/* $Id$
$State$
$Log$
+ Revision 1.90 2003/06/24 12:34:15 brouard
+ (Module): Some bugs corrected for windows. Also, when
+ mle=-1 a template is output in file "or"mypar.txt with the design
+ of the covariance matrix to be input.
+
Revision 1.89 2003/06/24 12:30:52 brouard
(Module): Some bugs corrected for windows. Also, when
mle=-1 a template is output in file "or"mypar.txt with the design
char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
char fullversion[]="$Revision$ $Date$";
-int erreur; /* Error number */
+int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
int npar=NPARMAX;
FILE *ficresilk;
FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
FILE *ficresprobmorprev;
-FILE *fichtm; /* Html File */
+FILE *fichtm, *fichtmcov; /* Html File */
FILE *ficreseij;
char filerese[FILENAMELENGTH];
FILE *ficresvij;
char fileregp[FILENAMELENGTH];
char popfile[FILENAMELENGTH];
-char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
+
+struct timeval start_time, end_time, curr_time, last_time, forecast_time;
+struct timezone tzp;
+extern int gettimeofday();
+struct tm tmg, tm, tmf, *gmtime(), *localtime();
+long time_value;
+extern long time();
+char strcurr[80], strfor[80];
#define NR_END 1
#define FREE_ARG char*
free_vector(pcom,1,n);
}
+char *asc_diff_time(long time_sec, char ascdiff[])
+{
+ long sec_left, days, hours, minutes;
+ days = (time_sec) / (60*60*24);
+ sec_left = (time_sec) % (60*60*24);
+ hours = (sec_left) / (60*60) ;
+ sec_left = (sec_left) %(60*60);
+ minutes = (sec_left) /60;
+ sec_left = (sec_left) % (60);
+ sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
+ return ascdiff;
+}
+
/*************** powell ************************/
void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
double (*func)(double []))
double del,t,*pt,*ptt,*xit;
double fp,fptt;
double *xits;
+ int niterf, itmp;
+
pt=vector(1,n);
ptt=vector(1,n);
xit=vector(1,n);
fp=(*fret);
ibig=0;
del=0.0;
- printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
- fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
- fprintf(ficrespow,"%d %.12f",*iter,*fret);
+ last_time=curr_time;
+ (void) gettimeofday(&curr_time,&tzp);
+ printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
+ fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
+ fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);
}
printf("\n");
fprintf(ficlog,"\n");
- fprintf(ficrespow,"\n");
+ fprintf(ficrespow,"\n");fflush(ficrespow);
+ if(*iter <=3){
+ tm = *localtime(&curr_time.tv_sec);
+ asctime_r(&tm,strcurr);
+ forecast_time=curr_time;
+ itmp = strlen(strcurr);
+ if(strcurr[itmp-1]=='\n')
+ 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);
+ for(niterf=10;niterf<=30;niterf+=10){
+ forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
+ tmf = *localtime(&forecast_time.tv_sec);
+ asctime_r(&tmf,strfor);
+/* strcpy(strfor,asctime(&tmf)); */
+ 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);
+ }
+ }
for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];
fptt=(*fret);
char *subdirf(char fileres[])
{
-
+ /* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/"); /* Add to the right */
strcat(tmpout,fileres);
wav[i]=mi;
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);
first=1;
j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
if(j==0) j=1; /* Survives at least one month after exam */
else if(j<0){
+ 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; /* Careful Patch */
+ 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("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,"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);
}
k=k+1;
/* 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){
+ nberr++;
printf("Error! Negative delay (%d) 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,"Error! Negative delay (%d) 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(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");
- fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
- fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
- fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
+ fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
+ fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
+ file %s<br>\n",optionfilehtmcov);
+ fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
+and drawn. It helps understanding how is the covariance between two incidences.\
+ They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+ fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
+It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
+would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
+standard deviations wide on each axis. <br>\
+ Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
+ and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
+To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
cov[1]=1;
tj=cptcoveff;
fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
- fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
+ fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s%d%1d%1d-%1d%1d.png\">\
%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+ fprintf(fichtm
cov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
+ fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
}else{
first=0;
- fprintf(fichtm," %d (%.3f),",(int) age, c12);
+ fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
fclose(ficresprob);
