Diff for /imach/src/imach.c between versions 1.112 and 1.133

version 1.112, 2006/01/30 09:55:26 version 1.133, 2009/07/06 10:21:25
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
   
     Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
   
     Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
   
     Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
     Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
     Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
   
     Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
     computation.
     In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   
     Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     Version 0.98h
   
     Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
   
     Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
   
     Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
   
     * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
     1.
     Version 0.98g
   
     Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
     1.
     Version 0.98g
   
     Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
   
     * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   
     Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
   
     Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
   
     Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
     (Module): Version 0.98d
   
     Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
     (Module): Version 0.98d
   
     Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
   
     Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
   
     Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
     filename with strsep.
   
     Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
   
   Revision 1.112  2006/01/30 09:55:26  brouard    Revision 1.112  2006/01/30 09:55:26  brouard
   (Module): Back to gnuplot.exe instead of wgnuplot.exe    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
Line 63 Line 174
   
   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 194 Line 305
   hPijx.    hPijx.
   
   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 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 223 Line 334
       begin-prev-date,...        begin-prev-date,...
   open gnuplot file    open gnuplot file
   open html file    open html file
   stable prevalence    period (stable) prevalence
    for age prevalim()     for age prevalim()
   h Pij x    h Pij x
   variance of p varprob    variance of p varprob
Line 235 Line 346
   varevsij()     varevsij() 
   if popbased==1 varevsij(,popbased)    if popbased==1 varevsij(,popbased)
   total life expectancies    total life expectancies
   Variance of stable prevalence    Variance of period (stable) prevalence
  end   end
 */  */
   
Line 270  extern int errno; Line 381  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 295  extern int errno; Line 406  extern int errno;
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";  char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite ";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  char strstart[80];
 int nvar;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   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 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,  *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 334  FILE *ficresprobmorprev; Line 447  FILE *ficresprobmorprev;
 FILE *fichtm, *fichtmcov; /* Html File */  FILE *fichtm, *fichtmcov; /* Html File */
 FILE *ficreseij;  FILE *ficreseij;
 char filerese[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
 FILE  *ficresvij;  FILE  *ficresvij;
 char fileresv[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  FILE  *ficresvpl;
 char fileresvpl[FILENAMELENGTH];  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 char command[FILENAMELENGTH];  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
Line 364  char strcurr[80], strfor[80]; Line 481  char strcurr[80], strfor[80];
   
 char *endptr;  char *endptr;
 long lval;  long lval;
   double dval;
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
Line 412  double dateintmean=0; Line 530  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 485  void replace_back_to_slash(char *s, char Line 603  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 929  void powell(double p[], double **xi, int Line 1061  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 1053  void powell(double p[], double **xi, int Line 1184  void powell(double p[], double **xi, int
   }     } 
 }   } 
   
 /**** Prevalence limit (stable prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 {  {
Line 1063  double **prevalim(double **prlim, int nl Line 1194  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 1145  double **pmij(double **ps, double *cov, Line 1276  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 1214  double ***hpxij(double ***po, int nhstep Line 1349  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 1230  double ***hpxij(double ***po, int nhstep Line 1365  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 1247  double ***hpxij(double ***po, int nhstep Line 1383  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 1259  double ***hpxij(double ***po, int nhstep Line 1396  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 1346  double func( double *x) Line 1483  double func( double *x)
   
         } else if  (s2==-2) {          } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += out[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= survp;            /*survp += out[s1][j]; */
         }            lli= log(survp);
           
         else if  (s2==-4) {  
           for (j=3,survp=0. ; j<=nlstate; j++)   
             survp += out[s1][j];  
           lli= survp;  
         }          }
                   
         else if  (s2==-5) {          else if  (s2==-4) { 
           for (j=1,survp=0. ; j<=2; j++)             for (j=3,survp=0. ; j<=nlstate; j++)  
             survp += out[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= survp;            lli= log(survp); 
         }          } 
   
   
           else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
           } 
           
         else{          else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
Line 1513  double funcone( double *x) Line 1650  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 1557  double funcone( double *x) Line 1694  double funcone( double *x)
        */         */
       if( s2 > nlstate && (mle <5) ){  /* Jackson */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         lli=log(out[s1][s2] - savm[s1][s2]);          lli=log(out[s1][s2] - savm[s1][s2]);
       } else if (mle==1){        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
         }else if (mle==1){
         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       } else if(mle==2){        } else if(mle==2){
         lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
Line 1571  double funcone( double *x) Line 1712  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 %1d %1d %1d %1d %3d %10.6f %6.4f\          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
  %10.6f %10.6f %10.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
Line 1659  void mlikeli(FILE *ficres,double p[], in Line 1800  void mlikeli(FILE *ficres,double p[], in
   
