--- imach/src/imach.c 2006/03/16 17:45:01 1.121 +++ imach/src/imach.c 2014/06/20 16:45:46 1.153 @@ -1,6 +1,157 @@ -/* $Id: imach.c,v 1.121 2006/03/16 17:45:01 lievre Exp $ +/* $Id: imach.c,v 1.153 2014/06/20 16:45:46 brouard Exp $ $State: Exp $ $Log: imach.c,v $ + Revision 1.153 2014/06/20 16:45:46 brouard + Summary: If 3 live state, convergence to period prevalence on same graph + Author: Brouard + + Revision 1.152 2014/06/18 17:54:09 brouard + Summary: open browser, use gnuplot on same dir than imach if not found in the path + + Revision 1.151 2014/06/18 16:43:30 brouard + *** empty log message *** + + Revision 1.150 2014/06/18 16:42:35 brouard + Summary: If gnuplot is not in the path try on same directory than imach binary (OSX) + Author: brouard + + Revision 1.149 2014/06/18 15:51:14 brouard + Summary: Some fixes in parameter files errors + Author: Nicolas Brouard + + Revision 1.148 2014/06/17 17:38:48 brouard + Summary: Nothing new + Author: Brouard + + Just a new packaging for OS/X version 0.98nS + + Revision 1.147 2014/06/16 10:33:11 brouard + *** empty log message *** + + Revision 1.146 2014/06/16 10:20:28 brouard + Summary: Merge + Author: Brouard + + Merge, before building revised version. + + Revision 1.145 2014/06/10 21:23:15 brouard + Summary: Debugging with valgrind + Author: Nicolas Brouard + + Lot of changes in order to output the results with some covariates + After the Edimburgh REVES conference 2014, it seems mandatory to + improve the code. + No more memory valgrind error but a lot has to be done in order to + continue the work of splitting the code into subroutines. + Also, decodemodel has been improved. Tricode is still not + optimal. nbcode should be improved. Documentation has been added in + the source code. + + Revision 1.143 2014/01/26 09:45:38 brouard + Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising + + * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... + (Module): Version 0.98nR Running ok, but output format still only works for three covariates. + + Revision 1.142 2014/01/26 03:57:36 brouard + Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2 + + * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... + + Revision 1.141 2014/01/26 02:42:01 brouard + * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested... + + Revision 1.140 2011/09/02 10:37:54 brouard + Summary: times.h is ok with mingw32 now. + + Revision 1.139 2010/06/14 07:50:17 brouard + After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree. + I remember having already fixed agemin agemax which are pointers now but not cvs saved. + + Revision 1.138 2010/04/30 18:19:40 brouard + *** empty log message *** + + Revision 1.137 2010/04/29 18:11:38 brouard + (Module): Checking covariates for more complex models + than V1+V2. A lot of change to be done. Unstable. + + Revision 1.136 2010/04/26 20:30:53 brouard + (Module): merging some libgsl code. Fixing computation + of likelione (using inter/intrapolation if mle = 0) in order to + get same likelihood as if mle=1. + Some cleaning of code and comments added. + + Revision 1.135 2009/10/29 15:33:14 brouard + (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. + + Revision 1.134 2009/10/29 13:18:53 brouard + (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code. + + Revision 1.133 2009/07/06 10:21:25 brouard + just nforces + + Revision 1.132 2009/07/06 08:22:05 brouard + Many tings + + Revision 1.131 2009/06/20 16:22:47 brouard + Some dimensions resccaled + + Revision 1.130 2009/05/26 06:44:34 brouard + (Module): Max Covariate is now set to 20 instead of 8. A + lot of cleaning with variables initialized to 0. Trying to make + V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better. + + Revision 1.129 2007/08/31 13:49:27 lievre + Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting + + Revision 1.128 2006/06/30 13:02:05 brouard + (Module): Clarifications on computing e.j + + Revision 1.127 2006/04/28 18:11:50 brouard + (Module): Yes the sum of survivors was wrong since + imach-114 because nhstepm was no more computed in the age + loop. Now we define nhstepma in the age loop. + (Module): In order to speed up (in case of numerous covariates) we + compute health expectancies (without variances) in a first step + and then all the health expectancies with variances or standard + deviation (needs data from the Hessian matrices) which slows the + computation. + In the future we should be able to stop the program is only health + expectancies and graph are needed without standard deviations. + + Revision 1.126 2006/04/28 17:23:28 brouard + (Module): Yes the sum of survivors was wrong since + imach-114 because nhstepm was no more computed in the age + loop. Now we define nhstepma in the age loop. + Version 0.98h + + Revision 1.125 2006/04/04 15:20:31 lievre + Errors in calculation of health expectancies. Age was not initialized. + Forecasting file added. + + Revision 1.124 2006/03/22 17:13:53 lievre + Parameters are printed with %lf instead of %f (more numbers after the comma). + The log-likelihood is printed in the log file + + Revision 1.123 2006/03/20 10:52:43 brouard + * imach.c (Module):
=(p+1))(v[j-p-1] = t[j]);
- }
-}
+/* for(j=0; j<= lg; j++) { */
+/* if (j>=(p+1))(v[j-p-1] = t[j]); */
+/* } */
+/* } */
/********************** nrerror ********************/
@@ -678,7 +938,9 @@ double **matrix(long nrl, long nrh, long
for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;
