Diff for /imach/src/imach.c between versions 1.123 and 1.131

version 1.123, 2006/03/20 10:52:43 version 1.131, 2009/06/20 16:22:47
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   
     Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
     Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
     Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
   
     Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
     computation.
     In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   
     Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     Version 0.98h
   
     Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
   
     Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
   
   Revision 1.123  2006/03/20 10:52:43  brouard    Revision 1.123  2006/03/20 10:52:43  brouard
   * imach.c (Module): <title> changed, corresponds to .htm file    * imach.c (Module): <title> changed, corresponds to .htm file
   name. <head> headers where missing.    name. <head> headers where missing.
Line 335  extern int errno; Line 375  extern int errno;
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define NCOVMAX 8 /* Maximum number of covariates */  #define NCOVMAX 20 /* Maximum number of covariates */
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /* Number of months per year */  #define YEARM 12. /* Number of months per year */
 #define AGESUP 130  #define AGESUP 130
Line 360  extern int errno; Line 400  extern int errno;
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";  char version[]="Imach version 0.98k, June 2006, 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, 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;  int nvar=0;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  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 */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav=0; /* Maxim number of waves */
 int jmin, jmax; /* min, max spacing between 2 waves */  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 int ijmin, ijmax; /* Individuals having jmin and jmax */   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 int gipmx, gsw; /* Global variables on the number of contributions   int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                    to the likelihood and the sum of weights (done by funcone)*/                     to the likelihood and the sum of weights (done by funcone)*/
 int mle, weightopt;  int mle=1, weightopt=0;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
            * wave mi and wave mi+1 is not an exact multiple of stepm. */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double jmean; /* 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,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficlog, *ficrespow;  FILE *ficlog, *ficrespow;
 int globpr; /* 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 */
 long ipmx; /* Number of contributions */  long ipmx=0; /* Number of contributions */
 double sw; /* Sum of weights */  double sw; /* Sum of weights */
 char filerespow[FILENAMELENGTH];  char filerespow[FILENAMELENGTH];
 char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
Line 484  double dateintmean=0; Line 524  double dateintmean=0;
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
 double *agedc, **covar, idx;  double *agedc, **covar, idx;
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
Line 1001  void powell(double p[], double **xi, int Line 1041  void powell(double p[], double **xi, int
     last_time=curr_time;      last_time=curr_time;
     (void) gettimeofday(&curr_time,&tzp);      (void) gettimeofday(&curr_time,&tzp);
     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     */  
    for (i=1;i<=n;i++) {     for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
Line 1135  double **prevalim(double **prlim, int nl Line 1174  double **prevalim(double **prlim, int nl
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double min, max, maxmin, maxmax,sumnew=0.;
   double **matprod2();    double **matprod2();
   double **out, cov[NCOVMAX], **pmij();    double **out, cov[NCOVMAX+1], **pmij();
   double **newm;    double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double agefin, delaymax=50 ; /* Max number of years to converge */
   
Line 1217  double **pmij(double **ps, double *cov, Line 1256  double **pmij(double **ps, double *cov,
           
     for(i=1; i<= nlstate; i++){      for(i=1; i<= nlstate; i++){
       s1=0;        s1=0;
       for(j=1; j<i; j++)        for(j=1; j<i; j++){
         s1+=exp(ps[i][j]);          s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
         for(j=i+1; j<=nlstate+ndeath; j++){
         s1+=exp(ps[i][j]);          s1+=exp(ps[i][j]);
           /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
       ps[i][i]=1./(s1+1.);        ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)        for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
Line 1286  double ***hpxij(double ***po, int nhstep Line 1329  double ***hpxij(double ***po, int nhstep
      */       */
   
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
   
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
Line 1302  double ***hpxij(double ***po, int nhstep Line 1345  double ***hpxij(double ***po, int nhstep
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        for (k=1; k<=cptcovn;k++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (k=1; k<=cptcovage;k++)        for (k=1; k<=cptcovage;k++)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for (k=1; k<=cptcovprod;k++)        for (k=1; k<=cptcovprod;k++)
Line 1319  double ***hpxij(double ***po, int nhstep Line 1363  double ***hpxij(double ***po, int nhstep
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
         po[i][j][h]=newm[i][j];          po[i][j][h]=newm[i][j];
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
          */  
       }        }
       /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
   /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
Line 1331  double ***hpxij(double ***po, int nhstep Line 1376  double ***hpxij(double ***po, int nhstep
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
Line 1585  double funcone( double *x) Line 1630  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as likeli but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   double llt;    double llt;
Line 1647  double funcone( double *x) Line 1692  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 2012  void pstamp(FILE *fichier) Line 2057  void pstamp(FILE *fichier)
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i, m, jk, k1,i1, j1, bool, z1,j;
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *pp, **prop;
Line 2181  void prevalence(double ***probs, double Line 2226  void prevalence(double ***probs, double
      We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
   */    */
     
