/* $Id$
$State$
$Log$
+ 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.
#include <time.h>
#include "timeval.h"
+#ifdef GSL
+#include <gsl/gsl_errno.h>
+#include <gsl/gsl_multimin.h>
+#endif
+
/* #include <libintl.h> */
/* #define _(String) gettext (String) */
/* $Id$ */
/* $State$ */
-char version[]="Imach version 0.98l, October 2009, INED-EUROREVES-Institut de longevite ";
+char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
char fullversion[]="$Revision$ $Date$";
char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];
double jmean=1; /* Mean space between 2 waves */
double **oldm, **newm, **savm; /* Working pointers to matrices */
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+/*FILE *fic ; */ /* Used in readdata only */
+FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
FILE *ficlog, *ficrespow;
int globpr=0; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */
}
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]]];
+ 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]);*/
lli= (savm[s1][s2]>(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];
dh[mi][i]=jk;
bh[mi][i]=0;
}else{ /* We want a negative bias in order to only have interpolation ie
- * at the price of an extra matrix product in likelihood */
+ * to avoid the price of an extra matrix product in likelihood */
dh[mi][i]=jk+1;
bh[mi][i]=ju;
}
/*********** Tricode ****************************/
void tricode(int *Tvar, int **nbcode, int imx)
{
-
+ /* Uses cptcovn+2*cptcovprod as the number of covariates */
/* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
- int cptcode=0;
+ int modmaxcovj=0; /* Modality max of covariates j */
cptcoveff=0;
for (k=0; k<maxncov; k++) Ndum[k]=0;
for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
- for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
- for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
- modality*/
- ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
- Ndum[ij]++; /*counts the occurence of this modality */
+ for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
+ for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
+ modality of this covariate Vj*/
+ ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
+ modality of the nth covariate of individual i. */
+ Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
/*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
- if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate (should be 0 or 1 now)
- Tvar[j]. If V=sex and male is 0 and
- female is 1, then cptcode=1.*/
+ if (ij > modmaxcovj) modmaxcovj=ij;
+ /* getting the maximum value of the modality of the covariate
+ (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
+ female is 1, then modmaxcovj=1.*/
}
- for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
- if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
- th covariate. In fact
- ncodemax[j]=2
- (dichotom. variables only) but
- it can be more */
+ for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*/
+ if( Ndum[i] != 0 )
+ ncodemax[j]++;
+ /* Number of modalities of the j th covariate. In fact
+ ncodemax[j]=2 (dichotom. variables only) but it could be more for
+ historical reasons */
} /* Ndum[-1] number of undefined modalities */
+ /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
ij=1;
- for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
- for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
+ for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
+ for (k=0; k<= maxncov; k++) { /* k=-1 ? NCOVMAX*/
if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
k is a modality. If we have model=V1+V1*sex
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[],\
}
+int readdata(char datafile[], int firstobs, int lastobs, int *imax)
+{
+ /*-------- data file ----------*/
+ FILE *fic;
+ char dummy[]=" ";
+ int i, j, n;
+ int linei, month, year,iout;
+ char line[MAXLINE], linetmp[MAXLINE];
+ char stra[80], strb[80];
+ char *stratrunc;
+ int lstra;
+ 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;
+ }
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
+ 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];
+ }
+
-int main(int argc, char *argv[])
-{
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
- int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
- int linei, month, year,iout;
- int jj, ll, li, lj, lk, imk;
- int numlinepar=0; /* Current linenumber of parameter file */
- int itimes;
- int NDIM=2;
- int vpopbased=0;
+ 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 %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
+ 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.") != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
+ 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 %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
+ 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.") != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
+ return 1;
+ }
+ if (year==9999) {
+ printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
+ fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