- /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
+ /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
+m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
+that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
*/
}
@@ -952,7 +1214,7 @@ 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;
}
@@ -981,9 +1243,8 @@ void powell(double p[], double **xi, int
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);
- */
+ fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
+/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);
@@ -1114,8 +1375,8 @@ double **prevalim(double **prlim, int nl
int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;
- double **matprod2();
- double **out, cov[NCOVMAX], **pmij();
+ /* double **matprod2(); */ /* test */
+ double **out, cov[NCOVMAX+1], **pmij();
double **newm;
double agefin, delaymax=50 ; /* Max number of years to converge */
@@ -1130,21 +1391,23 @@ double **prevalim(double **prlim, int nl
for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
newm=savm;
/* Covariates have to be included here again */
- cov[2]=agefin;
-
- for (k=1; k<=cptcovn;k++) {
- cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
- /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
- }
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
- for (k=1; k<=cptcovprod;k++)
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-
- /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
- /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
- out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-
+ cov[2]=agefin;
+
+ for (k=1; k<=cptcovn;k++) {
+ cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
+ }
+ /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+ /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
+ /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
+
+ /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+ /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+ /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+ /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
+ /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
+ out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
+
savm=oldm;
oldm=newm;
maxmax=0.;
@@ -1155,6 +1418,7 @@ double **prevalim(double **prlim, int nl
sumnew=0;
for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
prlim[i][j]= newm[i][j]/(1-sumnew);
+ /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
max=FMAX(max,prlim[i][j]);
min=FMIN(min,prlim[i][j]);
}
@@ -1171,37 +1435,56 @@ double **prevalim(double **prlim, int nl
double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
{
- double s1, s2;
+ /* According to parameters values stored in x and the covariate's values stored in cov,
+ computes the probability to be observed in state j being in state i by appying the
+ model to the ncovmodel covariates (including constant and age).
+ lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
+ and, according on how parameters are entered, the position of the coefficient xij(nc) of the
+ ncth covariate in the global vector x is given by the formula:
+ j=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
+ Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
+ sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
+ Outputs ps[i][j] the probability to be observed in j being in j according to
+ the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
+ */
+ double s1, lnpijopii;
/*double t34;*/
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 (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
+ /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
+ lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
+/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
}
- ps[i][j]=s2;
+ ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
}
}
- /*ps[3][2]=1;*/
for(i=1; i<= nlstate; i++){
s1=0;
- for(j=1; ji} pij/pii=(1-pii)/pii and thus pii is known from s1 */
ps[i][i]=1./(s1+1.);
+ /* Computing other pijs */
for(j=1; j(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
} else if (mle==4){ /* mle=4 no inter-extrapolation */
lli=log(out[s1][s2]); /* Original formula */
- } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
- lli=log(out[s1][s2]); /* Original formula */
+ } else{ /* mle=0 back to 1 */
+ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
+ /*lli=log(out[s1][s2]); */ /* Original formula */
} /* End of if */
ipmx +=1;
sw += weight[i];
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]); */
+ /*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]);
@@ -1832,7 +2132,7 @@ double hessii(double x[], double delta,
int i;
int l=1, lmax=20;
double k1,k2;
- double p2[NPARMAX+1];
+ double p2[MAXPARM+1]; /* identical to x */
double res;
double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
double fx;
@@ -1841,19 +2141,19 @@ double hessii(double x[], double delta,
fx=func(x);
for (i=1;i<=npar;i++) p2[i]=x[i];
- for(l=0 ; l <=lmax; l++){
+ for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
l1=pow(10,l);
delts=delt;
for(k=1 ; k ");
- m=cptcoveff;
+ m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
jj1=0;
@@ -3481,16 +3885,16 @@ fprintf(fichtm," \n ");
- m=cptcoveff;
+ m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}
jj1=0;
@@ -3556,11 +3960,14 @@ fprintf(fichtm," \n
File (multiple files are possible if covariates are present): %s\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
fprintf(fichtm,"\n
Probability is computed over estepm=%d months.
