41 brouard + (Module): Weights can have a decimal point as for + English (a comma might work with a correct LC_NUMERIC environment, + otherwise the weight is truncated). + Modification of warning when the covariates values are not 0 or + 1. + Version 0.98g + + Revision 1.121 2006/03/16 17:45:01 lievre + * imach.c (Module): Comments concerning covariates added + + * imach.c (Module): refinements in the computation of lli if + status=-2 in order to have more reliable computation if stepm is + not 1 month. Version 0.98f + + Revision 1.120 2006/03/16 15:10:38 lievre + (Module): refinements in the computation of lli if + status=-2 in order to have more reliable computation if stepm is + not 1 month. Version 0.98f + + Revision 1.119 2006/03/15 17:42:26 brouard + (Module): Bug if status = -2, the loglikelihood was + computed as likelihood omitting the logarithm. Version O.98e + + Revision 1.118 2006/03/14 18:20:07 brouard + (Module): varevsij Comments added explaining the second + table of variances if popbased=1 . + (Module): Covariances of eij, ekl added, graphs fixed, new html link. + (Module): Function pstamp added + (Module): Version 0.98d + + Revision 1.117 2006/03/14 17:16:22 brouard + (Module): varevsij Comments added explaining the second + table of variances if popbased=1 . + (Module): Covariances of eij, ekl added, graphs fixed, new html link. + (Module): Function pstamp added + (Module): Version 0.98d + + Revision 1.116 2006/03/06 10:29:27 brouard + (Module): Variance-covariance wrong links and + varian-covariance of ej. is needed (Saito). + + Revision 1.115 2006/02/27 12:17:45 brouard + (Module): One freematrix added in mlikeli! 0.98c + + Revision 1.114 2006/02/26 12:57:58 brouard + (Module): Some improvements in processing parameter + filename with strsep. + + Revision 1.113 2006/02/24 14:20:24 brouard + (Module): Memory leaks checks with valgrind and: + datafile was not closed, some imatrix were not freed and on matrix + allocation too. + + Revision 1.112 2006/01/30 09:55:26 brouard + (Module): Back to gnuplot.exe instead of wgnuplot.exe + + Revision 1.111 2006/01/25 20:38:18 brouard + (Module): Lots of cleaning and bugs added (Gompertz) + (Module): Comments can be added in data file. Missing date values + can be a simple dot '.'. + + Revision 1.110 2006/01/25 00:51:50 brouard + (Module): Lots of cleaning and bugs added (Gompertz) + + Revision 1.109 2006/01/24 19:37:15 brouard + (Module): Comments (lines starting with a #) are allowed in data. + + Revision 1.108 2006/01/19 18:05:42 lievre + Gnuplot problem appeared... + To be fixed + + Revision 1.107 2006/01/19 16:20:37 brouard + Test existence of gnuplot in imach path + + Revision 1.106 2006/01/19 13:24:36 brouard + Some cleaning and links added in html output + + Revision 1.105 2006/01/05 20:23:19 lievre + *** empty log message *** + + Revision 1.104 2005/09/30 16:11:43 lievre + (Module): sump fixed, loop imx fixed, and simplifications. + (Module): If the status is missing at the last wave but we know + that the person is alive, then we can code his/her status as -2 + (instead of missing=-1 in earlier versions) and his/her + contributions to the likelihood is 1 - Prob of dying from last + health status (= 1-p13= p11+p12 in the easiest case of somebody in + the healthy state at last known wave). Version is 0.98 + + Revision 1.103 2005/09/30 15:54:49 lievre + (Module): sump fixed, loop imx fixed, and simplifications. + + Revision 1.102 2004/09/15 17:31:30 brouard + Add the possibility to read data file including tab characters. + + Revision 1.101 2004/09/15 10:38:38 brouard + Fix on curr_time + + Revision 1.100 2004/07/12 18:29:06 brouard + Add version for Mac OS X. Just define UNIX in Makefile + + Revision 1.99 2004/06/05 08:57:40 brouard + *** empty log message *** + Revision 1.98 2004/05/16 15:05:56 brouard New version 0.97 . First attempt to estimate force of mortality directly from the data i.e. without the need of knowing the health @@ -143,7 +248,7 @@ hPijx. Also this programme outputs the covariance matrix of the parameters but also - of the life expectancies. It also computes the stable prevalence. + of the life expectancies. It also computes the period (stable) prevalence. Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr). Institut national d'études démographiques, Paris. @@ -172,7 +277,7 @@ begin-prev-date,... open gnuplot file open html file - stable prevalence + period (stable) prevalence for age prevalim() h Pij x variance of p varprob @@ -184,7 +289,7 @@ varevsij() if popbased==1 varevsij(,popbased) total life expectancies - Variance of stable prevalence + Variance of period (stable) prevalence end */ @@ -194,9 +299,16 @@ #include #include #include +#include #include -#include +#include +#include +#include +#include +extern int errno; + +/* #include */ #include #include "timeval.h" @@ -204,11 +316,11 @@ /* #define _(String) gettext (String) */ #define MAXLINE 256 + #define GNUPLOTPROGRAM "gnuplot" /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ #define FILENAMELENGTH 132 -/*#define DEBUG*/ -/*#define windows*/ + #define GLOCK_ERROR_NOPATH -1 /* empty path */ #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ @@ -224,19 +336,23 @@ #define AGESUP 130 #define AGEBASE 40 #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */ -#ifdef unix +#ifdef UNIX #define DIRSEPARATOR '/' +#define CHARSEPARATOR "/" #define ODIRSEPARATOR '\\' #else #define DIRSEPARATOR '\\' +#define CHARSEPARATOR "\\" #define ODIRSEPARATOR '/' #endif -/* $Id: imach.c,v 1.98 2004/05/16 15:05:56 brouard Exp $ */ +/* $Id: imach.c,v 1.122 2006/03/20 09:45:41 brouard Exp $ */ /* $State: Exp $ */ -char version[]="Imach version 0.70, May 2004, INED-EUROREVES "; -char fullversion[]="$Revision: 1.98 $ $Date: 2004/05/16 15:05:56 $"; +char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite "; +char fullversion[]="$Revision: 1.122 $ $Date: 2006/03/20 09:45:41 $"; +char strstart[80]; +char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ int nvar; int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; @@ -249,6 +365,7 @@ int popbased=0; int *wav; /* Number of waves for this individuual 0 is possible */ int maxwav; /* Maxim number of waves */ int jmin, jmax; /* min, max spacing between 2 waves */ +int ijmin, ijmax; /* Individuals having jmin and jmax */ int gipmx, gsw; /* Global variables on the number of contributions to the likelihood and the sum of weights (done by funcone)*/ int mle, weightopt; @@ -259,7 +376,7 @@ int **bh; /* bh[mi][i] is the bias (+ or double jmean; /* Mean space between 2 waves */ double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ -FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; +FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop; FILE *ficlog, *ficrespow; int globpr; /* Global variable for printing or not */ double fretone; /* Only one call to likelihood */ @@ -273,13 +390,17 @@ FILE *ficresprobmorprev; FILE *fichtm, *fichtmcov; /* Html File */ FILE *ficreseij; char filerese[FILENAMELENGTH]; +FILE *ficresstdeij; +char fileresstde[FILENAMELENGTH]; +FILE *ficrescveij; +char filerescve[FILENAMELENGTH]; FILE *ficresvij; char fileresv[FILENAMELENGTH]; FILE *ficresvpl; char fileresvpl[FILENAMELENGTH]; char title[MAXLINE]; char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; -char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; +char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; char command[FILENAMELENGTH]; int outcmd=0; @@ -301,6 +422,10 @@ long time_value; extern long time(); char strcurr[80], strfor[80]; +char *endptr; +long lval; +double dval; + #define NR_END 1 #define FREE_ARG