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
     free_matrix(xi,1,npar,1,npar);
   fclose(ficrespow);    fclose(ficrespow);
   printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
Line 1775  double hessii(double x[], double delta, Line 1917  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 1796  double hessii(double x[], double delta, Line 1938  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 1822  double hessij( double x[], double delti[ Line 1964  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 1926  void lubksb(double **a, int n, int *indx Line 2068  void lubksb(double **a, int n, int *indx
   }     } 
 }   } 
   
   void pstamp(FILE *fichier)
   {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 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;
   double pos,posprop, k2, dateintsum=0,k2cpt=0;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];    char fileresp[FILENAMELENGTH];
       
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
Line 2000  void  freqsummary(char fileres[], int ia Line 2146  void  freqsummary(char fileres[], int ia
       }        }
                 
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 fprintf(ficresp, "#Local time at start: %s", strstart);        pstamp(ficresp);
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 2029  fprintf(ficresp, "#Local time at start: Line 2175  fprintf(ficresp, "#Local time at start:
             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 2100  void prevalence(double ***probs, double Line 2246  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 2158  void prevalence(double ***probs, double Line 2304  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 2316  void  concatwav(int wav[], int **dh, int Line 2463  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 2354  void tricode(int *Tvar, int **nbcode, in Line 2507  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 2367  void tricode(int *Tvar, int **nbcode, in Line 2520  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 ij, int estepm,double delti[],double **matcov,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 */    /* Health expectancies, no variances */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    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,***varhe;    double ***p3mat;
     double eip;
   
     pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\n");
   
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* 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 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* 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
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     agelim=AGESUP;
     /* If stepm=6 months */
       /* 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 */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* 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,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   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
      to initial status i, ei. .
     */
     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 ***p3matp, ***p3matm, ***varhe;
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double *xp;    double *xp, *xm;
   double **gp, **gm;    double **gp, **gm;
   double ***gradg, ***trgradg;    double ***gradg, ***trgradg;
   int theta;    int theta;
   
     double eip, vip;
   
   varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   xp=vector(1,npar);    xp=vector(1,npar);
     xm=vector(1,npar);
   dnewm=matrix(1,nlstate*nlstate,1,npar);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       
   fprintf(ficreseij,"# Local time at start: %s", strstart);    pstamp(ficresstdeij);
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   fprintf(ficreseij,"# Age");    fprintf(ficresstdeij,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++){
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   fprintf(ficreseij,"\n");      fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
   if(estepm < stepm){    if(estepm < stepm){
     printf ("Problem %d lower than %d\n",estepm, stepm);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
Line 2428  void evsij(char fileres[], double ***eij Line 2712  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 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
   agelim=AGESUP;    agelim=AGESUP;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* nhstepm age range expressed in number of stepm */    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(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 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);  
     gp=matrix(0,nhstepm,1,nlstate*nlstate);  
     gm=matrix(0,nhstepm,1,nlstate*nlstate);  
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
    
   
       /* 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 */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
      for(theta=1; theta <=npar; theta++){         decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){         for(i=1; i<=npar; i++){ 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       
       cptj=0;  
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
           cptj=cptj+1;            for(h=0; h<=nhstepm-1; h++){
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           }            }
         }          }
       }        }
             
              for(ij=1; ij<= nlstate*nlstate; ij++)
       for(i=1; i<=npar; i++)   
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
         
       cptj=0;  
       for(j=1; j<= nlstate; j++){  
         for(i=1;i<=nlstate;i++){  
           cptj=cptj+1;  
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  
   
