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Diff for /imach/src/imach.c between versions 1.131 and 1.136

version 1.131, 2009/06/20 16:22:47 version 1.136, 2010/04/26 20:30:53
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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    Revision 1.131  2009/06/20 16:22:47  brouard
   Some dimensions resccaled    Some dimensions resccaled
   
Line 168 Line 186
   
   The same imach parameter file can be used but the option for mle should be -3.    The same imach parameter file can be used but the option for mle should be -3.
   
   Agnès, who wrote this part of the code, tried to keep most of the    Agnès, who wrote this part of the code, tried to keep most of the
   former routines in order to include the new code within the former code.    former routines in order to include the new code within the former code.
   
   The output is very simple: only an estimate of the intercept and of    The output is very simple: only an estimate of the intercept and of
Line 301 Line 319
   Also this programme outputs the covariance matrix of the parameters but also    Also this programme outputs the covariance matrix of the parameters but also
   of the life expectancies. It also computes the period (stable) prevalence.     of the life expectancies. It also computes the period (stable) prevalence. 
       
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
   from the European Union.    from the European Union.
   It is copyrighted identically to a GNU software product, ie programme and    It is copyrighted identically to a GNU software product, ie programme and
Line 363  extern int errno; Line 381  extern int errno;
 #include <time.h>  #include <time.h>
 #include "timeval.h"  #include "timeval.h"
   
   #ifdef GSL
   #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
   #endif
   
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
Line 400  extern int errno; Line 423  extern int errno;
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar=0;  int nvar=0, nforce=0; /* Number of variables, number of forces */
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
Line 427  int **bh; /* bh[mi][i] is the bias (+ or Line 450  int **bh; /* bh[mi][i] is the bias (+ or
 double jmean=1; /* Mean space between 2 waves */  double jmean=1; /* Mean space between 2 waves */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed 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;  FILE *ficlog, *ficrespow;
 int globpr=0; /* Global variable for printing or not */  int globpr=0; /* Global variable for printing or not */
 double fretone; /* Only one call to likelihood */  double fretone; /* Only one call to likelihood */
Line 597  void replace_back_to_slash(char *s, char Line 621  void replace_back_to_slash(char *s, char
   }    }
 }  }
   
   char *trimbb(char *out, char *in)
   { /* Trim multiple blanks in line */
     char *s;
     s=out;
     while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
         in++;
       }
       *out++ = *in++;
     }
     *out='\0';
     return s;
   }
   
 int nbocc(char *s, char occ)  int nbocc(char *s, char occ)
 {  {
   int i,j=0;    int i,j=0;
Line 1197  double **prevalim(double **prlim, int nl Line 1235  double **prevalim(double **prlim, int nl
       }        }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for (k=1; k<=cptcovprod;k++)        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 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 cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 1686  double funcone( double *x) Line 1724  double funcone( double *x)
         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 */          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 */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         lli=log(out[s1][s2]); /* Original formula */          lli=log(out[s1][s2]); /* Original formula */
       } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */        } else{  /* mle=0 back to 1 */
         lli=log(out[s1][s2]); /* Original formula */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
       } /* End of if */        } /* End of if */
       ipmx +=1;        ipmx +=1;
       sw += weight[i];        sw += weight[i];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        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){        if(globpr){
         fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
Line 1897  double hessii(double x[], double delta, Line 1936  double hessii(double x[], double delta,
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2;    double k1,k2;
   double p2[NPARMAX+1];    double p2[MAXPARM+1]; /* identical to x */
   double res;    double res;
   double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;    double fx;
Line 1918  double hessii(double x[], double delta, Line 1957  double hessii(double x[], double delta,
       /*res= (k1-2.0*fx+k2)/delt/delt; */        /*res= (k1-2.0*fx+k2)/delt/delt; */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
               