char* #define FTOL 1.0e-10 @@ -349,6 +474,7 @@ double *weight; int **s; /* Status */ double *agedc, **covar, idx; int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; +double *lsurv, *lpop, *tpop; double ftol=FTOL; /* Tolerance for computing Max Likelihood */ double ftolhess; /* Tolerance for computing hessian */ @@ -356,13 +482,17 @@ double ftolhess; /* Tolerance for comput /**************** split *************************/ static int split( char *path, char *dirc, char *name, char *ext, char *finame ) { + /* From a file name with (full) path (either Unix or Windows) we extract the directory (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 */ l1 = strlen(path ); /* length of path */ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); ss= strrchr( path, DIRSEPARATOR ); /* find last / */ - if ( ss == NULL ) { /* no directory, so use current */ + if ( ss == NULL ) { /* no directory, so determine current directory */ + strcpy( name, path ); /* we got the fullname name because no directory */ /*if(strrchr(path, ODIRSEPARATOR )==NULL) printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ /* get current working directory */ @@ -370,7 +500,8 @@ static int split( char *path, char *dirc if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { return( GLOCK_ERROR_GETCWD ); } - strcpy( name, path ); /* we've got it */ + /* got dirc from getcwd*/ + printf(" DIRC = %s \n",dirc); } else { /* strip direcotry from path */ ss++; /* after this, the filename */ l2 = strlen( ss ); /* length of filename */ @@ -378,21 +509,25 @@ static int split( char *path, char *dirc strcpy( name, ss ); /* save file name */ strncpy( dirc, path, l1 - l2 ); /* now the directory */ dirc[l1-l2] = 0; /* add zero */ + printf(" DIRC2 = %s \n",dirc); } + /* We add a separator at the end of dirc if not exists */ l1 = strlen( dirc ); /* length of directory */ - /*#ifdef windows - if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } -#else - if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } -#endif - */ + if( dirc[l1-1] != DIRSEPARATOR ){ + dirc[l1] = DIRSEPARATOR; + dirc[l1+1] = 0; + printf(" DIRC3 = %s \n",dirc); + } ss = strrchr( name, '.' ); /* find last / */ - ss++; - strcpy(ext,ss); /* save extension */ - l1= strlen( name); - l2= strlen(ss)+1; - strncpy( finame, name, l1-l2); - finame[l1-l2]= 0; + if (ss >0){ + ss++; + strcpy(ext,ss); /* save extension */ + l1= strlen( name); + l2= strlen(ss)+1; + strncpy( finame, name, l1-l2); + finame[l1-l2]= 0; + } + return( 0 ); /* we're done */ } @@ -425,8 +560,8 @@ int nbocc(char *s, char occ) void cutv(char *u,char *v, char*t, char occ) { - /* cuts string t into u and v where u is ended by char occ excluding it - and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) + /* cuts string t into u and v where u ends before first occurence of char 'occ' + and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') gives u="abcedf" and v="ghi2j" */ int i,lg,j,p=0; i=0; @@ -868,11 +1003,11 @@ void powell(double p[], double **xi, int fprintf(ficrespow,"\n");fflush(ficrespow); if(*iter <=3){ tm = *localtime(&curr_time.tv_sec); - strcpy(strcurr,asctime(&tmf)); + strcpy(strcurr,asctime(&tm)); /* asctime_r(&tm,strcurr); */ - forecast_time=curr_time; + forecast_time=curr_time; itmp = strlen(strcurr); - if(strcurr[itmp-1]=='\n') + 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); @@ -884,8 +1019,8 @@ void powell(double p[], double **xi, int 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 or\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 or\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(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); } } for (i=1;i<=n;i++) { @@ -979,7 +1114,7 @@ void powell(double p[], double **xi, int } } -/**** Prevalence limit (stable prevalence) ****************/ +/**** Prevalence limit (stable or period prevalence) ****************/ double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij) { @@ -1050,57 +1185,57 @@ double **pmij(double **ps, double *cov, int i,j,j1, nc, ii, jj; for(i=1; i<= nlstate; i++){ - for(j=1; ji s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/ + for(j=1; ji s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */ + } + ps[i][j]=s2; } - ps[i][j]=s2; } - } /*ps[3][2]=1;*/ - - for(i=1; i<= nlstate; i++){ - s1=0; - for(j=1; j 1 the results are less biased than in previous versions. @@ -1239,15 +1374,16 @@ double func( double *x) s1=s[mw[mi][i]][i]; s2=s[mw[mi+1][i]][i]; bbh=(double)bh[mi][i]/(double)stepm; - /* bias is positive if real duration + /* bias bh is positive if real duration * is higher than the multiple of stepm and negative otherwise. */ /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ if( s2 > nlstate){ - /* i.e. if s2 is a death state and if the date of death is known then the contribution - to the likelihood is the probability to die between last step unit time and current - step unit time, which is also the differences between probability to die before dh - and probability to die before dh-stepm . + /* i.e. if s2 is a death state and if the date of death is known + then the contribution to the likelihood is the probability to + die between last step unit time and current step unit time, + which is also equal to probability to die before dh + minus probability to die before dh-stepm . In version up to 0.92 likelihood was computed as if date of death was unknown. Death was treated as any other health state: the date of the interview describes the actual state @@ -1267,7 +1403,28 @@ double func( double *x) lower mortality. */ lli=log(out[s1][s2] - savm[s1][s2]); - }else{ + + + } else if (s2==-2) { + for (j=1,survp=0. ; j<=nlstate; j++) + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + /*survp += out[s1][j]; */ + lli= log(survp); + } + + else if (s2==-4) { + for (j=3,survp=0. ; j<=nlstate; j++) + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + lli= log(survp); + } + + else if (s2==-5) { + for (j=1,survp=0. ; j<=2; j++) + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + lli= log(survp); + } + + else{ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */ } @@ -1461,7 +1618,11 @@ double funcone( double *x) */ if( s2 > nlstate && (mle <5) ){ /* Jackson */ lli=log(out[s1][s2] - savm[s1][s2]); - } else if (mle==1){ + } else if (s2==-2) { + for (j=1,survp=0. ; j<=nlstate; j++) + survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; + lli= log(survp); + }else if (mle==1){ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ } else if(mle==2){ lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ @@ -1477,8 +1638,8 @@ double funcone( double *x) ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ if(globpr){ - fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\ - %10.6f %10.6f %10.6f ", \ + fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ + %11.6f %11.6f %11.6f ", \ num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); for(k=1,llt=0.,l=0.; k<=nlstate; k++){ @@ -1563,6 +1724,7 @@ void mlikeli(FILE *ficres,double p[], in powell(p,xi,npar,ftol,&iter,&fret,func); + 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)); @@ -1830,8 +1992,13 @@ void lubksb(double **a, int n, int *indx } } +void pstamp(FILE *fichier) +{ + fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart); +} + /************ Frequencies ********************/ -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) +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,z2,j; @@ -1839,7 +2006,6 @@ void freqsummary(char fileres[], int ia double ***freq; /* Frequencies */ double *pp, **prop; double pos,posprop, k2, dateintsum=0,k2cpt=0; - FILE *ficresp; char