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  
         }  
       }  
       for(j=1; j<= nlstate*nlstate; j++)  
         for(h=0; h<=nhstepm-1; h++){          for(h=0; h<=nhstepm-1; h++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
         }          }
      }       }/* End theta */
          
 /* End theta */      
       for(h=0; h<=nhstepm-1; h++)
      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);  
   
      for(h=0; h<=nhstepm-1; h++)  
       for(j=1; j<=nlstate*nlstate;j++)        for(j=1; j<=nlstate*nlstate;j++)
         for(theta=1; theta <=npar; theta++)          for(theta=1; theta <=npar; theta++)
           trgradg[h][j][theta]=gradg[h][theta][j];            trgradg[h][j][theta]=gradg[h][theta][j];
            
   
      for(i=1;i<=nlstate*nlstate;i++)       for(ij=1;ij<=nlstate*nlstate;ij++)
       for(j=1;j<=nlstate*nlstate;j++)        for(ji=1;ji<=nlstate*nlstate;ji++)
         varhe[i][j][(int)age] =0.;          varhe[ij][ji][(int)age] =0.;
   
      printf("%d|",(int)age);fflush(stdout);       printf("%d|",(int)age);fflush(stdout);
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
Line 2506  void evsij(char fileres[], double ***eij Line 2782  void evsij(char fileres[], double ***eij
       for(k=0;k<=nhstepm-1;k++){        for(k=0;k<=nhstepm-1;k++){
         matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         for(i=1;i<=nlstate*nlstate;i++)          for(ij=1;ij<=nlstate*nlstate;ij++)
           for(j=1;j<=nlstate*nlstate;j++)            for(ji=1;ji<=nlstate*nlstate;ji++)
             varhe[i][j][(int)age] += doldm[i][j]*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);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                       
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
         }          }
   
     fprintf(ficreseij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     cptj=0;      for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
         cptj++;          cptj= (j-1)*nlstate+i;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
       }        }
     fprintf(ficreseij,"\n");      fprintf(ficrescveij,"\n");
         
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);  
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("\n");    printf("\n");
   fprintf(ficlog,"\n");    fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(dnewm,1,nlstate*nlstate,1,npar);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
Line 2599  void varevsij(char optionfilefiname[], d Line 2897  void varevsij(char optionfilefiname[], d
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);    pstamp(ficresprobmorprev);
   fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2614  void varevsij(char optionfilefiname[], d Line 2912  void varevsij(char optionfilefiname[], d
   fprintf(fichtm,"\n<br>%s  <br>\n",digitp);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 /*   } */  /*   } */
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  fprintf(ficresvij, "#Local time at start: %s", strstart);    pstamp(ficresvij);
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(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
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   fprintf(ficresvij,"# Age");    fprintf(ficresvij,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
     for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   fprintf(ficresvij,"\n");    fprintf(ficresvij,"\n");
   
   xp=vector(1,npar);    xp=vector(1,npar);
Line 2641  void varevsij(char optionfilefiname[], d Line 2943  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 2708  void varevsij(char optionfilefiname[], d Line 3009  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 2818  void varevsij(char optionfilefiname[], d Line 3119  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 2860  void varprevlim(char fileres[], double * Line 3161  void varprevlim(char fileres[], double *
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double age,agelim;    double age,agelim;
   int theta;    int theta;
   fprintf(ficresvpl, "#Local time at start: %s", strstart);     
   fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");    pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   fprintf(ficresvpl,"# Age");    fprintf(ficresvpl,"# Age");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficresvpl," %1d-%1d",i,i);
Line 2975  void varprob(char optionfilefiname[], do Line 3277  void varprob(char optionfilefiname[], do
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fprintf(ficresprob, "#Local time at start: %s", strstart);    pstamp(ficresprob);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficresprob,"# Age");    fprintf(ficresprob,"# Age");
   fprintf(ficresprobcov, "#Local time at start: %s", strstart);    pstamp(ficresprobcov);
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   fprintf(ficresprobcov,"# Age");    fprintf(ficresprobcov,"# Age");
   fprintf(ficresprobcor, "#Local time at start: %s", strstart);    pstamp(ficresprobcor);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fprintf(ficresprobcov,"# Age");    fprintf(ficresprobcor,"# Age");
   