\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
/* fprintf(fichtm,"\n
Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year
\n", stepm,YEARM,digitp,digit);
@@ -3128,20 +3514,19 @@ void varprob(char optionfilefiname[], do
int i, j=0, i1, k1, l1, t, tj;
int k2, l2, j1, z1;
int k=0,l, cptcode;
- int first=1, first1;
+ int first=1, first1, first2;
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
double **dnewm,**doldm;
double *xp;
double *gp, *gm;
double **gradg, **trgradg;
double **mu;
- double age,agelim, cov[NCOVMAX];
+ double age,agelim, cov[NCOVMAX+1];
double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
int theta;
char fileresprob[FILENAMELENGTH];
char fileresprobcov[FILENAMELENGTH];
char fileresprobcor[FILENAMELENGTH];
-
double ***varpij;
strcpy(fileresprob,"prob");
@@ -3189,7 +3574,7 @@ void varprob(char optionfilefiname[], do
fprintf(ficresprobcov,"\n");
fprintf(ficresprobcor,"\n");
*/
- xp=vector(1,npar);
+ xp=vector(1,npar);
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
@@ -3214,12 +3599,13 @@ standard deviations wide on each axis. <
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
\n");
cov[1]=1;
- tj=cptcoveff;
+ /* tj=cptcoveff; */
+ tj = (int) pow(2,cptcoveff);
if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;
- for(t=1; t<=tj;t++){
- for(i1=1; i1<=ncodemax[t];i1++){
- j1++;
+ for(j1=1; j1<=tj;j1++){
+ /*for(i1=1; i1<=ncodemax[t];i1++){ */
+ /*j1++;*/
if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
@@ -3242,19 +3628,24 @@ To be simple, these graphs help to under
fprintf(ficresprobcor, "**********\n#");
}
+ gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+ trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ gp=vector(1,(nlstate)*(nlstate+ndeath));
+ gm=vector(1,(nlstate)*(nlstate+ndeath));
for (age=bage; age<=fage; age ++){
cov[2]=age;
for (k=1; k<=cptcovn;k++) {
- cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+ cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
+ * 1 1 1 1 1
+ * 2 2 1 1 1
+ * 3 1 2 1 1
+ */
+ /* nbcode[1][1]=0 nbcode[1][2]=1;*/
}
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
- gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
- trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- gp=vector(1,(nlstate)*(nlstate+ndeath));
- gm=vector(1,(nlstate)*(nlstate+ndeath));
for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)
@@ -3292,10 +3683,6 @@ To be simple, these graphs help to under
matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
- free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
- free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
- free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
- free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
pmij(pmmij,cov,ncovmodel,x,nlstate);
@@ -3329,20 +3716,25 @@ To be simple, these graphs help to under
i=0;
for (k=1; k<=(nlstate);k++){
for (l=1; l<=(nlstate+ndeath);l++){
- i=i++;
+ i++;
fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
for (j=1; j<=i;j++){
+ /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
}
}
}/* end of loop for state */
} /* end of loop for age */
-
+ free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+ free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+ free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+ free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+
/* Confidence intervalle of pij */
/*
- fprintf(ficgp,"\nset noparametric;unset label");
+ fprintf(ficgp,"\nunset parametric;unset label");
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
fprintf(fichtm,"\n
Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname);
@@ -3352,7 +3744,7 @@ To be simple, these graphs help to under
*/
/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
- first1=1;
+ first1=1;first2=2;
for (k2=1; k2<=(nlstate);k2++){
for (l2=1; l2<=(nlstate+ndeath);l2++){
if(l2==k2) continue;
@@ -3373,6 +3765,16 @@ To be simple, these graphs help to under
/* Computing eigen value of matrix of covariance */
lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+ if ((lc2 <0) || (lc1 <0) ){
+ if(first2==1){
+ first1=0;
+ printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
+ }
+ fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
+ /* lc1=fabs(lc1); */ /* If we want to have them positive */
+ /* lc2=fabs(lc2); */
+ }
+
/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/*v21=sqrt(1.-v11*v11); *//* error */
@@ -3392,7 +3794,7 @@ To be simple, these graphs help to under
first=0;
fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+ fprintf(ficgp,"\nset ter png small size 320, 240");
fprintf(fichtmcov,"\n
Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year-1\
:\
%s%d%1d%1d-%1d%1d.png, ",k1,l1,k2,l2,\