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, m, jk, k1, i1, j1, bool, z1,j;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *pp, **prop;
   double pos,posprop;     double pos,posprop; 
Line 2239  void prevalence(double ***probs, double Line 2284  void prevalence(double ***probs, double
           if( i <=  iagemax){             if( i <=  iagemax){ 
             if(posprop>=1.e-5){               if(posprop>=1.e-5){ 
               probs[i][jk][j1]= prop[jk][i]/posprop;                probs[i][jk][j1]= prop[jk][i]/posprop;
             }               } else
                 printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
           }             } 
         }/* end jk */           }/* end jk */ 
       }/* end i */         }/* end i */ 
Line 2397  void  concatwav(int wav[], int **dh, int Line 2443  void  concatwav(int wav[], int **dh, int
 void tricode(int *Tvar, int **nbcode, int imx)  void tricode(int *Tvar, int **nbcode, int imx)
 {  {
       
   int Ndum[20],ij=1, k, j, i, maxncov=19;    /*      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 cptcode=0;
   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;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    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       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                modality*/                                  modality*/ 
       ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
       Ndum[ij]++; /*store the modality */        Ndum[ij]++; /*counts the occurence of this modality */
       /*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 of covariable         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                                          Tvar[j]. If V=sex and male is 0 and 
                                        female is 1, then  cptcode=1.*/                                         female is 1, then  cptcode=1.*/
     }      }
   
     for (i=0; i<=cptcode; i++) {      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
       if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) 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 */
   
     ij=1;       ij=1; 
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
       for (k=0; k<= maxncov; k++) {        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
         if (Ndum[k] != 0) {          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
           nbcode[Tvar[j]][ij]=k;             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
           /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */                                       k is a modality. If we have model=V1+V1*sex 
                                                  then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           ij++;            ij++;
         }          }
         if (ij > ncodemax[j]) break;           if (ij > ncodemax[j]) break; 
Line 2435  void tricode(int *Tvar, int **nbcode, in Line 2483  void tricode(int *Tvar, int **nbcode, in
   
  for (k=0; k< maxncov; k++) Ndum[k]=0;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
  for (i=1; i<=ncovmodel-2; i++) {    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
    /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    ij=Tvar[i];     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
    Ndum[ij]++;     Ndum[ij]++;
  }   }
   
Line 2448  void tricode(int *Tvar, int **nbcode, in Line 2496  void tricode(int *Tvar, int **nbcode, in
      ij++;       ij++;
    }     }
  }   }
     ij--;
  cptcoveff=ij-1; /*Number of simple covariates*/   cptcoveff=ij; /*Number of simple covariates*/
 }  }
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
   double ***p3mat;    double ***p3mat;
   double eip;    double eip;
Line 2505  void evsij(char fileres[], double ***eij Line 2554  void evsij(char fileres[], double ***eij
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
   agelim=AGESUP;    agelim=AGESUP;
   /* nhstepm age range expressed in number of stepm */    /* If stepm=6 months */
   nstepm=(int) rint((agelim-age)*YEARM/stepm);       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   /* Typically if 20 years nstepm = 20*12/6=40 stepm */     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /* if (stepm >= YEARM) hstepm=1;*/    /* if (stepm >= YEARM) hstepm=1;*/
   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (age=bage; age<=fage; age ++){ 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           
Line 2551  void evsij(char fileres[], double ***eij Line 2610  void evsij(char fileres[], double ***eij
       
