--- imach/src/imach.c 2006/01/25 00:51:50 1.110 +++ imach/src/imach.c 2006/02/27 12:17:45 1.115 @@ -1,6 +1,26 @@ -/* $Id: imach.c,v 1.110 2006/01/25 00:51:50 brouard Exp $ +/* $Id: imach.c,v 1.115 2006/02/27 12:17:45 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + 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) @@ -284,11 +304,11 @@ extern int errno; #define ODIRSEPARATOR '/' #endif -/* $Id: imach.c,v 1.110 2006/01/25 00:51:50 brouard Exp $ */ +/* $Id: imach.c,v 1.115 2006/02/27 12:17:45 brouard Exp $ */ /* $State: Exp $ */ -char version[]="Imach version 0.98a, January 2006, INED-EUROREVES "; -char fullversion[]="$Revision: 1.110 $ $Date: 2006/01/25 00:51:50 $"; +char version[]="Imach version 0.98c, February 2006, INED-EUROREVES "; +char fullversion[]="$Revision: 1.115 $ $Date: 2006/02/27 12:17:45 $"; int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ int nvar; int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; @@ -332,7 +352,7 @@ FILE *ficresvpl; char fileresvpl[FILENAMELENGTH]; char title[MAXLINE]; char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; -char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; +char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; char command[FILENAMELENGTH]; int outcmd=0; @@ -1651,6 +1671,7 @@ 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)); @@ -2205,11 +2226,11 @@ 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 */ @@ -3226,6 +3247,8 @@ 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); @@ -4109,6 +4132,7 @@ int main(int argc, char *argv[]) int NDIM=2; char ca[32], cb[32], cc[32]; + char dummy[]=" "; /* FILE *fichtm; *//* Html File */ /* FILE *ficgp;*/ /*Gnuplot File */ struct stat info; @@ -4125,6 +4149,7 @@ int main(int argc, char *argv[]) char line[MAXLINE], linepar[MAXLINE]; char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; char pathr[MAXLINE], pathimach[MAXLINE]; + char **bp, *tok, *val; /* pathtot */ int firstobs=1, lastobs=10; int sdeb, sfin; /* Status at beginning and end */ int c, h , cpt,l; @@ -4202,7 +4227,17 @@ 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; /* Un peu sale */ + } } else{ strcpy(pathtot,argv[1]); @@ -4510,114 +4545,116 @@ int main(int argc, char *argv[]) i=1; linei=0; - while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { + 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\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n",lval, i,line,linei,j,maxwav); - exit(1); - } - s[j][i]=lval; + 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; + } - strcpy(line,stra); - cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ - } - else if(iout=sscanf(strb,".") != 0){ - month=99; - year=9999; - }else{ - printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d. Exiting.\n",strb, i,line,linei,j); - exit(1); - } - anint[j][i]= (double) year; - mint[j][i]= (double)month; - strcpy(line,stra); - } /* ENd Waves */ - + for (j=maxwav;j>=1;j--){ cutv(stra, strb,line,' '); - if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ - } - else if(iout=sscanf(strb,".") != 0){ - month=99; - year=9999; - }else{ - printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d. Exiting.\n",strb, i,line,linei,j); + 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); } - andc[i]=(double) year; - moisdc[i]=(double) month; + s[j][i]=lval; + strcpy(line,stra); - - cutv(stra, strb,line,' '); + cutv(stra, strb,line,' '); if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ } - else if(iout=sscanf(strb,".") != 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\nShould be a year of exam at wave %d. Exiting.\n",strb, i,line,linei,j); + 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); } - annais[i]=(double)(year); - moisnais[i]=(double)(month); + 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; + 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\nShould be a weight. Exiting.\n",lval, i,line,linei); + exit(1); + } + weight[i]=(double)(lval); + 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\nShould be a weight. Exiting.\n",lval, i,line,linei); + 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); } - weight[i]=(double)(lval); - 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\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, i,line,linei); - exit(1); - } - if(lval <-1 || lval >1){ - printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,i,line,linei,j); - exit(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); + if(lval <-1 || lval >1){ + printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). 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 */ @@ -4715,8 +4752,7 @@ 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*/ @@ -4981,7 +5017,7 @@ Interval (in months) between two waves: ximort[i][j]=(i == j ? 1.0 : 0.0); } - p[1]=0.1; p[NDIM]=0.1; + p[1]=0.0268; p[NDIM]=0.083; /*printf("%lf %lf", p[1], p[2]);*/ @@ -5600,11 +5636,11 @@ 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);*/ @@ -5619,7 +5655,8 @@ 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); @@ -5654,32 +5691,29 @@ Interval (in months) between two waves: /*------ End -----------*/ chdir(path); -#ifndef UNIX - /* strcpy(plotcmd,"\""); */ -#endif - strcpy(plotcmd,pathimach); /*strcat(plotcmd,CHARSEPARATOR);*/ - strcat(plotcmd,GNUPLOTPROGRAM); + sprintf(plotcmd,"gnuplot"); #ifndef UNIX - strcat(plotcmd,".exe"); - /* strcat(plotcmd,"\"");*/ + sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); #endif - if(stat(plotcmd,&info)){ + if(!stat(plotcmd,&info)){ printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); - } - -#ifndef UNIX - strcpy(plotcmd,"\""); -#endif - strcat(plotcmd,pathimach); - strcat(plotcmd,GNUPLOTPROGRAM); -#ifndef UNIX - strcat(plotcmd,".exe"); - strcat(plotcmd,"\""); + 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 - strcat(plotcmd," "); - strcat(plotcmd,optionfilegnuplot); - printf("Starting graphs with: %s",plotcmd);fflush(stdout); + }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("\n Problem with gnuplot\n");