@@ -3423,7 +3825,7 @@ To be simple, these graphs help to under
} /* k12 */
} /*l1 */
}/* k1 */
- } /* loop covariates */
+ /* } /* loop covariates */
}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
@@ -3460,14 +3862,16 @@ void printinghtml(char fileres[], char t
- Period (stable) prevalence in each health state: %s
\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
fprintf(fichtm,"\
- - (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",
+ - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates 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,"\
+ - Population projections by age and states: \
+ %s
\n", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
fprintf(fichtm," \n
");
}
/* Pij */
- fprintf(fichtm,"
- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png
\
-",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ fprintf(fichtm,"
- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d_1.png
\
+",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */
fprintf(fichtm,"
- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png
\
-",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d_2.png
\
+",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Period (stable) prevalence in each health state */
for(cpt=1; cpt
\
-",subdirf2(optionfilefiname,"p"),cpt,jj1,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
- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : %s%d%d.png
\
@@ -3523,11 +3927,11 @@ fprintf(fichtm," \n
\n
\n",
+ - 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,"\
- - 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"));
+ - Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors (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,"t"),subdirf2(fileres,"t"));
fprintf(fichtm,"\
- Standard deviation of period (stable) prevalences: %s
\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
@@ -3541,7 +3945,7 @@ fprintf(fichtm," \n
\n",\
- fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
+ optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
@@ -5176,7 +5883,8 @@ Interval (in months) between two waves:
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
if (mle==-3){
- ximort=matrix(1,NDIM,1,NDIM);
+ ximort=matrix(1,NDIM,1,NDIM);
+/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);
ageexmed=vector(1,n);
agecens=vector(1,n);
@@ -5214,25 +5922,110 @@ Interval (in months) between two waves:
ximort[i][j]=(i == j ? 1.0 : 0.0);
}
- p[1]=0.0268; p[NDIM]=0.083;
+ /*p[1]=0.0268; p[NDIM]=0.083;*/
/*printf("%lf %lf", p[1], p[2]);*/
+#ifdef GSL
+ printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
+#elsedef
printf("Powell\n"); fprintf(ficlog,"Powell\n");
+#endif
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);
}
+#ifdef GSL
+ fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
+#elsedef
fprintf(ficrespow,"# Powell\n# iter -2*LL");
+#endif
/* 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");
+#ifdef GSL
+ /* gsl starts here */
+ T = gsl_multimin_fminimizer_nmsimplex;
+ gsl_multimin_fminimizer *sfm = NULL;
+ gsl_vector *ss, *x;
+ gsl_multimin_function minex_func;
+
+ /* Initial vertex size vector */
+ ss = gsl_vector_alloc (NDIM);
+
+ if (ss == NULL){
+ GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
+ }
+ /* Set all step sizes to 1 */
+ gsl_vector_set_all (ss, 0.001);
+
+ /* Starting point */
+
+ x = gsl_vector_alloc (NDIM);
+
+ if (x == NULL){
+ gsl_vector_free(ss);
+ GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
+ }
+
+ /* Initialize method and iterate */
+ /* p[1]=0.0268; p[NDIM]=0.083; */
+/* gsl_vector_set(x, 0, 0.0268); */
+/* gsl_vector_set(x, 1, 0.083); */
+ gsl_vector_set(x, 0, p[1]);
+ gsl_vector_set(x, 1, p[2]);
+
+ minex_func.f = &gompertz_f;
+ minex_func.n = NDIM;
+ minex_func.params = (void *)&p; /* ??? */
+
+ sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
+ gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
+
+ printf("Iterations beginning .....\n\n");
+ printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
+
+ iteri=0;
+ while (rval == GSL_CONTINUE){
+ iteri++;
+ status = gsl_multimin_fminimizer_iterate(sfm);
+
+ if (status) printf("error: %s\n", gsl_strerror (status));
+ fflush(0);
+
+ if (status)
+ break;
+
+ rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
+ ssval = gsl_multimin_fminimizer_size (sfm);
+
+ if (rval == GSL_SUCCESS)
+ printf ("converged to a local maximum at\n");
+
+ printf("%5d ", iteri);
+ for (it = 0; it < NDIM; it++){
+ printf ("%10.5f ", gsl_vector_get (sfm->x, it));
+ }
+ printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
+ }
- powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
+
+ gsl_vector_free(x); /* initial values */
+ gsl_vector_free(ss); /* inital step size */
+ for (it=0; it