   
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
Line 2996  void varprob(char optionfilefiname[], do Line 3298  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 3149  To be simple, these graphs help to under Line 3451  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 3234  To be simple, these graphs help to under Line 3536  To be simple, these graphs help to under
   }    }
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   fclose(ficresprob);    fclose(ficresprob);
   fclose(ficresprobcov);    fclose(ficresprobcov);
Line 3262  void printinghtml(char fileres[], char t Line 3566  void printinghtml(char fileres[], char t
  - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - 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,"\
  - Life expectancies by age and initial health status (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 3285  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 3592  fprintf(fichtm," \n<ul><li><b>Graphs</b>
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
 <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);       <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
 <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Stable prevalence in each health state */         /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<nlstate;cpt++){         for(cpt=1; cpt<nlstate;cpt++){
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
 <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }         }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }       }
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
Line 3319  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 3626  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
  fprintf(fichtm,"\   fprintf(fichtm,"\
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - 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,"\
  - Health expectancies with their variances (no covariance): <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 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"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
Line 3356  prevalence (with 95%% confidence interva Line 3671  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 3368  health expectancies in states (1) and (2 Line 3686  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 3395  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 3713  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\"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 ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
Line 3445  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 3763  plot [%.f:%.f] \"%s\" every :::%d::%d u
       
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(2*cpt-2);        /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       fprintf(ficgp,"set ter png small\n\        fprintf(ficgp,"set ter png small\n\
 set size 0.65,0.65\n\  set size 0.65,0.65\n\
Line 3459  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 3778  plot [%.f:%.f] \"%s\" every :::%d::%d u
                   
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                   
       }         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
     }      }
   }    }
       
Line 4102  void printinggnuplotmort(char fileres[], Line 4423  void printinggnuplotmort(char fileres[],
   
   
   
   
 /***********************************************/  /***********************************************/
 /**************** Main Program *****************/  /**************** Main Program *****************/
 /***********************************************/  /***********************************************/
Line 4115  int main(int argc, char *argv[]) Line 4437  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 4132  int main(int argc, char *argv[]) Line 4455  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 */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */    int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;    int c,  h , cpt,l;
Line 4169  int main(int argc, char *argv[]) Line 4494  int main(int argc, char *argv[])
   char z[1]="c", occ;    char z[1]="c", occ;
   
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   char strstart[80], *strt, strtend[80];    char  *strt, strtend[80];
   char *stratrunc;    char *stratrunc;
   int lstra;    int lstra;
   
Line 4211  int main(int argc, char *argv[]) Line 4536  int main(int argc, char *argv[])
   printf("\n%s\n%s",version,fullversion);    printf("\n%s\n%s",version,fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     scanf("%s",pathtot);      fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
   }    }
   else{    else{
     strcpy(pathtot,argv[1]);      strcpy(pathtot,argv[1]);
Line 4229  int main(int argc, char *argv[]) Line 4564  int main(int argc, char *argv[])
   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */    /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);    chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
   strcpy(command,"mkdir ");    strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);    strcat(command,optionfilefiname);
   if((outcmd=system(command)) != 0){    if((outcmd=system(command)) != 0){
Line 4323  int main(int argc, char *argv[]) Line 4660  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){
       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 4338  int main(int argc, char *argv[]) Line 4682  int main(int argc, char *argv[])
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     fclose (ficparo);      fclose (ficparo);
     fclose (ficlog);      fclose (ficlog);
       goto end;
     exit(0);      exit(0);
   }    }
   else if(mle==-3) {    else if(mle==-3) {
Line 4368  int main(int argc, char *argv[]) Line 4713  int main(int argc, char *argv[])
         j++;          j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){          if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
           exit(1);            exit(1);
         }          }
         fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficparo,"%1d%1d",i1,j1);
Line 4450  int main(int argc, char *argv[]) Line 4797  int main(int argc, char *argv[])
     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 4495  int main(int argc, char *argv[]) Line 4845  int main(int argc, char *argv[])
   