fileresp[FILENAMELENGTH]; pp=vector(1,nlstate); @@ -1851,7 +2017,7 @@ void freqsummary(char fileres[], int ia fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); exit(0); } - freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3); + freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3); j1=0; j=cptcoveff; @@ -1864,8 +2030,8 @@ void freqsummary(char fileres[], int ia j1++; /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]); scanf("%d", i);*/ - for (i=-1; i<=nlstate+ndeath; i++) - for (jk=-1; jk<=nlstate+ndeath; jk++) + 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; @@ -1904,7 +2070,7 @@ void freqsummary(char fileres[], int ia } /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/ - + pstamp(ficresp); if (cptcovn>0) { fprintf(ficresp, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); @@ -1990,7 +2156,7 @@ void freqsummary(char fileres[], int ia dateintmean=dateintsum/k2cpt; fclose(ficresp); - free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3); + free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3); free_vector(pp,1,nlstate); free_matrix(prop,1,nlstate,iagemin, iagemax+3); /* End of Freq */ @@ -2099,7 +2265,7 @@ void concatwav(int wav[], int **dh, int mi=0; m=firstpass; while(s[m][i] <= nlstate){ - if(s[m][i]>=1) + if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5) mw[++mi][i]=m; if(m >=lastpass) break; @@ -2117,11 +2283,11 @@ void concatwav(int wav[], int **dh, int if(mi==0){ nbwarn++; if(first==0){ - printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i); + printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i); first=1; } if(first==1){ - fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i); + fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i); } } /* end mi==0 */ } /* End individuals */ @@ -2139,13 +2305,19 @@ void concatwav(int wav[], int **dh, int nberr++; printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); j=1; /* Temporary Dangerous patch */ - printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm); + printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); - fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm); + fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm); } k=k+1; - if (j >= jmax) jmax=j; - if (j <= jmin) jmin=j; + if (j >= jmax){ + jmax=j; + ijmax=i; + } + if (j <= jmin){ + jmin=j; + ijmin=i; + } sum=sum+j; /*if (j<0) printf("j=%d num=%d \n",j,i);*/ /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ @@ -2153,10 +2325,17 @@ void concatwav(int wav[], int **dh, int } else{ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); - /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ +/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */ + k=k+1; - if (j >= jmax) jmax=j; - else if (j <= jmin)jmin=j; + if (j >= jmax) { + jmax=j; + ijmax=i; + } + else if (j <= jmin){ + jmin=j; + ijmin=i; + } /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ if(j<0){ @@ -2199,8 +2378,8 @@ void concatwav(int wav[], int **dh, int } /* end wave */ } jmean=sum/k; - printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); - fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); + 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); } /*********** Tricode ****************************/ @@ -2246,7 +2425,7 @@ void tricode(int *Tvar, int **nbcode, in for (k=0; k< maxncov; k++) Ndum[k]=0; for (i=1; i<=ncovmodel-2; i++) { - /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ + /* 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]; Ndum[ij]++; } @@ -2264,31 +2443,151 @@ void tricode(int *Tvar, int **nbcode, in /*********** Health Expectancies ****************/ -void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov ) +void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] ) { - /* Health expectancies */ - int i, j, nhstepm, hstepm, h, nstepm, k, cptj; + /* Health expectancies, no variances */ + int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2; double age, agelim, hf; - double ***p3mat,***varhe; + double ***p3mat; + double eip; + + pstamp(ficreseij); + fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n"); + fprintf(ficreseij,"# Age"); + for(i=1; i<=nlstate;i++){ + for(j=1; j<=nlstate;j++){ + fprintf(ficreseij," e%1d%1d ",i,j); + } + fprintf(ficreseij," e%1d. ",i); + } + fprintf(ficreseij,"\n"); + + + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + /* We compute the life expectancy from trapezoids spaced every estepm months + * This is mainly to measure the difference between two models: for example + * if stepm=24 months pijx are given only every 2 years and by summing them + * we are calculating an estimate of the Life Expectancy assuming a linear + * progression in between and thus overestimating or underestimating according + * to the curvature of the survival function. If, for the same date, we + * estimate the model with stepm=1 month, we can keep estepm to 24 months + * to compare the new estimate of Life expectancy with the same linear + * hypothesis. A more precise result, taking into account a more precise + * curvature will be obtained if estepm is as small as stepm. */ + + /* For example we decided to compute the life expectancy with the smallest unit */ + /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. + nhstepm is the number of hstepm from age to agelim + nstepm is the number of stepm from age to agelin. + Look at hpijx to understand the reason of that which relies in memory size + and note for a fixed period like estepm months */ + /* We decided (b) to get a life expectancy respecting the most precise curvature of the + survival function given by stepm (the optimization length). Unfortunately it + means that if the survival funtion is printed only each two years of age and if + you sum them up and add 1 year (area under the trapezoids) you won't get the same + results. So we changed our mind and took the option of the best precision. + */ + hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ + + agelim=AGESUP; + /* nhstepm age range expressed in number of stepm */ + nstepm=(int) rint((agelim-age)*YEARM/stepm); + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + + for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ + /* Computed by stepm unit matrices, product of hstepm matrices, stored + in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ + + hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); + + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ + + printf("%d|",(int)age);fflush(stdout); + fprintf(ficlog,"%d|",(int)age);fflush(ficlog); + + /* Computing expectancies */ + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++) + for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ + eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; + + /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ + + } + + fprintf(ficreseij,"%3.0f",age ); + for(i=1; i<=nlstate;i++){ + eip=0; + for(j=1; j<=nlstate;j++){ + eip +=eij[i][j][(int)age]; + fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] ); + } + fprintf(ficreseij,"%9.4f", eip ); + } + fprintf(ficreseij,"\n"); + + } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + printf("\n"); + fprintf(ficlog,"\n"); + +} + +void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] ) + +{ + /* Covariances of health expectancies eij and of total life expectancies according + to initial status i, ei. . + */ + int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji; + double age, agelim, hf; + double ***p3matp, ***p3matm, ***varhe; double **dnewm,**doldm; - double *xp; + double *xp, *xm; double **gp, **gm; double ***gradg, ***trgradg; int theta; + double