 }  }
   
 void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
    to initial status i, ei. .     to initial status i, ei. .
   */    */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
   double ***p3matp, ***p3matm, ***varhe;    double ***p3matp, ***p3matm, ***varhe;
   double **dnewm,**doldm;    double **dnewm,**doldm;
Line 2631  void cvevsij(char fileres[], double ***e Line 2691  void cvevsij(char fileres[], double ***e
   /* If stepm=6 months */    /* If stepm=6 months */
   /* nhstepm age range expressed in number of stepm */    /* nhstepm age range expressed in number of stepm */
   agelim=AGESUP;    agelim=AGESUP;
   nstepm=(int) rint((agelim-age)*YEARM/stepm);     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   /* Typically if 20 years nstepm = 20*12/6=40 stepm */     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /* if (stepm >= YEARM) hstepm=1;*/    /* if (stepm >= YEARM) hstepm=1;*/
   nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
Line 2644  void cvevsij(char fileres[], double ***e Line 2704  void cvevsij(char fileres[], double ***e
   gm=matrix(0,nhstepm,1,nlstate*nlstate);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   for (age=bage; age<=fage; age ++){     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
     /* Computing  Variances of health expectancies */      /* Computing  Variances of health expectancies */
Line 2698  void cvevsij(char fileres[], double ***e Line 2763  void cvevsij(char fileres[], double ***e
             varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       }        }
     }      }
   
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
Line 2825  void varevsij(char optionfilefiname[], d Line 2891  void varevsij(char optionfilefiname[], d
   pstamp(ficresvij);    pstamp(ficresvij);
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   if(popbased==1)    if(popbased==1)
     fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   else    else
     fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   fprintf(ficresvij,"# Age");    fprintf(ficresvij,"# Age");
Line 2853  void varevsij(char optionfilefiname[], d Line 2919  void varevsij(char optionfilefiname[], d
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      nhstepm is the number of hstepm from age to agelim        nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin.        nstepm is the number of stepm from age to agelin. 
      Look at hpijx to understand the reason of that which relies in memory size       Look at function hpijx to understand why (it is linked to memory size questions) */
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      survival function given by stepm (the optimization length). Unfortunately it       survival function given by stepm (the optimization length). Unfortunately it
      means that if the survival funtion is printed every two years of age and if       means that if the survival funtion is printed every two years of age and if
Line 2920  void varevsij(char optionfilefiname[], d Line 2985  void varevsij(char optionfilefiname[], d
         }          }
       }        }
   
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
         for(h=0; h<=nhstepm; h++){          for(h=0; h<=nhstepm; h++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
Line 3030  void varevsij(char optionfilefiname[], d Line 3095  void varevsij(char optionfilefiname[], d
   free_vector(gmp,nlstate+1,nlstate+ndeath);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
Line 3209  void varprob(char optionfilefiname[], do Line 3274  void varprob(char optionfilefiname[], do
   fprintf(ficresprobcov,"\n");    fprintf(ficresprobcov,"\n");
   fprintf(ficresprobcor,"\n");    fprintf(ficresprobcor,"\n");
  */   */
  xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
Line 3362  To be simple, these graphs help to under Line 3427  To be simple, these graphs help to under
   
       /* Confidence intervalle of pij  */        /* Confidence intervalle of pij  */
       /*        /*
         fprintf(ficgp,"\nset noparametric;unset label");          fprintf(ficgp,"\nunset parametric;unset label");
         fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
Line 3480  void printinghtml(char fileres[], char t Line 3545  void printinghtml(char fileres[], char t
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n",
            estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
Line 3543  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 3610  fprintf(fichtm," \n<ul><li><b>Graphs</b>
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
          estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"t"),subdirf2(fileres,"t"));           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
          subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
Line 3580  prevalence (with 95%% confidence interva Line 3647  prevalence (with 95%% confidence interva
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2): %s%d.png<br>\  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
 <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
Line 3592  health expectancies in states (1) and (2 Line 3662  health expectancies in states (1) and (2
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng;    int ng=0;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
 /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 3619  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 3689  plot [%.f:%.f] \"%s\" every :::%d::%d u
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else        fprintf(ficgp," \%%*lf (\%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
Line 4343  int main(int argc, char *argv[]) Line 4413  int main(int argc, char *argv[])
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
     int vpopbased=0;
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32], cc[32];
   char dummy[]="                         ";    char dummy[]="                         ";
Line 4568  int main(int argc, char *argv[]) Line 4639  int main(int argc, char *argv[])
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   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*/    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
     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);
       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);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   delti=delti3[1][1];    delti=delti3[1][1];
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
Line 4694  run imach with mle=-1 to get a correct t Line 4771  run imach with mle=-1 to get a correct t
     ungetc(c,ficpar);      ungetc(c,ficpar);
       
     matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);        fscanf(ficpar,"%s",&str);
       if(mle==1)        if(mle==1)
Line 4757  run imach with mle=-1 to get a correct t Line 4837  run imach with mle=-1 to get a correct t
   for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
   mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,1,n);
   anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,1,n);
   s=imatrix(1,maxwav+1,1,n);    s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,8);    ncodemax=ivector(1,8);
   