 #ifdef DEBUG  #ifdef DEBUGHESS
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 #endif  #endif
Line 1944  double hessij( double x[], double delti[ Line 1983  double hessij( double x[], double delti[
   int i;    int i;
   int l=1, l1, lmax=20;    int l=1, l1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[NPARMAX+1];    double p2[MAXPARM+1];
   int k;    int k;
   
   fx=func(x);    fx=func(x);
Line 2155  void  freqsummary(char fileres[], int ia Line 2194  void  freqsummary(char fileres[], int ia
             pos += freq[jk][m][i];              pos += freq[jk][m][i];
           if(pp[jk]>=1.e-10){            if(pp[jk]>=1.e-10){
             if(first==1){              if(first==1){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }              }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }else{            }else{
Line 2410  void  concatwav(int wav[], int **dh, int Line 2449  void  concatwav(int wav[], int **dh, int
             dh[mi][i]=jk;              dh[mi][i]=jk;
             bh[mi][i]=0;              bh[mi][i]=0;
           }else{ /* We want a negative bias in order to only have interpolation ie            }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;              dh[mi][i]=jk+1;
             bh[mi][i]=ju;              bh[mi][i]=ju;
           }            }
Line 2442  void  concatwav(int wav[], int **dh, int Line 2481  void  concatwav(int wav[], int **dh, int
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)  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 */    /*      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 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;     cptcoveff=0; 
     
   for (k=0; k<maxncov; k++) Ndum[k]=0;    for (k=0; k<maxncov; k++) Ndum[k]=0;
   for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */    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       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
                                modality*/                                  modality of this covariate Vj*/ 
       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
       Ndum[ij]++; /*counts the occurence of this modality */                                        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);*/        /*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)         if (ij > modmaxcovj) modmaxcovj=ij; 
                                        Tvar[j]. If V=sex and male is 0 and         /* getting the maximum value of the modality of the covariate
                                        female is 1, then  cptcode=1.*/           (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 ?*/      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 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 */        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 */      } /* Ndum[-1] number of undefined modalities */
   
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     ij=1;       ij=1; 
     for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
       for (k=0; k<= maxncov; k++) { /* k=-1 ?*/        for (k=0; k<= maxncov; k++) { /* k=-1 ? NCOVMAX*/
         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */          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.             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                      k is a modality. If we have model=V1+V1*sex                                        k is a modality. If we have model=V1+V1*sex 
Line 3458  To be simple, these graphs help to under Line 3504  To be simple, these graphs help to under
                   /* Computing eigen value of matrix of covariance */                    /* Computing eigen value of matrix of covariance */
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;                    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.;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: 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. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       fprintf(ficlog,"Error: 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", lc1, lc2, v1, v2, cv12);fflush(ficlog);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                   /* Eigen vectors */                    /* Eigen vectors */
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                   /*v21=sqrt(1.-v11*v11); *//* error */                    /*v21=sqrt(1.-v11*v11); *//* error */
Line 4349  double gompertz(double x[]) Line 4402  double gompertz(double x[])
   return -2*L*num/sump;    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 ***********/  /******************* Printing html file ***********/
 void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \  void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
Line 4396  void printinggnuplotmort(char fileres[], Line 4490  void printinggnuplotmort(char fileres[],
   
 }   } 
   
   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;
     }
   
 /***********************************************/    i=1;
 /**************** Main Program *****************/    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[])      for (j=maxwav;j>=1;j--){
 {        cutv(stra, strb,line,' '); 
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);        if(strb[0]=='.') { /* Missing status */
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;          lval=-1;
   int linei, month, year,iout;        }else{
   int jj, ll, li, lj, lk, imk;          errno=0;
   int numlinepar=0; /* Current linenumber of parameter file */          lval=strtol(strb,&endptr,10); 
   int itimes;        /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
   int NDIM=2;          if( strb[0]=='\0' || (*endptr != '\0')){
   int vpopbased=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[]="                         ";      annais[i]=(double)(year);
   /*  FILE *fichtm; *//* Html File */      moisnais[i]=(double)(month); 
   /* FILE *ficgp;*/ /*Gnuplot File */      strcpy(line,stra);
   struct stat info;      
   double agedeb, agefin,hf;      cutv(stra, strb,line,' '); 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      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;    *imax=i-1; /* Number of individuals */
   double **xi,tmp,delta;    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 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];  int decodemodel ( char model[], int lastobs)
   char  *strt, strtend[80];  {
   char *stratrunc;    int i, j, k;
   int lstra;    int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
   long total_usecs;    if (strlen(model) >1){ /* If there is at least 1 covariate */
        j=0, j1=0, k1=1, k2=1;
 /*   setlocale (LC_ALL, ""); */      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); */  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
 /*   textdomain (PACKAGE); */  /*   textdomain (PACKAGE); */
 /*   setlocale (LC_CTYPE, ""); */  /*   setlocale (LC_CTYPE, ""); */
Line 4633  int main(int argc, char *argv[]) Line 5113  int main(int argc, char *argv[])
   