eip, vip; + varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); xp=vector(1,npar); + xm=vector(1,npar); dnewm=matrix(1,nlstate*nlstate,1,npar); doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); - fprintf(ficreseij,"# Health expectancies\n"); - fprintf(ficreseij,"# Age"); - for(i=1; i<=nlstate;i++) + pstamp(ficresstdeij); + fprintf(ficresstdeij,"# Health expectancies with standard errors\n"); + fprintf(ficresstdeij,"# Age"); + for(i=1; i<=nlstate;i++){ for(j=1; j<=nlstate;j++) - fprintf(ficreseij," %1d-%1d (SE)",i,j); - fprintf(ficreseij,"\n"); + fprintf(ficresstdeij," e%1d%1d (SE)",i,j); + fprintf(ficresstdeij," e%1d. ",i); + } + fprintf(ficresstdeij,"\n"); + pstamp(ficrescveij); + fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n"); + fprintf(ficrescveij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate;j++){ + cptj= (j-1)*nlstate+i; + for(i2=1; i2<=nlstate;i2++) + for(j2=1; j2<=nlstate;j2++){ + cptj2= (j2-1)*nlstate+i2; + if(cptj2 <= cptj) + fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2); + } + } + fprintf(ficrescveij,"\n"); + if(estepm < stepm){ printf ("Problem %d lower than %d\n",estepm, stepm); } @@ -2318,77 +2617,64 @@ void evsij(char fileres[], double ***eij */ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ + /* If stepm=6 months */ + /* nhstepm age range expressed in number of stepm */ agelim=AGESUP; - for (age=bage; age<=fage; age ++){ /* If stepm=6 months */ - /* nhstepm age range expressed in number of stepm */ - nstepm=(int) rint((agelim-age)*YEARM/stepm); - /* Typically if 20 years nstepm = 20*12/6=40 stepm */ - /* if (stepm >= YEARM) hstepm=1;*/ - nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); - gp=matrix(0,nhstepm,1,nlstate*nlstate); - gm=matrix(0,nhstepm,1,nlstate*nlstate); + nstepm=(int) rint((agelim-age)*YEARM/stepm); + /* Typically if 20 years nstepm = 20*12/6=40 stepm */ + /* if (stepm >= YEARM) hstepm=1;*/ + nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ + + p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); + trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); + gp=matrix(0,nhstepm,1,nlstate*nlstate); + gm=matrix(0,nhstepm,1,nlstate*nlstate); + + for (age=bage; age<=fage; age ++){ /* Computed by stepm unit matrices, product of hstepm matrices, stored in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ - hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij); - hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ /* Computing Variances of health expectancies */ - - for(theta=1; theta <=npar; theta++){ + /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to + decrease memory allocation */ + for(theta=1; theta <=npar; theta++){ for(i=1; i<=npar; i++){ xp[i] = x[i] + (i==theta ?delti[theta]:0); + xm[i] = x[i] - (i==theta ?delti[theta]:0); } - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); + hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); + hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); - cptj=0; for(j=1; j<= nlstate; j++){ for(i=1; i<=nlstate; i++){ - cptj=cptj+1; - for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){ - gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; + for(h=0; h<=nhstepm-1; h++){ + gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.; + gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.; } } } - - for(i=1; i<=npar; i++) - xp[i] = x[i] - (i==theta ?delti[theta]:0); - hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); - - cptj=0; - for(j=1; j<= nlstate; j++){ - for(i=1;i<=nlstate;i++){ - cptj=cptj+1; - for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){ - - gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.; - } - } - } - for(j=1; j<= nlstate*nlstate; j++) + for(ij=1; ij<= nlstate*nlstate; ij++) for(h=0; h<=nhstepm-1; h++){ - gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; + gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta]; } - } - -/* End theta */ - - trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); - - for(h=0; h<=nhstepm-1; h++) + }/* End theta */ + + + for(h=0; h<=nhstepm-1; h++) for(j=1; j<=nlstate*nlstate;j++) for(theta=1; theta <=npar; theta++) trgradg[h][j][theta]=gradg[h][theta][j]; - + - for(i=1;i<=nlstate*nlstate;i++) - for(j=1;j<=nlstate*nlstate;j++) - varhe[i][j][(int)age] =0.; + for(ij=1;ij<=nlstate*nlstate;ij++) + for(ji=1;ji<=nlstate*nlstate;ji++) + varhe[ij][ji][(int)age] =0.; printf("%d|",(int)age);fflush(stdout); fprintf(ficlog,"%d|",(int)age);fflush(ficlog); @@ -2396,39 +2682,60 @@ void evsij(char fileres[], double ***eij for(k=0;k<=nhstepm-1;k++){ matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); - for(i=1;i<=nlstate*nlstate;i++) - for(j=1;j<=nlstate*nlstate;j++) - varhe[i][j][(int)age] += doldm[i][j]*hf*hf; + for(ij=1;ij<=nlstate*nlstate;ij++) + for(ji=1;ji<=nlstate*nlstate;ji++) + varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf; } } /* Computing expectancies */ + hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++) for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){ - eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf; + eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf; -/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ + /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/ } - fprintf(ficreseij,"%3.0f",age ); - cptj=0; + fprintf(ficresstdeij,"%3.0f",age ); + for(i=1; i<=nlstate;i++){ + eip=0.; + vip=0.; + for(j=1; j<=nlstate;j++){ + eip += eij[i][j][(int)age]; + for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */ + vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age]; + fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) ); + } + fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip)); + } + fprintf(ficresstdeij,"\n"); + + fprintf(ficrescveij,"%3.0f",age ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++){ - cptj++; - fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) ); + cptj= (j-1)*nlstate+i; + for(i2=1; i2<=nlstate;i2++) + for(j2=1; j2<=nlstate;j2++){ + cptj2= (j2-1)*nlstate+i2; + if(cptj2 <= cptj) + fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]); + } } - fprintf(ficreseij,"\n"); + fprintf(ficrescveij,"\n"); - free_matrix(gm,0,nhstepm,1,nlstate*nlstate); - free_matrix(gp,0,nhstepm,1,nlstate*nlstate); - free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); - free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); } + free_matrix(gm,0,nhstepm,1,nlstate*nlstate); + free_matrix(gp,0,nhstepm,1,nlstate*nlstate); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); + free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); + free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); printf("\n"); fprintf(ficlog,"\n"); + free_vector(xm,1,npar); free_vector(xp,1,npar); free_matrix(dnewm,1,nlstate*nlstate,1,npar); free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); @@ -2436,7 +2743,7 @@ void evsij(char fileres[], double ***eij } /************ Variance ******************/ -void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav) +void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[]) { /* Variance of health expectancies */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/ @@ -2487,7 +2794,9 @@ void varevsij(char optionfilefiname[], d fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev); } printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); + pstamp(ficresprobmorprev); fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); fprintf(ficresprobmorprev,"# Age cov=%-d",ij); for(j=nlstate+1; j<=(nlstate+ndeath);j++){ @@ -2497,16 +2806,21 @@ void varevsij(char optionfilefiname[], d } fprintf(ficresprobmorprev,"\n"); fprintf(ficgp,"\n# Routine varevsij"); + /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ fprintf(fichtm,"\n