Line 4781  run imach with mle=-1 to get a correct t Line 4861  run imach with mle=-1 to get a correct t
   
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
       cutv(stra, strb,line,' ');         cutv(stra, strb,line,' '); 
       errno=0;        if(strb[0]=='.') { /* Missing status */
       lval=strtol(strb,&endptr,10);           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
       /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/        /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
       if( strb[0]=='\0' || (*endptr != '\0')){          if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %d %s 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);            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);
         exit(1);            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;        s[j][i]=lval;
               
Line 4798  run imach with mle=-1 to get a correct t Line 4883  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 interview (mm/yyyy or .) at wave %d.  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 interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
         exit(1);          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;         anint[j][i]= (double) year; 
       mint[j][i]= (double)month;         mint[j][i]= (double)month; 
Line 4813  run imach with mle=-1 to get a correct t Line 4899  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 death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);        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);
       exit(1);          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;       andc[i]=(double) year; 
     moisdc[i]=(double) month;       moisdc[i]=(double) month; 
Line 4828  run imach with mle=-1 to get a correct t Line 4915  run imach with mle=-1 to get a correct t
       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 %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
       exit(1);        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);      annais[i]=(double)(year);
     moisnais[i]=(double)(month);       moisnais[i]=(double)(month); 
Line 4839  run imach with mle=-1 to get a correct t Line 4927  run imach with mle=-1 to get a correct t
     dval=strtod(strb,&endptr);       dval=strtod(strb,&endptr); 
     if( strb[0]=='\0' || (*endptr != '\0')){      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);        printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
       exit(1);        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;       weight[i]=dval; 
     strcpy(line,stra);      strcpy(line,stra);
           
     for (j=ncovcol;j>=1;j--){      for (j=ncovcol;j>=1;j--){
       cutv(stra, strb,line,' ');         cutv(stra, strb,line,' '); 
       errno=0;        if(strb[0]=='.') { /* Missing status */
       lval=strtol(strb,&endptr,10);           lval=-1;
       if( strb[0]=='\0' || (*endptr != '\0')){        }else{
         printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);          errno=0;
         exit(1);          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){        if(lval <-1 || lval >1){
         printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \          printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
Line 4862  run imach with mle=-1 to get a correct t Line 4957  run imach with mle=-1 to get a correct t
  and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\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 \   output of IMaCh is often meaningless.\n \
  Exiting.\n",lval,linei, i,line,j);   Exiting.\n",lval,linei, i,line,j);
         exit(1);          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);        covar[j][i]=(double)(lval);
       strcpy(line,stra);        strcpy(line,stra);
     }       }  
     lstra=strlen(stra);      lstra=strlen(stra);
            
     if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */      if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
       stratrunc = &(stra[lstra-9]);        stratrunc = &(stra[lstra-9]);
       num[i]=atol(stratrunc);        num[i]=atol(stratrunc);
Line 4900  run imach with mle=-1 to get a correct t Line 5004  run imach with mle=-1 to get a correct t
      else weight[i]=1;*/       else weight[i]=1;*/
   
   /* Calculation of the number of parameters from char model */    /* Calculation of the number of parameters from char model */
   Tvar=ivector(1,15); /* 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 */
   Tprod=ivector(1,15);     Tprod=ivector(1,15); 
   Tvaraff=ivector(1,15);     Tvaraff=ivector(1,15); 
   Tvard=imatrix(1,15,1,2);    Tvard=imatrix(1,15,1,2);
Line 4910  run imach with mle=-1 to get a correct t Line 5014  run imach with mle=-1 to get a correct t
     j=0, j1=0, k1=1, k2=1;      j=0, j1=0, k1=1, k2=1;
     j=nbocc(model,'+'); /* j=Number of '+' */      j=nbocc(model,'+'); /* j=Number of '+' */
     j1=nbocc(model,'*'); /* j1=Number of '*' */      j1=nbocc(model,'*'); /* j1=Number of '*' */
     cptcovn=j+1;       cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
     cptcovprod=j1; /*Number of products */      cptcovprod=j1; /*Number of products  V1*V2 =1 */
           
     strcpy(modelsav,model);       strcpy(modelsav,model); 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
       printf("Error. Non available option model=%s ",model);        printf("Error. Non available option model=%s ",model);
       fprintf(ficlog,"Error. Non available option model=%s ",model);        fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
       goto end;        goto end;
     }      }
           
