--- imach/src/imach.c 2011/09/02 10:37:54 1.140 +++ imach/src/imach.c 2014/01/26 02:42:01 1.141 @@ -1,6 +1,9 @@ -/* $Id: imach.c,v 1.140 2011/09/02 10:37:54 brouard Exp $ +/* $Id: imach.c,v 1.141 2014/01/26 02:42:01 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + 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. @@ -391,10 +394,12 @@ #include extern int errno; -#include -/* +#ifdef LINUX #include #include "timeval.h" +#else +#include +#endif #ifdef GSL #include @@ -404,7 +409,7 @@ extern int errno; /* #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"*/ @@ -435,11 +440,11 @@ extern int errno; #define ODIRSEPARATOR '/' #endif -/* $Id: imach.c,v 1.140 2011/09/02 10:37:54 brouard Exp $ */ +/* $Id: imach.c,v 1.141 2014/01/26 02:42:01 brouard Exp $ */ /* $State: Exp $ */ -char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite "; -char fullversion[]="$Revision: 1.140 $ $Date: 2011/09/02 10:37:54 $"; +char version[]="Imach version 0.98n, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Sicentific Research 25293121)"; +char fullversion[]="$Revision: 1.141 $ $Date: 2014/01/26 02:42:01 $"; char strstart[80]; char optionfilext[10], optionfilefiname[FILENAMELENGTH]; int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ @@ -562,8 +567,14 @@ double dateintmean=0; double *weight; int **s; /* Status */ -double *agedc, **covar, idx; -int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff; +double *agedc; +double **covar; /**< covar[i,j], value of jth covariate for individual i, + * covar=matrix(0,NCOVMAX,1,n); + * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */ +double idx; +int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ +int **codtab; /**< codtab=imatrix(1,100,1,10); */ +int **Tvard, *Tprod, cptcovprod, *Tvaraff; double *lsurv, *lpop, *tpop; double ftol=FTOL; /* Tolerance for computing Max Likelihood */ @@ -1094,7 +1105,7 @@ char *asc_diff_time(long time_sec, char sec_left = (sec_left) %(60*60); minutes = (sec_left) /60; sec_left = (sec_left) % (60); - sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left); + sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left); return ascdiff; } @@ -1800,7 +1811,7 @@ double funcone( double *x) ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */ if(globpr){ - fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ + fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\ %11.6f %11.6f %11.6f ", \ num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i], 2*weight[i]*lli,out[s1][s2],savm[s1][s2]); @@ -2542,7 +2553,7 @@ 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 ****************************/ @@ -3936,7 +3947,7 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1); else fprintf(ficgp," exp(p%d+p%d*x",i,i+1); - ij=1; + ij=1;/* To be checked else nbcode[0][0] wrong */ for(j=3; j <=ncovmodel; j++) { if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); @@ -4608,8 +4619,8 @@ 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; } } @@ -4623,8 +4634,8 @@ int readdata(char datafile[], int firsto 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; @@ -4639,8 +4650,8 @@ int readdata(char datafile[], int firsto 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; @@ -4654,13 +4665,13 @@ int readdata(char datafile[], int firsto 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; } @@ -4672,8 +4683,8 @@ 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; } @@ -4688,13 +4699,13 @@ 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 \ @@ -4703,7 +4714,7 @@ 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 \ @@ -4765,6 +4776,11 @@ int decodemodel ( char model[], int last fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog); return 1; } + if (strstr(model,"v") !=0){ + printf("Error. 'v' must be in upper case 'V' model=%s ",model); + fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog); + return 1; + } /* 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 */ @@ -5161,7 +5177,7 @@ 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); } @@ -5177,7 +5193,8 @@ int main(int argc, char *argv[]) ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); numlinepar++; - puts(line); + fputs(line, stdout); + //puts(line); fputs(line,ficparo); fputs(line,ficlog); } @@ -5230,7 +5247,7 @@ 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); } @@ -5280,7 +5297,7 @@ 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); } @@ -5321,7 +5338,7 @@ 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); } @@ -5412,12 +5429,14 @@ 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(1,15); /* 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) */ + Tvard=imatrix(1,15,1,2); /* 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(1,15); /* 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 @@ -5476,11 +5495,10 @@ run imach with mle=-1 to get a correct t 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 */ h++; - if (h>m) { + if (h>m) h=1; - codtab[h][k]=j; - codtab[h][Tvar[k]]=j; - } + codtab[h][k]=j; + codtab[h][Tvar[k]]=j; printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); } } @@ -5508,7 +5526,8 @@ run imach with mle=-1 to get a correct t else{ fprintf(ficgp,"\n# %s\n", version); fprintf(ficgp,"# %s\n", optionfilegnuplot); - fprintf(ficgp,"set missing 'NaNq'\n"); + //fprintf(ficgp,"set missing 'NaNq'\n"); + fprintf(ficgp,"set datafile missing 'NaNq'\n"); } /* fclose(ficgp);*/ /*--------- index.htm --------*/ @@ -5947,7 +5966,7 @@ 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); @@ -5967,7 +5986,7 @@ 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); @@ -5981,7 +6000,7 @@ 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); @@ -5997,7 +6016,7 @@ 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); @@ -6374,10 +6393,9 @@ Interval (in months) between two waves: /*---------- End : free ----------------*/ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); - } /* mle==-3 arrives here for freeing */ endfree: - free_matrix(prlim,1,nlstate,1,nlstate); + free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */ free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); @@ -6418,9 +6436,9 @@ Interval (in months) between two waves: 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 was %d Sec.\n", end_time.tv_sec -start_time.tv_sec); + printf("Total time was %ld 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); + fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec); /* 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);