  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

  • \n"); fprintf(fichtm,"\n
    %s
    \n",digitp); /* } */ varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - - fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n"); + pstamp(ficresvij); + fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are "); + if(popbased==1) + fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)"); + else + fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n"); fprintf(ficresvij,"# Age"); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate;j++) - fprintf(ficresvij," Cov(e%1d, e%1d)",i,j); + fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j); fprintf(ficresvij,"\n"); xp=vector(1,npar); @@ -2734,7 +3048,7 @@ void varevsij(char optionfilefiname[], d } /* end varevsij */ /************ Variance of prevlim ******************/ -void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) +void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[]) { /* Variance of prevalence limit */ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/ @@ -2747,8 +3061,9 @@ void varprevlim(char fileres[], double * double **gradg, **trgradg; double age,agelim; int theta; - - fprintf(ficresvpl,"# Standard deviation of stable prevalences \n"); + + pstamp(ficresvpl); + fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n"); fprintf(ficresvpl,"# Age"); for(i=1; i<=nlstate;i++) fprintf(ficresvpl," %1d-%1d",i,i); @@ -2817,7 +3132,7 @@ 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) +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 k2, l2, j1, z1; @@ -2862,13 +3177,15 @@ void varprob(char optionfilefiname[], do fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov); printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor); - + pstamp(ficresprob); fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n"); fprintf(ficresprob,"# Age"); + pstamp(ficresprobcov); fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n"); fprintf(ficresprobcov,"# Age"); + pstamp(ficresprobcor); fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n"); - fprintf(ficresprobcov,"# Age"); + fprintf(ficresprobcor,"# Age"); for(i=1; i<=nlstate;i++) @@ -3119,6 +3436,8 @@ To be simple, these graphs help to under } free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); + free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); + free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); free_vector(xp,1,npar); fclose(ficresprob); fclose(ficresprobcov); @@ -3137,20 +3456,24 @@ void printinghtml(char fileres[], char t double jprev2, double mprev2,double anprev2){ int jj1, k1, i1, cpt; - fprintf(fichtm,"
    • Result files (first order: no variance)

      \n \ + fprintf(fichtm,""); + fprintf(fichtm,"
      • Result files (first order: no variance)

        \n \ - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): %s
        \n ", jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p")); fprintf(fichtm,"\ - Estimated transition probabilities over %d (stepm) months: %s
        \n ", stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij")); fprintf(fichtm,"\ - - Stable prevalence in each health state: %s
        \n", + - Period (stable) prevalence in each health state: %s
        \n", subdirf2(fileres,"pl"),subdirf2(fileres,"pl")); fprintf(fichtm,"\ - - Life expectancies by age and initial health status (estepm=%2d months): \ + - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \ %s
        \n
      • ", estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e")); + fprintf(fichtm," \n
        • Graphs
        • "); m=cptcoveff; @@ -3167,20 +3490,20 @@ 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); + 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); /* 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); - /* Stable prevalence in each health state */ + 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); + /* Period (stable) prevalence in each health state */ for(cpt=1; cpt- Stable prevalence in each health state : p%s%d%d.png
            \ -",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1); + fprintf(fichtm,"
            - 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,"\n
            - Health life expectancies by age and initial health state (%d): %s%d%d.png
            \ -",cpt,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 : %s%d%d.png
            \ +",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1); } } /* end i1 */ }/* End k1 */ @@ -3188,7 +3511,7 @@ fprintf(fichtm," \n
            • Graphs fprintf(fichtm,"\ -\n
            • Result files (second order: variances)

              \n\ +\n
            • Result files (second order: variances)

              \n\ - Parameter file with estimated parameters and covariance matrix: %s
              \n", rfileres,rfileres); fprintf(fichtm," - Variance of one-step probabilities: %s
              \n", @@ -3201,13 +3524,21 @@ fprintf(fichtm," \n
              • Graphs - Correlation matrix of one-step probabilities: %s
                \n", subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor")); fprintf(fichtm,"\ - - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): %s
                \n", + - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm=%2d months): \ + %s
                \n
              • ", + estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve")); + fprintf(fichtm,"\ + - (a) Health expectancies by health status at initial age (eij) and standard errors (in parentheses) (b) life expectancies and standard errors (ei.=ei1+ei2+...)(estepm=%2d months): \ + %s
                \n", + estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde")); + fprintf(fichtm,"\ + - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): %s
                \n", estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v")); fprintf(fichtm,"\ - - Health expectancies with their variances (no covariance): %s
                \n", + - Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors: %s
                \n", subdirf2(fileres,"t"),subdirf2(fileres,"t")); fprintf(fichtm,"\ - - Standard deviation of stable prevalences: %s
                \n",\ + - Standard deviation of period (stable) prevalences: %s
                \n",\ subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl")); /* if(popforecast==1) fprintf(fichtm,"\n */ @@ -3279,7 +3610,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); } - fprintf(ficgp,"\" t\"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 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)"); @@ -3327,7 +3658,8 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u for (k1=1; k1<= m ; k1 ++) { for (cpt=1; cpt<= nlstate ; cpt ++) { - k=2+nlstate*(2*cpt-2); + /* 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\ @@ -3341,9 +3673,11 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u */ for (i=1; i< nlstate ; i ++) { - fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1); + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1); + /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/ } + fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt); } } @@ -3902,28 +4236,28 @@ double gompertz(double x[]) { double A,B,L=0.0,sump=0.,num=0.; int i,n=0; /* n is the size of the sample */ + for (i=0;i<=imx-1 ; i++) { sump=sump+weight[i]; - sump=sump+1; + /* sump=sump+1;*/ num=num+1; } - /* for (i=1; i<=imx; i++) + /* for (i=0; i<=imx; i++) if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ - for (i=0;i<=imx-1 ; i++) + for (i=1;i<=imx ; i++) { - if (cens[i]==1 & wav[i]>1) - A=-x[1]/(x[2])* - (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12))); + if (cens[i] == 1 && wav[i]>1) + A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); - if (cens[i]==0 & wav[i]>1) - A=-x[1]/(x[2])* - (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12))) - +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM); + if (cens[i] == 0 && wav[i]>1) + A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) + +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); - if (wav[i]>1 & agecens[i]>15) { + /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ + if (wav[i] > 1 ) { /* ??? */ L=L+A*weight[i]; /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/ } @@ -3937,8 +4271,8 @@ double gompertz(double x[]) /******************* Printing html file ***********/ void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \ int lastpass, int stepm, int weightopt, char model[],\ - int imx, double p[],double **matcov){ - int i; + int imx, double p[],double **matcov,double agemortsup){ + int i,k; fprintf(fichtm,"