- Observed (cross-sectional) and period (incidence based) \
-prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png
\
-",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
+prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png
\
+",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}
fprintf(fichtm,"\n
- Total life expectancy by age and \
-health expectancies in states (1) and (2): %s%d.png
\
+health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
+true period expectancies (those weighted with period prevalences are also\
+ drawn in addition to the population based expectancies computed using\
+ observed and cahotic prevalences: %s%d.png
\
",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */
}/* End k1 */
@@ -3572,8 +3979,8 @@ health expectancies in states (1) and (2
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
char dirfileres[132],optfileres[132];
- int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
- int ng;
+ int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
+ int ng=0;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
@@ -3587,38 +3994,38 @@ void printinggnuplot(char fileres[], cha
strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");
/* 1eme*/
+ fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
for (cpt=1; cpt<= nlstate ; cpt ++) {
- for (k1=1; k1<= m ; k1 ++) {
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
- fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
+ for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
+ fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
+ fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\
set ylabel \"Probability\" \n\
-set ter png small\n\
-set size 0.65,0.65\n\
+set ter png small size 320, 240\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
}
- fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+ fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
- fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+ fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
- fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
+ fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
}
}
/*2 eme*/
-
+ fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
- fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+ fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;
@@ -3634,14 +4041,14 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
- fprintf(ficgp,"\" t\"\" w l 0,");
+ fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
- if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
- else fprintf(ficgp,"\" t\"\" w l 0,");
+ if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
+ else fprintf(ficgp,"\" t\"\" w l lt 0,");
}
}
@@ -3652,8 +4059,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
/* k=2+nlstate*(2*cpt-2); */
k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
- fprintf(ficgp,"set ter png small\n\
-set size 0.65,0.65\n\
+ fprintf(ficgp,"set ter png small size 320, 240\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
/*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
@@ -3673,28 +4079,29 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
}
/* CV preval stable (period) */
- for (k1=1; k1<= m ; k1 ++) {
- for (cpt=1; cpt<=nlstate ; cpt ++) {
+ for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
k=3;
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+ fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
+ fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
+ l=(nlstate+ndeath)*(cpt-1)+1;
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-set ter png small\nset size 0.65,0.65\n\
+set ter png small size 320, 240\n\
unset log y\n\
-plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-
- for (i=1; i< nlstate ; i ++)
- fprintf(ficgp,"+$%d",k+i+1);
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-
- l=3+(nlstate+ndeath)*cpt;
- fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
- for (i=1; i< nlstate ; i ++) {
- l=3+(nlstate+ndeath)*cpt;
- fprintf(ficgp,"+$%d",l+i+1);
- }
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
- }
- }
+plot [%.f:%.f] ", ageminpar, agemaxpar);
+ for (i=1; i<= nlstate ; i ++){
+ if(i==1)
+ fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
+ else
+ fprintf(ficgp,", '' ");
+ fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l,k+l);
+ for (j=1; j<= (nlstate-1) ; j ++)
+ fprintf(ficgp,"+$%d",k+l+j);
+ fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
+ } /* nlstate */
+ fprintf(ficgp,"\n");
+ } /* end cpt state*/
+ } /* end covariate */
/* proba elementaires */
for(i=1,jk=1; i <=nlstate; i++){
@@ -3708,15 +4115,15 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
}
}
}
-
+ /*goto avoid;*/
for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
