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Diff for /imach/src/imach.c between versions 1.131 and 1.135

version 1.131, 2009/06/20 16:22:47 version 1.135, 2009/10/29 15:33:14
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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.
   
     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 180
   
   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 313
   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 400  extern int errno; Line 412  extern int errno;
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";  char version[]="Imach version 0.98l, October 2009, 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 597  void replace_back_to_slash(char *s, char Line 609  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 1692  double funcone( double *x) Line 1718  double funcone( double *x)
       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 1923  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 1944  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 1970  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 2181  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 2464  void tricode(int *Tvar, int **nbcode, in Line 2490  void tricode(int *Tvar, int **nbcode, in
     }      }
   
     for (i=0; i<=cptcode; i++) { /* i=-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 */        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 */
     } /* Ndum[-1] number of undefined modalities */      } /* Ndum[-1] number of undefined modalities */
   
     ij=1;       ij=1; 
Line 3458  To be simple, these graphs help to under Line 3488  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 4431  int main(int argc, char *argv[]) Line 4468  int main(int argc, char *argv[])
   double ***mobaverage;    double ***mobaverage;
   int *indx;    int *indx;
   char line[MAXLINE], linepar[MAXLINE];    char line[MAXLINE], linepar[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char linetmp[MAXLINE];
       char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char **bp, *tok, *val; /* pathtot */    char **bp, *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
Line 4635  int main(int argc, char *argv[]) Line 4673  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*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     /* where is ncovprod ?*/
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */    ncovmodel=2+cptcovn; /*Number of variables = 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 4858  run imach with mle=-1 to get a correct t Line 4897  run imach with mle=-1 to get a correct t
       printf("Comment line\n%s\n",line);        printf("Comment line\n%s\n",line);
       continue;        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--){      for (j=maxwav;j>=1;j--){
       cutv(stra, strb,line,' ');         cutv(stra, strb,line,' '); 
Line 4914  run imach with mle=-1 to get a correct t Line 4958  run imach with mle=-1 to get a correct t
       month=99;        month=99;
       year=9999;        year=9999;
     }else{      }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);        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 %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);fflush(ficlog);        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;          goto end;
   
     }      }
     annais[i]=(double)(year);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month); 
Line 5040  run imach with mle=-1 to get a correct t Line 5090  run imach with mle=-1 to get a correct t
           cptcovprod--;            cptcovprod--;
           cutv(strb,stre,strd,'V');            cutv(strb,stre,strd,'V');
           Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */            Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
           cptcovage++; /* Sum the number of covariates including ages as a product */            cptcovage++; /* Sums the number of covariates including age as a product */
           Tage[cptcovage]=i;  /* Tage[1] =2 */            Tage[cptcovage]=i;  /* Tage[1] =2 */
           /*printf("stre=%s ", stre);*/            /*printf("stre=%s ", stre);*/
         }          }
Line 5141  run imach with mle=-1 to get a correct t Line 5191  run imach with mle=-1 to get a correct t
             agev[m][i]=1;              agev[m][i]=1;
           else if(agev[m][i] <agemin){             else if(agev[m][i] <agemin){ 
             agemin=agev[m][i];              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);*/              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){            else if(agev[m][i] >agemax){
             agemax=agev[m][i];              agemax=agev[m][i];
Line 5436  Interval (in months) between two waves: Line 5486  Interval (in months) between two waves:
   } /* 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.1.135

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