                • Result files

                  \n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):
                  "); fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year

                  ",p[1],p[2],agegomp); @@ -3946,6 +4280,15 @@ void printinghtmlmort(char fileres[], ch fprintf(fichtm," p[%d] = %lf [%f ; %f]
                  \n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); fprintf(fichtm,"

                  "); fprintf(fichtm,"
                "); + +fprintf(fichtm,"
                • Life table

                  \n
                  "); + + fprintf(fichtm,"\nAge lx qx d(x,x+1) Lx Tx e
                  "); + + for (k=agegomp;k<(agemortsup-2);k++) + fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf
                  \n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]); + + fflush(fichtm); } @@ -3975,6 +4318,7 @@ void printinggnuplotmort(char fileres[], + /***********************************************/ /**************** Main Program *****************/ /***********************************************/ @@ -3983,14 +4327,17 @@ int main(int argc, char *argv[]) { int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; + int linei, month, year,iout; int jj, ll, li, lj, lk, imk; int numlinepar=0; /* Current linenumber of parameter file */ int itimes; int NDIM=2; char ca[32], cb[32], cc[32]; + char dummy[]=" "; /* FILE *fichtm; *//* Html File */ /* FILE *ficgp;*/ /*Gnuplot File */ + struct stat info; double agedeb, agefin,hf; double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; @@ -4003,7 +4350,8 @@ int main(int argc, char *argv[]) int *indx; char line[MAXLINE], linepar[MAXLINE]; char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; - char pathr[MAXLINE]; + char pathr[MAXLINE], pathimach[MAXLINE]; + char **bp, *tok, *val; /* pathtot */ int firstobs=1, lastobs=10; int sdeb, sfin; /* Status at beginning and end */ int c, h , cpt,l; @@ -4013,6 +4361,8 @@ int main(int argc, char *argv[]) int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ int mobilav=0,popforecast=0; int hstepm, nhstepm; + int agemortsup; + float sumlpop=0.; double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; @@ -4037,7 +4387,7 @@ int main(int argc, char *argv[]) char z[1]="c", occ; char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; - char strstart[80], *strt, strtend[80]; + char *strt, strtend[80]; char *stratrunc; int lstra; @@ -4079,7 +4429,17 @@ int main(int argc, char *argv[]) printf("\n%s\n%s",version,fullversion); if(argc <=1){ printf("\nEnter the parameter file name: "); - scanf("%s",pathtot); + fgets(pathr,FILENAMELENGTH,stdin); + i=strlen(pathr); + if(pathr[i-1]=='\n') + pathr[i-1]='\0'; + for (tok = pathr; tok != NULL; ){ + printf("Pathr |%s|\n",pathr); + while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); + printf("val= |%s| pathr=%s\n",val,pathr); + strcpy (pathtot, val); + if(pathr[0] == '\0') break; /* Dirty */ + } } else{ strcpy(pathtot,argv[1]); @@ -4089,9 +4449,17 @@ int main(int argc, char *argv[]) printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ /* cutv(path,optionfile,pathtot,'\\');*/ + /* Split argv[0], imach program to get pathimach */ + printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]); + split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); + printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname); + /* strcpy(pathimach,argv[0]); */ + /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */ split(pathtot,path,optionfile,optionfilext,optionfilefiname); - printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); - chdir(path); + printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); + chdir(path); /* Can be a relative path */ + if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */ + printf("Current directory %s!\n",pathcd); strcpy(command,"mkdir "); strcat(command,optionfilefiname); if((outcmd=system(command)) != 0){ @@ -4115,12 +4483,12 @@ int main(int argc, char *argv[]) } fprintf(ficlog,"Log filename:%s\n",filelog); fprintf(ficlog,"\n%s\n%s",version,fullversion); - fprintf(ficlog,"\nEnter the parameter file name: "); - fprintf(ficlog,"pathtot=%s\n\ + fprintf(ficlog,"\nEnter the parameter file name: \n"); + fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ path=%s \n\ optionfile=%s\n\ optionfilext=%s\n\ - optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); + optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); printf("Local time (at start):%s",strstart); fprintf(ficlog,"Local time (at start): %s",strstart); @@ -4257,7 +4625,6 @@ int main(int argc, char *argv[]) } fflush(ficlog); - p=param[1][1]; /* Reads comments: lines beginning with '#' */ @@ -4358,8 +4725,8 @@ int main(int argc, char *argv[]) /*-------- data file ----------*/ if((fic=fopen(datafile,"r"))==NULL) { - printf("Problem with datafile: %s\n", datafile);goto end; - fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; + printf("Problem while opening datafile: %s\n", datafile);goto end; + fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end; } n= lastobs; @@ -4381,40 +4748,125 @@ int main(int argc, char *argv[]) ncodemax=ivector(1,8); i=1; - while (fgets(line, MAXLINE, fic) != NULL) { - if ((i >= firstobs) && (i <=lastobs)) { - - for (j=maxwav;j>=1;j--){ - cutv(stra, strb,line,' '); s[j][i]=atoi(strb); - strcpy(line,stra); - cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra); + linei=0; + while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { + linei=linei+1; + for(j=strlen(line); j>=0;j--){ /* Untabifies line */ + if(line[j] == '\t') + line[j] = ' '; + } + for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ + ; + }; + line[j+1]=0; /* Trims blanks at end of line */ + if(line[0]=='#'){ + fprintf(ficlog,"Comment line\n%s\n",line); + printf("Comment line\n%s\n",line); + continue; + } + + for (j=maxwav;j>=1;j--){ + cutv(stra, strb,line,' '); + errno=0; + lval=strtol(strb,&endptr,10); + /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%d' at line number %d %s 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); + exit(1); } - - cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); - - cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); - - cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); - for (j=ncovcol;j>=1;j--){ - cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); - } - lstra=strlen(stra); - if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ - stratrunc = &(stra[lstra-9]); - num[i]=atol(stratrunc); + s[j][i]=lval; + + strcpy(line,stra); + cutv(stra, strb,line,' '); + if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + } + else if(iout=sscanf(strb,"%s.") != 