fclose(ficresprobcov);
fclose(ficresprobcor);
- /* fclose(ficgp);*/
+ fflush(ficgp);
+ fflush(fichtmcov);
}
} /* end of prwizard */
+
/***********************************************/
/**************** Main Program *****************/
/***********************************************/
int lstra;
long total_usecs;
- struct timeval start_time, end_time, curr_time;
- struct timezone tzp;
- extern int gettimeofday();
- struct tm tmg, tm, *gmtime(), *localtime();
- long time_value;
- extern long time();
/* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
(void) gettimeofday(&start_time,&tzp);
+ curr_time=start_time;
tm = *localtime(&start_time.tv_sec);
tmg = *gmtime(&start_time.tv_sec);
strcpy(strstart,asctime(&tm));
* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
*/
+ nberr=0; /* Number of errors and warnings */
+ nbwarn=0;
getcwd(pathcd, size);
printf("\n%s\n%s",version,fullversion);
printf("Localtime (at start):%s",strstart);
fprintf(ficlog,"Localtime (at start): %s",strstart);
fflush(ficlog);
+/* (void) gettimeofday(&curr_time,&tzp); */
+/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
/* */
strcpy(fileres,"r");
s[m][i]=-1;
}
if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
+ nberr++;
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
s[m][i]=-1;
}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
+ nberr++;
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
/*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
else {
if ((int)andc[i]!=9999){
+ nbwarn++;
printf("Warning negative age at death: %ld line:%d\n",num[i],i);
fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
agev[m][i]=-1;
for (i=1; i<=imx; i++) {
for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {
+ nberr++;
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
goto end;
/* fclose(ficgp);*/
/*--------- index.htm --------*/
- strcpy(optionfilehtm,optionfilefiname);
+ strcpy(optionfilehtm,optionfilefiname); /* Main html file */
strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);
}
+ strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
+ strcat(optionfilehtmcov,"-cov.htm");
+ if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
+ printf("Problem with %s \n",optionfilehtmcov), exit(0);
+ }
+ else{
+ fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
+<hr size=\"2\" color=\"#EC5E5E\"> \n\
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
+ fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+ }
+
fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
- Log file of the run: <a href=\"%s\">%s</a><br>\n\
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
- Date and time at start: %s</ul>\n",\
- fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
- model,fileres,fileres,\
+ fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+ fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
- /*fclose(fichtm);*/
fflush(fichtm);
strcpy(pathr,path);
fflush(ficgp);
- if(erreur >0){
- printf("End of Imach with error or warning %d\n",erreur);
- fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+ if((nberr >0) || (nbwarn>0)){
+ printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
+ fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
}else{
- printf("End of Imach\n");
- fprintf(ficlog,"End of Imach\n");
+ printf("End of Imach\n");
+ fprintf(ficlog,"End of Imach\n");
}
printf("See log file on %s\n",filelog);
- fclose(ficlog);
/* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
(void) gettimeofday(&end_time,&tzp);
tm = *localtime(&end_time.tv_sec);
tmg = *gmtime(&end_time.tv_sec);
strcpy(strtend,asctime(&tm));
printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend);
- fprintf(ficlog,"Localtime at start %s\nLocal time at end %s",strstart, strtend);
- /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
+ fprintf(ficlog,"Localtime 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. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
- fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
+ printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
+ fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
+ fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
fclose(fichtm);
+ fclose(fichtmcov);
fclose(ficgp);
+ fclose(ficlog);
/*------ End -----------*/
- end:
-#ifdef windows
- /* chdir(pathcd);*/
-#endif
chdir(path);
- /*system("wgnuplot graph.plt");*/
- /*system("../gp37mgw/wgnuplot graph.plt");*/
- /*system("cd ../gp37mgw");*/
- /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
strcpy(plotcmd,GNUPLOTPROGRAM);
strcat(plotcmd," ");
strcat(plotcmd,optionfilegnuplot);
printf("Starting graphs with: %s",plotcmd);fflush(stdout);
- system(plotcmd);
+ if((outcmd=system(plotcmd)) != 0){
+ printf(" Problem with gnuplot\n");
+ }
printf(" Wait...");
-
- /*#ifdef windows*/
while (z[0] != 'q') {
/* chdir(path); */
- printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+ printf("\nType e to edit output files, g to graph again and q for exiting: ");
scanf("%s",z);
- if (z[0] == 'c') system("./imach");
- else if (z[0] == 'e') system(optionfilehtm);
+/* if (z[0] == 'c') system("./imach"); */
+ if (z[0] == 'e') system(optionfilehtm);
else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);
}
- /*#endif */
+ end:
+ while (z[0] != 'q') {
+ printf("\nType q for exiting: ");
+ scanf("%s",z);
+ }
}
git://henry.ined.fr / .git / commitdiff