for(jk=1; jk <=m; jk++) {
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
+ fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
if (ng==2)
fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
else
fprintf(ficgp,"\nset title \"Probability\"\n");
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
+ fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;
for(k2=1; k2<=nlstate; k2++) {
k3=i;
@@ -3726,13 +4133,13 @@ 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]]]);
- ij++;
- }
- else
+ /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
+ /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
+ /* ij++; */
+ /* } */
+ /* else */
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")/(1");
@@ -3741,11 +4148,11 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
ij=1;
for(j=3; j <=ncovmodel; j++){
- if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
- fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
- ij++;
- }
- else
+ /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
+ /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
+ /* ij++; */
+ /* } */
+ /* else */
fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")");
@@ -3758,6 +4165,7 @@ plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1
} /* end k2 */
} /* end jk */
} /* end ng */
+ avoid:
fflush(ficgp);
} /* end gnuplot */
@@ -4259,6 +4667,47 @@ double gompertz(double x[])
return -2*L*num/sump;
}
+#ifdef GSL
+/******************* Gompertz_f Likelihood ******************************/
+double gompertz_f(const gsl_vector *v, void *params)
+{
+ double A,B,LL=0.0,sump=0.,num=0.;
+ double *x= (double *) v->data;
+ 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;*/
+ num=num+1;
+ }
+
+
+ /* 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]);*/
+ printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
+ for (i=1;i<=imx ; i++)
+ {
+ if (cens[i] == 1 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
+
+ if (cens[i] == 0 && wav[i]>1)
+ A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
+ +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
+
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+ if (wav[i] > 1 ) { /* ??? */
+ LL=LL+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]);*/
+ }
+ }
+
+ /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
+ printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
+
+ return -2*LL*num/sump;
+}
+#endif
+
/******************* Printing html file ***********/
void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\
@@ -4300,87 +4749,548 @@ void printinggnuplotmort(char fileres[],
strcpy(optfileres,"vpl");
fprintf(ficgp,"set out \"graphmort.png\"\n ");
fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
- fprintf(ficgp, "set ter png small\n set log y\n");
- fprintf(ficgp, "set size 0.65,0.65\n");
+ fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
+ /* fprintf(ficgp, "set size 0.65,0.65\n"); */
fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
}
-
-
-
-
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
-
-int main(int argc, char *argv[])
+int readdata(char datafile[], int firstobs, int lastobs, int *imax)
{
- 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];
+ /*-------- data file ----------*/
+ FILE *fic;
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;
-
- double fret;
- double **xi,tmp,delta;
+ int i, j, n;
+ int linei, month, year,iout;
+ char line[MAXLINE], linetmp[MAXLINE];
+ char stra[80], strb[80];
+ char *stratrunc;
+ int lstra;
- double dum; /* Dummy variable */
- double ***p3mat;
- double ***mobaverage;
- int *indx;
- 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;
- int ju,jl, mi;
- int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
- int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
- 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;
- double bage, fage, age, agelim, agebase;
- double ftolpl=FTOL;
- double **prlim;
- double *severity;
- double ***param; /* Matrix of parameters */
- double *p;
- double **matcov; /* Matrix of covariance */
- double ***delti3; /* Scale */
- double *delti; /* Scale */
- double ***eij, ***vareij;
- double **varpl; /* Variances of prevalence limits by age */
- double *epj, vepp;
- double kk1, kk2;
- double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
- double **ximort;
- char *alph[]={"a","a","b","c","d","e"}, str[4];
- int *dcwave;
+ if((fic=fopen(datafile,"r"))==NULL) {
+ printf("Problem while opening datafile: %s\n", datafile);return 1;
+ fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
+ }
+
+ i=1;
+ 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;
+ }
+ trimbb(linetmp,line); /* Trims multiple blanks in line */
+ for (j=0; line[j]!='\0';j++){
+ line[j]=linetmp[j];
+ }