+ return 1;
- char ca[32], cb[32], cc[32];
- char dummy[]=" ";
- /* FILE *fichtm; *//* Html File */
- /* FILE *ficgp;*/ /*Gnuplot File */
- struct stat info;
- double agedeb, agefin,hf;
- double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+ }
+ annais[i]=(double)(year);
+ moisnais[i]=(double)(month);
+ strcpy(line,stra);
+
+ cutv(stra, strb,line,' ');
+ errno=0;
+ dval=strtod(strb,&endptr);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
+ fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
+ 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 '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
+ fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
+ return 1;
+ }
+ }
+ if(lval <-1 || lval >1){
+ printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+ For example, for multinomial values like 1, 2 and 3,\n \
+ build V1=0 V2=0 for the reference value (1),\n \
+ V1=1 V2=0 for (2) \n \
+ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+ output of IMaCh is often meaningless.\n \
+ Exiting.\n",lval,linei, i,line,j);
+ fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
+ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
+ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
+ For example, for multinomial values like 1, 2 and 3,\n \
+ build V1=0 V2=0 for the reference value (1),\n \
+ V1=1 V2=0 for (2) \n \
+ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
+ output of IMaCh is often meaningless.\n \
+ Exiting.\n",lval,linei, i,line,j);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 */
- double fret;
- double **xi,tmp,delta;
+ *imax=i-1; /* Number of individuals */
+ fclose(fic);
+
+ return (0);
+ endread:
+ printf("Exiting readdata: ");
+ fclose(fic);
+ return (1);
- double dum; /* Dummy variable */
- double ***p3mat;
- double ***mobaverage;
- int *indx;
- char line[MAXLINE], linepar[MAXLINE];
- char linetmp[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;
- char z[1]="c", occ;
+}
- char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
- char *strt, strtend[80];
- char *stratrunc;
- int lstra;
+int decodemodel ( char model[], int lastobs)
+{
+ int i, j, k;
+ int i1, j1, k1, k2;
+ char modelsav[80];
+ char stra[80], strb[80], strc[80], strd[80],stre[80];
- long total_usecs;
-
-/* setlocale (LC_ALL, ""); */
-/* bindtextdomain (PACKAGE, LOCALEDIR); */
+ if (strlen(model) >1){ /* If there is at least 1 covariate */
+ j=0, j1=0, k1=1, k2=1;
+ j=nbocc(model,'+'); /* j=Number of '+' */
+ j1=nbocc(model,'*'); /* j1=Number of '*' */
+ cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
+ but the covariates which are product must be computed and stored. */
+ cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */
+
+ strcpy(modelsav,model);
+ if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+ printf("Error. Non available option model=%s ",model);
+ fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
+ return 1;
+ }
+
+ /* This loop fills the array Tvar from the string 'model'.*/
+ /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
+ /* modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4
+ i=1 Tvar[1]=3 Tage[1]=1
+ i=2 Tvar[2]=2
+ i=3 Tvar[3]=1
+ i=4 Tvar[4]= 4
+ i=5 Tvar[5]
+ for (k=1; k<=cptcovn;k++) {
+ cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ */
+ for(k=1; k<=(j+1);k++){
+ cutv(strb,stra,modelsav,'+'); /* keeps in strb after the first '+'
+ modelsav=V3*age+V2+V1+V4 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 V3*age+V2+V1+V4 strb=V3*age */
+ cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
+ if (strcmp(strc,"age")==0) { /* Vn*age */
+ cptcovprod--;
+ cutv(strb,stre,strd,'V'); /* stre="V3" */
+ Tvar[k]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3, and Tvar[3]=2 */
+ cptcovage++; /* Sums the number of covariates which include age as a product */
+ Tage[cptcovage]=k; /* Tage[1] =2 */
+ /*printf("stre=%s ", stre);*/
+ }
+ else if (strcmp(strd,"age")==0) { /* or age*Vn */
+ cptcovprod--;
+ cutv(strb,stre,strc,'V');
+ Tvar[k]=atoi(stre);
+ cptcovage++;
+ Tage[cptcovage]=k;
+ }
+ else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
+ cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
+ Tvar[k]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
+ If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
+ cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+ Tprod[k1]=k; /* Tprod[1] */
+ Tvard[k1][1]=atoi(strc); /* m*/
+ Tvard[k1][2]=atoi(stre); /* n */
+ Tvar[cptcovn+k2]=Tvard[k1][1];
+ Tvar[cptcovn+k2+1]=Tvard[k1][2];
+ for (i=1; i<=lastobs;i++) /* Computes the new covariate which is a product of covar[n][i]* covar[m][i]
+ and is stored at ncovol+k1 */
+ covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
+ k1++;
+ k2=k2+2;
+ }
+ }
+ else { /* no more sum */
+ /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+ /* scanf("%d",i);*/
+ cutv(strd,strc,strb,'V');
+ Tvar[i]=atoi(strc);
+ }
+ strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+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);