     /* This loop fills the array Tvar from the string 'model'.*/      /* 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--){      for(i=(j+1); i>=1;i--){
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */         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 */        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
       /*scanf("%d",i);*/        /*scanf("%d",i);*/
       if (strchr(strb,'*')) {  /* Model includes a product */        if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *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 */          if (strcmp(strc,"age")==0) { /* Vn*age */
           cptcovprod--;            cptcovprod--;
           cutv(strb,stre,strd,'V');            cutv(strb,stre,strd,'V');
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/            Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
           cptcovage++;            cptcovage++; /* Sum the number of covariates including ages as a product */
             Tage[cptcovage]=i;            Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/            /*printf("stre=%s ", stre);*/
         }          }
         else if (strcmp(strd,"age")==0) { /* or age*Vn */          else if (strcmp(strd,"age")==0) { /* or age*Vn */
           cptcovprod--;            cptcovprod--;
Line 4944  run imach with mle=-1 to get a correct t Line 5051  run imach with mle=-1 to get a correct t
           cptcovage++;            cptcovage++;
           Tage[cptcovage]=i;            Tage[cptcovage]=i;
         }          }
         else {  /* Age is not in the model */          else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/            cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
           Tvar[i]=ncovcol+k1;            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 */            cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
           Tprod[k1]=i;            Tprod[k1]=i;  /* Tprod[1]  */
           Tvard[k1][1]=atoi(strc); /* m*/            Tvard[k1][1]=atoi(strc); /* m*/
           Tvard[k1][2]=atoi(stre); /* n */            Tvard[k1][2]=atoi(stre); /* n */
           Tvar[cptcovn+k2]=Tvard[k1][1];            Tvar[cptcovn+k2]=Tvard[k1][1];
Line 4965  run imach with mle=-1 to get a correct t Line 5073  run imach with mle=-1 to get a correct t
       cutv(strd,strc,strb,'V');        cutv(strd,strc,strb,'V');
       Tvar[i]=atoi(strc);        Tvar[i]=atoi(strc);
       }        }
       strcpy(modelsav,stra);          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);        /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
         scanf("%d",i);*/          scanf("%d",i);*/
     } /* end of loop + */      } /* end of loop + */
Line 5095  run imach with mle=-1 to get a correct t Line 5203  run imach with mle=-1 to get a correct t
   
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
   Tcode=ivector(1,100);  
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
   ncodemax[1]=1;    ncodemax[1]=1;
   if (cptcovn > 0) tricode(Tvar,nbcode,imx);    if (cptcovn > 0) tricode(Tvar,nbcode,imx);
Line 5105  run imach with mle=-1 to get a correct t Line 5212  run imach with mle=-1 to get a correct t
   h=0;    h=0;
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
   for(k=1;k<=cptcoveff; k++){    for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
     for(i=1; i <=(m/pow(2,k));i++){      for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
       for(j=1; j <= ncodemax[k]; j++){        for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
         for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          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) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            if (h>m) 
           /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/              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]]);
         }           } 
       }        }
     }      }
Line 5120  run imach with mle=-1 to get a correct t Line 5228  run imach with mle=-1 to get a correct t
      codtab[1][2]=1;codtab[2][2]=2; */       codtab[1][2]=1;codtab[2][2]=2; */
   /* for(i=1; i <=m ;i++){     /* for(i=1; i <=m ;i++){ 
      for(k=1; k <=cptcovn; k++){       for(k=1; k <=cptcovn; k++){
      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);         printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
      }       }
      printf("\n");       printf("\n");
      }       }
Line 5148  run imach with mle=-1 to get a correct t Line 5256  run imach with mle=-1 to get a correct t
     strcat(optionfilehtm,"-mort");      strcat(optionfilehtm,"-mort");
   strcat(optionfilehtm,".htm");    strcat(optionfilehtm,".htm");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
     printf("Problem with %s \n",optionfilehtm), exit(0);      printf("Problem with %s \n",optionfilehtm);
       exit(0);
   }    }
   
   strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */    strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
Line 5327  Interval (in months) between two waves: Line 5436  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 */
     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]);
Line 5357  Interval (in months) between two waves: Line 5466  Interval (in months) between two waves:
           fprintf(ficlog,"%d%d ",i,k);            fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficres,"%1d%1d ",i,k);
           for(j=1; j <=ncovmodel; j++){            for(j=1; j <=ncovmodel; j++){
             printf("%f ",p[jk]);              printf("%lf ",p[jk]);
             fprintf(ficlog,"%f ",p[jk]);              fprintf(ficlog,"%lf ",p[jk]);
             fprintf(ficres,"%f ",p[jk]);              fprintf(ficres,"%lf ",p[jk]);
             jk++;               jk++; 
           }            }
           printf("\n");            printf("\n");
Line 5600  Interval (in months) between two waves: Line 5709  Interval (in months) between two waves:
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;          k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
         fprintf(ficrespl,"\n#******");          fprintf(ficrespl,"\n#******");
         printf("\n#******");          printf("\n#******");
         fprintf(ficlog,"\n#******");          fprintf(ficlog,"\n#******");
Line 5706  Interval (in months) between two waves: Line 5816  Interval (in months) between two waves:
     }      }
       
   
     /*---------- Health expectancies and variances ------------*/      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
     strcpy(filerest,"t");      prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     strcat(filerest,fileres);      /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
     if((ficrest=fopen(filerest,"w"))==NULL) {          ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;      */
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;  
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
     }      }
     printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);   
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);   
   
   
       /*---------- Health expectancies, no variances ------------*/
   
     strcpy(filerese,"e");      strcpy(filerese,"e");
     strcat(filerese,fileres);      strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
Line 5726  Interval (in months) between two waves: Line 5842  Interval (in months) between two waves:
     }      }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
     strcpy(fileresstde,"stde");      strcpy(fileresstde,"stde");
     strcat(fileresstde,fileres);      strcat(fileresstde,fileres);
Line 5754  Interval (in months) between two waves: Line 5901  Interval (in months) between two waves:
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */  
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);  
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\  
         ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);  
     */  
   
     if (mobilav!=0) {  
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){  
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);  
         printf(" Error in movingaverage mobilav=%d\n",mobilav);  
       }  
     }  
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;           k=k+1; 
Line 5776  Interval (in months) between two waves: Line 5909  Interval (in months) between two waves:
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");          fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");  
         fprintf(ficresstdeij,"\n#****** ");          fprintf(ficresstdeij,"\n#****** ");
         fprintf(ficrescveij,"\n#****** ");          fprintf(ficrescveij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
           fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }          }
         fprintf(ficreseij,"******\n");  
         fprintf(ficresstdeij,"******\n");          fprintf(ficresstdeij,"******\n");
         fprintf(ficrescveij,"******\n");          fprintf(ficrescveij,"******\n");
   
Line 5795  Interval (in months) between two waves: Line 5925  Interval (in months) between two waves:
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);            cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
         cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);    
     
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;  
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);  
         if(popbased==1){  
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);  
         }  
   
         pstamp(ficrest);          pstamp(ficrest);
         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            oldm=oldms;savm=savms;
         fprintf(ficrest,"\n");            varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);            epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){            for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {              if (vpopbased==1) {
             if(mobilav ==0){                if(mobilav ==0){
               for(i=1; i<=nlstate;i++)                  for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];                    prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */                 }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)                  for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];                    prlim[i][i]=mobaverage[(int)age][i][k];
                 }
             }              }
           }  
                   
           fprintf(ficrest," %4.0f",age);              fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {                for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];                  epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                  /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
             }              }
             epj[nlstate+1] +=epj[j];  
           }  
   
           for(i=1, vepp=0.;i <=nlstate;i++)              for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)                for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];                  vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));              fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){              for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
           }            }
           fprintf(ficrest,"\n");  
         }          }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 5853  Interval (in months) between two waves: Line 5984  Interval (in months) between two waves:
     free_matrix(mint,1,maxwav,1,n);      free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);      free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);      free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);  
     fclose(ficresstdeij);      fclose(ficresstdeij);
     fclose(ficrescveij);      fclose(ficrescveij);
     fclose(ficresvij);      fclose(ficresvij);
Line 5892  Interval (in months) between two waves: Line 6022  Interval (in months) between two waves:
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
    endfree:
   free_matrix(prlim,1,nlstate,1,nlstate);    free_matrix(prlim,1,nlstate,1,nlstate);
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
Line 5909  Interval (in months) between two waves: Line 6040  Interval (in months) between two waves:
     free_ivector(Tprod,1,15);      free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);      free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);      free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);  
   
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);      free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     free_imatrix(codtab,1,100,1,10);      free_imatrix(codtab,1,100,1,10);

Removed from v.1.123  
changed lines
  Added in v.1.131


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