0){ + month=99; + year=9999; + }else{ + printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j); + exit(1); + } + anint[j][i]= (double) year; + mint[j][i]= (double)month; + strcpy(line,stra); + } /* ENd Waves */ + + cutv(stra, strb,line,' '); + if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + } + else if(iout=sscanf(strb,"%s.",dummy) != 0){ + month=99; + year=9999; + }else{ + printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line); + exit(1); + } + andc[i]=(double) year; + moisdc[i]=(double) month; + strcpy(line,stra); + + cutv(stra, strb,line,' '); + if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ + } + else if(iout=sscanf(strb,"%s.") != 0){ + month=99; + year=9999; + }else{ + printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j); + exit(1); + } + annais[i]=(double)(year); + moisnais[i]=(double)(month); + strcpy(line,stra); + + cutv(stra, strb,line,' '); + errno=0; + dval=strtod(strb,&endptr); + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei); + exit(1); + } + weight[i]=dval; + strcpy(line,stra); + + for (j=ncovcol;j>=1;j--){ + cutv(stra, strb,line,' '); + errno=0; + lval=strtol(strb,&endptr,10); + if( strb[0]=='\0' || (*endptr != '\0')){ + printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line); + exit(1); + } + if(lval <-1 || lval >1){ + printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \ + Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \ + for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \ + For example, for multinomial values like 1, 2 and 3,\n \ + build V1=0 V2=0 for the reference value (1),\n \ + V1=1 V2=0 for (2) \n \ + and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \ + output of IMaCh is often meaningless.\n \ + Exiting.\n",lval,linei, i,line,j); + exit(1); } - else - num[i]=atol(stra); - - /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ - printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ - - i=i+1; - } - } + covar[j][i]=(double)(lval); + strcpy(line,stra); + } + lstra=strlen(stra); + + if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ + stratrunc = &(stra[lstra-9]); + num[i]=atol(stratrunc); + } + else + num[i]=atol(stra); + /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ + printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ + + i=i+1; + } /* End loop reading data */ + fclose(fic); /* printf("ii=%d", ij); scanf("%d",i);*/ imx=i-1; /* Number of individuals */ @@ -4428,12 +4880,12 @@ int main(int argc, char *argv[]) if (s[4][i]==9) s[4][i]=-1; printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/ - for (i=1; i<=imx; i++) + /* for (i=1; i<=imx; i++) */ /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08; else weight[i]=1;*/ - /* Calculation of the number of parameter from char model*/ + /* Calculation of the number of parameters from char model */ Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ Tprod=ivector(1,15); Tvaraff=ivector(1,15); @@ -4512,8 +4964,7 @@ int main(int argc, char *argv[]) printf("cptcovprod=%d ", cptcovprod); fprintf(ficlog,"cptcovprod=%d ", cptcovprod); - scanf("%d ",i); - fclose(fic);*/ + scanf("%d ",i);*/ /* if(mle==1){*/ if (weightopt != 1) { /* Maximisation without weights*/ @@ -4546,7 +4997,7 @@ int main(int argc, char *argv[]) for (i=1; i<=imx; i++) { agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); for(m=firstpass; (m<= lastpass); m++){ - if(s[m][i] >0){ + 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) @@ -4562,8 +5013,7 @@ int main(int argc, char *argv[]) } } else if(s[m][i] !=9){ /* Standard case, age in fractional - years but with the precision of a - month */ + years but with the precision of a month */ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); if((int)mint[m][i]==99 || (int)anint[m][i]==9999) agev[m][i]=1; @@ -4705,11 +5155,13 @@ Title=%s
                  Datafile=%s Firstpass=%d La \n\
                  \
                  • Parameter files

                    \n\ + - Parameter file: %s.%s
                    \n\ - Copy of the parameter file: o%s
                    \n\ - Log file of the run: %s
                    \n\ - Gnuplot file name: %s
                    \n\ - Date and time at start: %s
                  \n",\ fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\ + optionfilefiname,optionfilext,optionfilefiname,optionfilext,\ fileres,fileres,\ filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart); fflush(fichtm); @@ -4720,7 +5172,7 @@ Title=%s
                  Datafile=%s Firstpass=%d La /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart); fprintf(fichtm,"\n"); fprintf(fichtm,"
                  Total number of observations=%d
                  \n\ @@ -4739,6 +5191,7 @@ 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*/ + if (mle==-3){ ximort=matrix(1,NDIM,1,NDIM); cens=ivector(1,n); @@ -4748,9 +5201,9 @@ Interval (in months) between two waves: for (i=1; i<=imx; i++){ dcwave[i]=-1; - for (j=1; j<=lastpass; j++) - if (s[j][i]>nlstate) { - dcwave[i]=j; + for (m=firstpass; m<=lastpass; m++) + if (s[m][i]>nlstate) { + dcwave[i]=m; /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ break; } @@ -4759,12 +5212,16 @@ Interval (in months) between two waves: for (i=1; i<=imx; i++) { if (wav[i]>0){ ageexmed[i]=agev[mw[1][i]][i]; - j=wav[i];agecens[i]=1.; - if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i]; - cens[i]=1; - - if (ageexmed[i]<1) cens[i]=-1; - if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ; + j=wav[i]; + agecens[i]=1.; + + if (ageexmed[i]> 1 && wav[i] > 0){ + agecens[i]=agev[mw[j][i]][i]; + cens[i]= 1; + }else if (ageexmed[i]< 1) + cens[i]= -1; + if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass) + cens[i]=0 ; } else cens[i]=-1; } @@ -4773,29 +5230,29 @@ Interval (in months) between two waves: for (j=1;j<=NDIM;j++) ximort[i][j]=(i == j ? 1.0 : 0.0); } - - p[1]=0.1; p[2]=0.1; + + p[1]=0.0268; p[NDIM]=0.083; /*printf("%lf %lf", p[1], p[2]);*/ - printf("Powell\n"); fprintf(ficlog,"Powell\n"); - strcpy(filerespow,"pow-mort"); - strcat(filerespow,fileres); - if((ficrespow=fopen(filerespow,"w"))==NULL) { - printf("Problem with resultfile: %s\n", filerespow); - fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); - } - fprintf(ficrespow,"# Powell\n# iter -2*LL"); - /* for (i=1;i<=nlstate;i++) - for(j=1;j<=nlstate+ndeath;j++) - if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); - */ - fprintf(ficrespow,"\n"); - + printf("Powell\n"); fprintf(ficlog,"Powell\n"); + strcpy(filerespow,"pow-mort"); + strcat(filerespow,fileres); + if((ficrespow=fopen(filerespow,"w"))==NULL) { + printf("Problem with resultfile: %s\n", filerespow); + fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); + } + fprintf(ficrespow,"# Powell\n# iter -2*LL"); + /* for (i=1;i<=nlstate;i++) + for(j=1;j<=nlstate+ndeath;j++) + if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); + */ + fprintf(ficrespow,"\n"); + powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); fclose(ficrespow); - hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); + hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); for(i=1; i <=NDIM; i++) for(j=i+1;j<=NDIM;j++) @@ -4812,14 +5269,49 @@ Interval (in months) between two waves: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp); for (i=1;i<=NDIM;i++) printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i])); - replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */ + + lsurv=vector(1,AGESUP); + lpop=vector(1,AGESUP); + tpop=vector(1,AGESUP); + lsurv[agegomp]=100000; + + for (k=agegomp;k<=AGESUP;k++) { + agemortsup=k; + if (p[1]*exp(p[2]*(k-agegomp))>1) break; + } + + for (k=agegomp;k=1 */ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ @@ -5045,7 +5537,7 @@ 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);*/ - replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */ + replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */ printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\ @@ -5067,17 +5559,18 @@ Interval (in months) between two waves: fclose(ficres); - /*--------------- Prevalence limit (stable prevalence) --------------*/ + /*--------------- Prevalence limit (period or stable prevalence) --------------*/ strcpy(filerespl,"pl"); strcat(filerespl,fileres); if((ficrespl=fopen(filerespl,"w"))==NULL) { - printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end; - fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end; + 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 stable prevalence: result on file '%s' \n", filerespl); - fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl); - fprintf(ficrespl,"#Stable prevalence \n"); + 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"); @@ -5137,7 +5630,7 @@ Interval (in months) between two waves: 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++){ @@ -5174,7 +5667,7 @@ Interval (in months) between two waves: } } - varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax); + varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart); fclose(ficrespij); @@ -5207,8 +5700,8 @@ Interval (in months) between two waves: printf("Problem with total LE resultfile: %s\n", filerest);goto end; fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end; } - printf("Computing Total LEs with variances: file '%s' \n", filerest); - fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); + printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); + fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); strcpy(filerese,"e"); @@ -5220,6 +5713,24 @@ 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); + strcpy(fileresstde,"stde"); + strcat(fileresstde,fileres); + if((ficresstdeij=fopen(fileresstde,"w"))==NULL) { + printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); + fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0); + } + printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); + fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde); + + strcpy(filerescve,"cve"); + strcat(filerescve,fileres); + if((ficrescveij=fopen(filerescve,"w"))==NULL) { + printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); + fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0); + } + printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); + fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve); + strcpy(fileresv,"v"); strcat(fileresv,fileres); if((ficresvij=fopen(fileresv,"w"))==NULL) { @@ -5252,9 +5763,16 @@ Interval (in months) between two waves: fprintf(ficrest,"******\n"); fprintf(ficreseij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) + fprintf(ficresstdeij,"\n#****** "); + fprintf(ficrescveij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) { fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + } fprintf(ficreseij,"******\n"); + fprintf(ficresstdeij,"******\n"); + fprintf(ficrescveij,"******\n"); fprintf(ficresvij,"\n#****** "); for(j=1;j<=cptcoveff;j++) @@ -5263,17 +5781,18 @@ Interval (in months) between two waves: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; - evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); + evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); + cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; - varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav); + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart); if(popbased==1){ - varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav); + varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart); } - - fprintf(ficrest,"#Total LEs with variances: e.. (std) "); + pstamp(ficrest); + fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) "); for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i); fprintf(ficrest,"\n"); @@ -5321,19 +5840,21 @@ Interval (in months) between two waves: free_ivector(cod,1,n); free_ivector(tab,1,NCOVMAX); fclose(ficreseij); + fclose(ficresstdeij); + fclose(ficrescveij); fclose(ficresvij); fclose(ficrest); fclose(ficpar); - /*------- Variance of stable prevalence------*/ + /*------- Variance of period (stable) prevalence------*/ strcpy(fileresvpl,"vpl"); strcat(fileresvpl,fileres); if((ficresvpl=fopen(fileresvpl,"w"))==NULL) { - printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl); + printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl); exit(0); } - printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl); + 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++){ @@ -5345,7 +5866,7 @@ Interval (in months) between two waves: varpl=matrix(1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; - varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); + 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); } } @@ -5357,11 +5878,11 @@ Interval (in months) between two waves: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); } /* mle==-3 arrives here for freeing */ + free_matrix(prlim,1,nlstate,1,nlstate); 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); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); - free_matrix(covar,0,NCOVMAX,1,n); free_matrix(matcov,1,npar,1,npar); /*free_vector(delti,1,npar);*/ @@ -5376,7 +5897,8 @@ Interval (in months) between two waves: free_ivector(Tage,1,15); free_ivector(Tcode,1,100); - + free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); + free_imatrix(codtab,1,100,1,10); fflush(fichtm); fflush(ficgp); @@ -5394,7 +5916,7 @@ Interval (in months) between two waves: tm = *localtime(&end_time.tv_sec); tmg = *gmtime(&end_time.tv_sec); strcpy(strtend,asctime(&tm)); - printf("Local time at start %s\nLocaltime at end %s",strstart, strtend); + 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)); @@ -5410,13 +5932,38 @@ Interval (in months) between two waves: fclose(ficlog); /*------ End -----------*/ - chdir(path); - strcpy(plotcmd,GNUPLOTPROGRAM); - strcat(plotcmd," "); - strcat(plotcmd,optionfilegnuplot); - printf("Starting graphs with: %s",plotcmd);fflush(stdout); + + printf("Before Current directory %s!\n",pathcd); + if(chdir(pathcd) != 0) + printf("Can't move to directory %s!\n",path); + if(getcwd(pathcd,MAXLINE) > 0) + printf("Current directory %s!\n",pathcd); + /*strcat(plotcmd,CHARSEPARATOR);*/ + sprintf(plotcmd,"gnuplot"); +#ifndef UNIX + sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); +#endif + if(!stat(plotcmd,&info)){ + printf("Error 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); + }else + strcpy(pplotcmd,plotcmd); +#ifdef UNIX + strcpy(plotcmd,GNUPLOTPROGRAM); + if(!stat(plotcmd,&info)){ + printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); + }else + strcpy(pplotcmd,plotcmd); +#endif + }else + strcpy(pplotcmd,plotcmd); + + sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); + printf("Starting graphs with: %s\n",plotcmd);fflush(stdout); + if((outcmd=system(plotcmd)) != 0){ - printf(" Problem with gnuplot\n"); + printf("\n Problem with gnuplot\n"); } printf(" Wait..."); while (z[0] != 'q') { @@ -5424,7 +5971,10 @@ Interval (in months) between two waves: printf("\nType e to edit output files, g to graph again and q for exiting: "); scanf("%s",z); /* if (z[0] == 'c') system("./imach"); */ - if (z[0] == 'e') system(optionfilehtm); + if (z[0] == 'e') { + printf("Starting browser with: %s",optionfilehtm);fflush(stdout); + system(optionfilehtm); + } else if (z[0] == 'g') system(plotcmd); else if (z[0] == 'q') exit(0); }