+ 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(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\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<lastpass); m++){
+ printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
+}
+
+}*/
+
+
+ printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+ fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+
+ return (0);
+ endread:
+ printf("Exiting calandcheckages: ");
+ return (1);
+}
+
+
+/***********************************************/
+/**************** Main Program *****************/
+/***********************************************/
+
+int main(int argc, char *argv[])
+{
+#ifdef GSL
+ const gsl_multimin_fminimizer_type *T;
+ size_t iteri = 0, it;
+ int rval = GSL_CONTINUE;
+ int status = GSL_SUCCESS;
+ double ssval;
+#endif
+ 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;
+ int vpopbased=0;
+
+ char ca[32], cb[32], cc[32];
+ /* 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;
+
+ 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, jk,aa,bb, stepsize, ij;
+ int jnais,jdc,jint4,jint1,jint2,jint3,*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 ***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;
+
+ char z[1]="c", occ;
+
+ /*char *strt;*/
+ char strtend[80];
+
+ long total_usecs;
+
+/* setlocale (LC_ALL, ""); */
+/* bindtextdomain (PACKAGE, LOCALEDIR); */
/* textdomain (PACKAGE); */
/* setlocale (LC_CTYPE, ""); */
/* setlocale (LC_MESSAGES, ""); */
covar=matrix(0,NCOVMAX,1,n);
- cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
- if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
- /* where is ncovprod ?*/
- ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
+ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
+ /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
+ v1+v2*age+v2*v3 makes cptcovn = 3
+ */
+ if (strlen(model)>1)
+ cptcovn=nbocc(model,'+')+1;
+ /* ncovprod */
+ ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
npar= nforce*ncovmodel; /* Number of parameters like aij*/
fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */
- /*-------- data file ----------*/
- if((fic=fopen(datafile,"r"))==NULL) {
- printf("Problem while opening datafile: %s\n", datafile);goto end;
- fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
- }
n= lastobs;
- severity = vector(1,maxwav);
- outcome=imatrix(1,maxwav+1,1,n);
num=lvector(1,n);
moisnais=vector(1,n);
annais=vector(1,n);
tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,8);
- 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 %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
- fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
- goto end;
- }
- }
- s[j][i]=lval;
-
- strcpy(line,stra);
- cutv(stra, strb,line,' ');
- if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
- }
- else if(iout=sscanf(strb,"%s.") != 0){
- month=99;
- year=9999;
- }else{
- printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
- fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
- goto end;
- }
- 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 for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
- fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
- goto end;
- }
- 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 for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
- fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
- goto end;
- }
- if (year==9999) {
- printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
- fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
- goto end;
-
- }
- annais[i]=(double)(year);
- moisnais[i]=(double)(month);
- strcpy(line,stra);
-
- cutv(stra, strb,line,' ');
- errno=0;
- dval=strtod(strb,&endptr);
- if( strb[0]=='\0' || (*endptr != '\0')){
- printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
- fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
- fflush(ficlog);
- goto end;
- }
- 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 '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
- fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
- goto end;
- }
- }
- if(lval <-1 || lval >1){
- printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
- Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
- for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
- For example, for multinomial values like 1, 2 and 3,\n \
- build V1=0 V2=0 for the reference value (1),\n \
- V1=1 V2=0 for (2) \n \
- and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
- output of IMaCh is often meaningless.\n \
- Exiting.\n",lval,linei, i,line,j);
- fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
- Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
- for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
- For example, for multinomial values like 1, 2 and 3,\n \
- build V1=0 V2=0 for the reference value (1),\n \
- V1=1 V2=0 for (2) \n \
- and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
- output of IMaCh is often meaningless.\n \
- Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
- goto end;
- }
- 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 */