   /*-------- data file ----------*/    /*-------- data file ----------*/
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem with datafile: %s\n", datafile);goto end;      printf("Problem while opening datafile: %s\n", datafile);goto end;
     fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;      fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
   }    }
   
   n= lastobs;    n= lastobs;
Line 4513  int main(int argc, char *argv[]) Line 4863  int main(int argc, char *argv[])
   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 4534  int main(int argc, char *argv[]) Line 4884  int main(int argc, char *argv[])
       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,' '); 
       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 4554  int main(int argc, char *argv[]) Line 4914  int main(int argc, char *argv[])
         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 4569  int main(int argc, char *argv[]) Line 4930  int main(int argc, char *argv[])
       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 4584  int main(int argc, char *argv[]) Line 4946  int main(int argc, char *argv[])
       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 4592  int main(int argc, char *argv[]) Line 4955  int main(int argc, char *argv[])
           
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     errno=0;      errno=0;
     lval=strtol(strb,&endptr,10);       dval=strtod(strb,&endptr); 
     if( strb[0]=='\0' || (*endptr != '\0')){      if( strb[0]=='\0' || (*endptr != '\0')){
       printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, 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]=(double)(lval);       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 %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);          printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
         exit(1);   Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           goto end;
       }        }
       covar[j][i]=(double)(lval);        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 4628  int main(int argc, char *argv[]) Line 5015  int main(int argc, char *argv[])
           
     i=i+1;      i=i+1;
   } /* End loop reading  data */    } /* End loop reading  data */
     fclose(fic);
   /* printf("ii=%d", ij);    /* printf("ii=%d", ij);
      scanf("%d",i);*/       scanf("%d",i);*/
   imx=i-1; /* Number of individuals */    imx=i-1; /* Number of individuals */
Line 4647  int main(int argc, char *argv[]) Line 5035  int main(int argc, char *argv[])
      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 4657  int main(int argc, char *argv[]) Line 5045  int main(int argc, char *argv[])
     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++; /* Sums the number of covariates including age 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 4691  int main(int argc, char *argv[]) Line 5082  int main(int argc, char *argv[])
           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 4712  int main(int argc, char *argv[]) Line 5104  int main(int argc, char *argv[])
       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 4725  int main(int argc, char *argv[]) Line 5117  int main(int argc, char *argv[])
   printf("cptcovprod=%d ", cptcovprod);    printf("cptcovprod=%d ", cptcovprod);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
   scanf("%d ",i);    scanf("%d ",i);*/
   fclose(fic);*/  
   
     /*  if(mle==1){*/      /*  if(mle==1){*/
   if (weightopt != 1) { /* Maximisation without weights*/    if (weightopt != 1) { /* Maximisation without weights*/
Line 4843  int main(int argc, char *argv[]) Line 5234  int main(int argc, char *argv[])
   
   /* 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 4853  int main(int argc, char *argv[]) Line 5243  int main(int argc, char *argv[])
   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 4868  int main(int argc, char *argv[]) Line 5259  int main(int argc, char *argv[])
      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 4896  int main(int argc, char *argv[]) Line 5287  int main(int argc, char *argv[])
     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 4905  int main(int argc, char *argv[]) Line 5297  int main(int argc, char *argv[])
     printf("Problem with %s \n",optionfilehtmcov), exit(0);      printf("Problem with %s \n",optionfilehtmcov), exit(0);
   }    }
   else{    else{
   fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \    fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   
   fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \    fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
 \n\  \n\
 <hr  size=\"2\" color=\"#EC5E5E\">\  <hr  size=\"2\" color=\"#EC5E5E\">\
  <ul><li><h4>Parameter files</h4>\n\   <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\   - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
  - Date and time at start: %s</ul>\n",\   - Date and time at start: %s</ul>\n",\
           fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\            optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
           fileres,fileres,\            fileres,fileres,\
           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
   fflush(fichtm);    fflush(fichtm);
Line 5060  Interval (in months) between two waves: Line 5454  Interval (in months) between two waves:
       printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);        printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
           