+
+
+ for (j=maxwav;j>=1;j--){
+ cutv(stra, strb, line, ' ');
+ if(strb[0]=='.') { /* Missing status */
+ lval=-1;
+ }else{
+ 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 '%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;
+ }
+ }
+ 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.",dummy) != 0){
+ month=99;
+ year=9999;
+ }else{
+ 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;
+ 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 %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;
+ 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.", dummy) != 0){
+ month=99;
+ year=9999;
+ }else{
+ 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 %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;
+
+ }
+ 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 %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;
+ }
+ weight[i]=dval;
+ strcpy(line,stra);
+
+ for (j=ncovcol;j>=1;j--){
+ cutv(stra, strb,line,' ');
+ if(strb[0]=='.') { /* Missing status */
+ lval=-1;
+ }else{
+ errno=0;
+ lval=strtol(strb,&endptr,10);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ 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 '%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 \
+ 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);
+ 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 \
+ 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);fflush(ficlog);
+ return 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 */
+
+ *imax=i-1; /* Number of individuals */
+ fclose(fic);
+
+ return (0);
+ endread:
+ printf("Exiting readdata: ");
+ fclose(fic);
+ return (1);
+
+
+
+}
+void removespace(char *str) {
+ char *p1 = str, *p2 = str;
+ do
+ while (*p2 == ' ')
+ p2++;
+ while (*p1++ = *p2++);
+}
+
+int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
+ * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
+ * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
+ * - cptcovn or number of covariates k of the models excluding age*products =6
+ * - cptcovage number of covariates with age*products =2
+ * - cptcovs number of simple covariates
+ * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
+ * which is a new column after the 9 (ncovcol) variables.
+ * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
+ * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
+ * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
+ * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
+ */
+{
+ int i, j, k, ks;
+ int i1, j1, k1, k2;
+ char modelsav[80];
+ char stra[80], strb[80], strc[80], strd[80],stre[80];
+
+ /*removespace(model);*/
+ if (strlen(model) >1){ /* If there is at least 1 covariate */
+ j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
+ j=nbocc(model,'+'); /**< j=Number of '+' */
+ j1=nbocc(model,'*'); /**< j1=Number of '*' */
+ cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
+ cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
+ /* including age products which are counted in cptcovage.
+ /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
+ cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
+ cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
+ strcpy(modelsav,model);
+ if (strstr(model,"AGE") !=0){
+ printf("Error. AGE must be in lower case 'age' model=%s ",model);
+ fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
+ 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;
+ }
+
+ /* Design
+ * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
+ * < ncovcol=8 >
+ * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
+ * k= 1 2 3 4 5 6 7 8
+ * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
+ * covar[k,i], value of kth covariate if not including age for individual i:
+ * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
+ * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
+ * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
+ * Tage[++cptcovage]=k
+ * if products, new covar are created after ncovcol with k1
+ * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
+ * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
+ * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
+ * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
+ * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
+ * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
+ * < ncovcol=8 >
+ * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
+ * k= 1 2 3 4 5 6 7 8 9 10 11 12
+ * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
+ * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
+ * p Tprod[1]@2={ 6, 5}
+ *p Tvard[1][1]@4= {7, 8, 5, 6}
+ * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
+ * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ *How to reorganize?
+ * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
+ * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
+ * {2, 1, 4, 8, 5, 6, 3, 7}
+ * Struct []
+ */
+
+ /* This loop fills the array Tvar from the string 'model'.*/
+ /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+ /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
+ /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
+ /* k=3 V4 Tvar[k=3]= 4 (from V4) */
+ /* k=2 V1 Tvar[k=2]= 1 (from V1) */
+ /* k=1 Tvar[1]=2 (from V2) */
+ /* k=5 Tvar[5] */
+ /* for (k=1; k<=cptcovn;k++) { */
+ /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
+ /* } */
+ /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
+ /*
+ * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
+ for(k=cptcovt; k>=1;k--) /**< Number of covariates */
+ Tvar[k]=0;
+ cptcovage=0;
+ for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
+ cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
+ modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
+ if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
+ /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+ /*scanf("%d",i);*/
+ if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
+ cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+ if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
+ /* covar is not filled and then is empty */
+ cptcovprod--;
+ cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
+ Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
+ cptcovage++; /* Sums the number of covariates which include age as a product */
+ Tage[cptcovage]=k; /* Tage[1] = 4 */
+ /*printf("stre=%s ", stre);*/
+ } else if (strcmp(strd,"age")==0) { /* or age*Vn */
+ cptcovprod--;
+ cutl(stre,strb,strc,'V');
+ Tvar[k]=atoi(stre);
+ cptcovage++;
+ Tage[cptcovage]=k;
+ } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
+ /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
+ cptcovn++;
+ cptcovprodnoage++;k1++;
+ cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+ Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
+ because this model-covariate is a construction we invent a new column
+ ncovcol + k1
+ If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
+ Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
+ cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
+ Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
+ Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
+ Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
+ k2=k2+2;
+ Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
+ Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
+ for (i=1; i<=lastobs;i++){
+ /* Computes the new covariate which is a product of
+ covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
+ covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+ }
+ } /* End age is not in the model */
+ } /* End if model includes a product */
+ else { /* no more sum */
+ /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+ /* scanf("%d",i);*/
+ cutl(strd,strc,strb,'V');
+ ks++; /**< Number of simple covariates */
+ cptcovn++;
+ Tvar[k]=atoi(strd);
+ }
+ strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
+ /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ scanf("%d",i);*/
+ } /* end of loop + */
+ } /* end model */
+
+ /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
+ If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
+
+ /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+ printf("cptcovprod=%d ", cptcovprod);
+ fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+
+ scanf("%d ",i);*/
+
+
+ return (0); /* with covar[new additional covariate if product] and Tage if age */
+ endread:
+ printf("Exiting decodemodel: ");
+ return (1);
+}
+
+calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
+{
+ int i, m;
+
+ for (i=1; i<=imx; i++) {
+ for(m=2; (m<= maxwav); m++) {
+ if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
+ anint[m][i]=9999;
+ 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 */
+ }
+ }
+ }
+
+ 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 || 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)
+ agev[m][i]=agedc[i];
+ /*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;
+ }
+ }
+ }
+ else if(s[m][i] !=9){ /* Standard case, age in fractional
+ 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;
+ else if(agev[m][i] < *agemin){
+ *agemin=agev[m][i];
+ printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
+ }
+ else if(agev[m][i] >*agemax){
+ *agemax=agev[m][i];
+ printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
+ }
+ /*agev[m][i]=anint[m][i]-annais[i];*/
+ /* agev[m][i] = age[i]+2*m;*/
+ }
+ else { /* =9 */
+ agev[m][i]=1;
+ s[m][i]=-1;
+ }
+ }
+ else /*= 0 Unknown */
+ 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);
+ return 1;
+ }
+ }
+ }
+
+ /*for (i=1; i<=imx; i++){
+ for (m=firstpass; (m
%s \
+ fprintf(fichtmcov,"\n
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n",\
- fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+ optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}
- fprintf(fichtm,"\n
%s \
+ fprintf(fichtm,"\n
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n\
\n\
@@ -5143,7 +5850,7 @@ Title=%s
Datafile=%s Firstpass=%d La
- Log file of the run: %s
\n\
- Gnuplot file name: %s
\n\
- Date and time at start: %s
Local time at start %s
Local time at end %s
",strstart, strtend);
+ fprintf(fichtm,"
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtm);
+ fprintf(fichtmcov,"
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtmcov);
fclose(ficgp);
fclose(ficlog);
@@ -5946,7 +6679,11 @@ Interval (in months) between two waves:
printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
if((outcmd=system(plotcmd)) != 0){
- printf("\n Problem with gnuplot\n");
+ printf("\n Problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+ printf("\n Trying on same directory\n");
+ sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
+ if((outcmd=system(plotcmd)) != 0)
+ printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
}
printf(" Wait...");
while (z[0] != 'q') {
@@ -5955,8 +6692,13 @@ Interval (in months) between two waves:
scanf("%s",z);
/* if (z[0] == 'c') system("./imach"); */
if (z[0] == 'e') {
- printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
- system(optionfilehtm);
+#ifdef OSX
+ sprintf(pplotcmd, "open %s", optionfilehtm);
+#else
+ sprintf(pplotcmd, "%s", optionfilehtm);
+#endif
+ printf("Starting browser with: %s",pplotcmd);fflush(stdout);
+ system(pplotcmd);
}
else if (z[0] == 'g') system(plotcmd);
else if (z[0] == 'q') exit(0);