-
- /* for (i=1; i<=imx; i++){
- if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
- if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
- if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
- }*/
- /* for (i=1; i<=imx; i++){
- if (s[4][i]==9) s[4][i]=-1;
- printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
-
- /* for (i=1; i<=imx; i++) */
-
- /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
- else weight[i]=1;*/
+ /* Reads data from file datafile */
+ if (readdata(datafile, firstobs, lastobs, &imx)==1)
+ goto end;
/* Calculation of the number of parameters from char model */
Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tvaraff=ivector(1,15);
Tvard=imatrix(1,15,1,2);
Tage=ivector(1,15);
-
- if (strlen(model) >1){ /* If there is at least 1 covariate */
- j=0, j1=0, k1=1, k2=1;
- j=nbocc(model,'+'); /* j=Number of '+' */
- j1=nbocc(model,'*'); /* j1=Number of '*' */
- cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
- cptcovprod=j1; /*Number of products V1*V2 =1 */
-
- strcpy(modelsav,model);
- if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
- printf("Error. Non available option model=%s ",model);
- fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
- goto end;
- }
-
- /* 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 */
- for(i=(j+1); i>=1;i--){
- cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
- modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4
- stra=V2
- */
- 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 V1+V3*age+V2 strb=V3*age*/
- cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
- if (strcmp(strc,"age")==0) { /* Vn*age */
- cptcovprod--;
- cutv(strb,stre,strd,'V');
- Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */
- cptcovage++; /* Sums the number of covariates including age as a product */
- Tage[cptcovage]=i; /* Tage[1] =2 */
- /*printf("stre=%s ", stre);*/
- }
- else if (strcmp(strd,"age")==0) { /* or age*Vn */
- cptcovprod--;
- cutv(strb,stre,strc,'V');
- Tvar[i]=atoi(stre);
- cptcovage++;
- Tage[cptcovage]=i;
- }
- else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
- cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
- Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
- If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
- cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
- Tprod[k1]=i; /* Tprod[1] */
- Tvard[k1][1]=atoi(strc); /* m*/
- Tvard[k1][2]=atoi(stre); /* n */
- Tvar[cptcovn+k2]=Tvard[k1][1];
- Tvar[cptcovn+k2+1]=Tvard[k1][2];
- for (k=1; k<=lastobs;k++)
- covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
- k1++;
- k2=k2+2;
- }
- }
- else { /* no more sum */
- /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
- /* scanf("%d",i);*/
- cutv(strd,strc,strb,'V');
- Tvar[i]=atoi(strc);
- }
- strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+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);*/
+ if(decodemodel(model, lastobs) == 1)
+ goto end;
/* if(mle==1){*/
if (weightopt != 1) { /* Maximisation without weights*/
for(i=1;i<=n;i++) weight[i]=1.0;
}
+
/*-calculation of age at interview from date of interview and age at death -*/
agev=matrix(1,maxwav,1,imx);
- 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(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\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);
- goto end;
- }
- }
- }
-
- /*for (i=1; i<=imx; i++){
- for (m=firstpass; (m<lastpass); m++){
- printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-}
-
-}*/
-
+ if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
+ goto end;
- printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
- fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
agegomp=(int)agemin;
- free_vector(severity,1,maxwav);
- free_imatrix(outcome,1,maxwav+1,1,n);
free_vector(moisnais,1,n);
free_vector(annais,1,n);
/* free_matrix(mint,1,maxwav,1,n);
for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
h++;
- if (h>m)
- h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+ if (h>m) {
+ h=1;
+ codtab[h][k]=j;
+ codtab[h][Tvar[k]]=j;
+ }
printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
}
}
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);
/*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 */
- powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+ 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);
+ }
+
+ 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<NDIM; it++){
+ p[it+1]=gsl_vector_get(sfm->x,it);
+ fprintf(ficrespow," %.12lf", p[it]);
+ }
+ gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
+#endif
+#ifdef POWELL
+ powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
+#endif
fclose(ficrespow);
hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
free_vector(lsurv,1,AGESUP);
free_vector(lpop,1,AGESUP);
free_vector(tpop,1,AGESUP);
+#ifdef GSL
+ free_ivector(cens,1,n);
+ free_vector(agecens,1,n);
+ free_ivector(dcwave,1,n);
+ free_matrix(ximort,1,NDIM,1,NDIM);
+#endif
} /* Endof if mle==-3 */
else{ /* For mle >=1 */
git://henry.ined.fr / .git / commitdiff