           
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
           
     printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \      printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
Line 5073  Interval (in months) between two waves: Line 5467  Interval (in months) between two waves:
   } /* Endof if mle==-3 */    } /* Endof if mle==-3 */
       
   else{ /* For mle >=1 */    else{ /* For mle >=1 */
         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++)
Line 5103  Interval (in months) between two waves: Line 5497  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 5297  Interval (in months) between two waves: Line 5691  Interval (in months) between two waves:
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/      /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/      /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
           
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\      printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
Line 5319  Interval (in months) between two waves: Line 5713  Interval (in months) between two waves:
     fclose(ficres);      fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       
     strcpy(filerespl,"pl");      strcpy(filerespl,"pl");
     strcat(filerespl,fileres);      strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {      if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;        printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;        fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
     }      }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);      printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);      fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl, "#Local time at start: %s", strstart);      pstamp(ficrespl);
     fprintf(ficrespl,"#Stable prevalence \n");      fprintf(ficrespl,"# Period (stable) prevalence \n");
     fprintf(ficrespl,"#Age ");      fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");      fprintf(ficrespl,"\n");
Line 5346  Interval (in months) between two waves: Line 5740  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 5390  Interval (in months) between two waves: Line 5785  Interval (in months) between two waves:
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/      /* hstepm=1;   aff par mois*/
     fprintf(ficrespij, "#Local time at start: %s", strstart);      pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     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++){
Line 5452  Interval (in months) between two waves: Line 5847  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 LEs with variances: file '%s' \n", filerest);   
     fprintf(ficlog,"Computing Total LEs with variances: 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 5472  Interval (in months) between two waves: Line 5873  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");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"v");      strcpy(fileresv,"v");
     strcat(fileresv,fileres);      strcat(fileresv,fileres);
Line 5482  Interval (in months) between two waves: Line 5932  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 5504  Interval (in months) between two waves: Line 5940  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#****** ");
         for(j=1;j<=cptcoveff;j++)           fprintf(ficrescveij,"\n#****** ");
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(j=1;j<=cptcoveff;j++) {
         fprintf(ficreseij,"******\n");            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(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");          fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
Line 5516  Interval (in months) between two waves: Line 5956  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, delti, matcov, strstart);            cvevsij(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;          pstamp(ficrest);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         if(popbased==1){            oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);            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);
         fprintf(ficrest, "#Local time at start: %s", strstart);            else
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            fprintf(ficrest,"# Age e.. (std) ");
         fprintf(ficrest,"\n");            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 5573  Interval (in months) between two waves: Line 6015  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(ficrescveij);
     fclose(ficresvij);      fclose(ficresvij);
     fclose(ficrest);      fclose(ficrest);
     fclose(ficpar);      fclose(ficpar);
       
     /*------- Variance of stable prevalence------*/         /*------- Variance of period (stable) prevalence------*/   
   
     strcpy(fileresvpl,"vpl");      strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);      strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);        printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
       exit(0);        exit(0);
     }      }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);      printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
     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++){
Line 5610  Interval (in months) between two waves: Line 6053  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(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);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);      free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);      free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/      /*free_vector(delti,1,npar);*/
Line 5627  Interval (in months) between two waves: Line 6071  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(codtab,1,100,1,10);
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       
Line 5656  Interval (in months) between two waves: Line 6100  Interval (in months) between two waves:
   fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);    fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
   /*  printf("Total time was %d uSec.\n", total_usecs);*/    /*  printf("Total time was %d uSec.\n", total_usecs);*/
 /*   if(fileappend(fichtm,optionfilehtm)){ */  /*   if(fileappend(fichtm,optionfilehtm)){ */
   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
   fclose(fichtm);    fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
   fclose(fichtmcov);    fclose(fichtmcov);
   fclose(ficgp);    fclose(ficgp);
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
   
   chdir(path);  
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
   sprintf(plotcmd,"gnuplot");    sprintf(plotcmd,"gnuplot");
 #ifndef UNIX  #ifndef UNIX

Removed from v.1.112  
changed lines
  Added in v.1.133


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