         
   covar=matrix(0,NCOVMAX,1,n);     covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */    */
     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 */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/    nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
   if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){    if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
     printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);      printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
     fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);      fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
Line 4817  run imach with mle=-1 to get a correct t Line 5302  run imach with mle=-1 to get a correct t
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* 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;    n= lastobs;
   severity = vector(1,maxwav);  
   outcome=imatrix(1,maxwav+1,1,n);  
   num=lvector(1,n);    num=lvector(1,n);
   moisnais=vector(1,n);    moisnais=vector(1,n);
   annais=vector(1,n);    annais=vector(1,n);
Line 4841  run imach with mle=-1 to get a correct t Line 5319  run imach with mle=-1 to get a correct t
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,8);    ncodemax=ivector(1,8);
   
   i=1;    /* Reads data from file datafile */
   linei=0;    if (readdata(datafile, firstobs, lastobs, &imx)==1)
   while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {      goto end;
     linei=linei+1;  
     for(j=strlen(line); j>=0;j--){  /* Untabifies line */  
       if(line[j] == '\t')  
         line[j] = ' ';  
     }  
     for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){  
       ;  
     };  
     line[j+1]=0;  /* Trims blanks at end of line */  
     if(line[0]=='#'){  
       fprintf(ficlog,"Comment line\n%s\n",line);  
       printf("Comment line\n%s\n",line);  
       continue;  
     }  
   
     for (j=maxwav;j>=1;j--){  
       cutv(stra, strb,line,' ');   
       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 %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);  
       fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);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;*/  
   
   /* Calculation of the number of parameters from char model */    /* 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 */    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 */
Line 5009  run imach with mle=-1 to get a correct t Line 5329  run imach with mle=-1 to get a correct t
   Tvaraff=ivector(1,15);     Tvaraff=ivector(1,15); 
   Tvard=imatrix(1,15,1,2);    Tvard=imatrix(1,15,1,2);
   Tage=ivector(1,15);          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++; /* Sum the number of covariates including ages 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(mle==1){*/
   if (weightopt != 1) { /* Maximisation without weights*/    if (weightopt != 1) { /* Maximisation without weights*/
     for(i=1;i<=n;i++) weight[i]=1.0;      for(i=1;i<=n;i++) weight[i]=1.0;
   }    }
   
     /*-calculation of age at interview from date of interview and age at death -*/      /*-calculation of age at interview from date of interview and age at death -*/
   agev=matrix(1,maxwav,1,imx);    agev=matrix(1,maxwav,1,imx);
   
   for (i=1; i<=imx; i++) {    if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
     for(m=2; (m<= maxwav); m++) {      goto end;
       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]);  
 }  
   
 }*/  
   
   
   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;    agegomp=(int)agemin;
   free_vector(severity,1,maxwav);  
   free_imatrix(outcome,1,maxwav+1,1,n);  
   free_vector(moisnais,1,n);    free_vector(moisnais,1,n);
   free_vector(annais,1,n);    free_vector(annais,1,n);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
Line 5217  run imach with mle=-1 to get a correct t Line 5378  run imach with mle=-1 to get a correct t
       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */        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 */           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++;            h++;
           if (h>m)             if (h>m) {
             h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              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]]);            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]]);
         }           } 
       }        }
Line 5316  Interval (in months) between two waves: Line 5480  Interval (in months) between two waves:
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
   if (mle==-3){    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);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
Line 5358  Interval (in months) between two waves: Line 5523  Interval (in months) between two waves:
     /*printf("%lf %lf", p[1], p[2]);*/      /*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");      printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
     strcpy(filerespow,"pow-mort");       strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);      strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {      if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);        printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"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");      fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
     /*  for (i=1;i<=nlstate;i++)      /*  for (i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate+ndeath;j++)          for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */      */
     fprintf(ficrespow,"\n");      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<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);      fclose(ficrespow);
           
     hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
Line 5433  Interval (in months) between two waves: Line 5683  Interval (in months) between two waves:
     free_vector(lsurv,1,AGESUP);      free_vector(lsurv,1,AGESUP);
     free_vector(lpop,1,AGESUP);      free_vector(lpop,1,AGESUP);
     free_vector(tpop,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 */    } /* Endof if mle==-3 */
       
   else{ /* For mle >=1 */    else{ /* For mle >=1 */
     globpr=1;/* debug */      globpr=0;/* debug */
     /*    likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone);*/ /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
Removed from v.1.131  
changed lines
  Added in v.1.136

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