Diff for /imach/src/imach.c between versions 1.8 and 1.127

version 1.8, 2001/05/02 17:54:31 version 1.127, 2006/04/28 18:11:50
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.127  2006/04/28 18:11:50  brouard
   individuals from different ages are interviewed on their health status    (Module): Yes the sum of survivors was wrong since
   or degree of  disability. At least a second wave of interviews    imach-114 because nhstepm was no more computed in the age
   ("longitudinal") should  measure each new individual health status.    loop. Now we define nhstepma in the age loop.
   Health expectancies are computed from the transistions observed between    (Module): In order to speed up (in case of numerous covariates) we
   waves and are computed for each degree of severity of disability (number    compute health expectancies (without variances) in a first step
   of life states). More degrees you consider, more time is necessary to    and then all the health expectancies with variances or standard
   reach the Maximum Likelihood of the parameters involved in the model.    deviation (needs data from the Hessian matrices) which slows the
   The simplest model is the multinomial logistic model where pij is    computation.
   the probabibility to be observed in state j at the second wave conditional    In the future we should be able to stop the program is only health
   to be observed in state i at the first wave. Therefore the model is:    expectancies and graph are needed without standard deviations.
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.126  2006/04/28 17:23:28  brouard
   age", you should modify the program where the markup    (Module): Yes the sum of survivors was wrong since
     *Covariates have to be included here again* invites you to do it.    imach-114 because nhstepm was no more computed in the age
   More covariates you add, less is the speed of the convergence.    loop. Now we define nhstepma in the age loop.
     Version 0.98h
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.125  2006/04/04 15:20:31  lievre
   individual missed an interview, the information is not rounded or lost, but    Errors in calculation of health expectancies. Age was not initialized.
   taken into account using an interpolation or extrapolation.    Forecasting file added.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    Revision 1.124  2006/03/22 17:13:53  lievre
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Parameters are printed with %lf instead of %f (more numbers after the comma).
   unobserved intermediate  states. This elementary transition (by month or    The log-likelihood is printed in the log file
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.123  2006/03/20 10:52:43  brouard
   and the contribution of each individual to the likelihood is simply hPijx.    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    * imach.c (Module): Weights can have a decimal point as for
      English (a comma might work with a correct LC_NUMERIC environment,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    otherwise the weight is truncated).
            Institut national d'études démographiques, Paris.    Modification of warning when the covariates values are not 0 or
   This software have been partly granted by Euro-REVES, a concerted action    1.
   from the European Union.    Version 0.98g
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.122  2006/03/20 09:45:41  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (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).
 #include <math.h>    Modification of warning when the covariates values are not 0 or
 #include <stdio.h>    1.
 #include <stdlib.h>    Version 0.98g
 #include <unistd.h>  
     Revision 1.121  2006/03/16 17:45:01  lievre
 #define MAXLINE 256    * imach.c (Module): Comments concerning covariates added
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    * imach.c (Module): refinements in the computation of lli if
 #define windows    status=-2 in order to have more reliable computation if stepm is
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    not 1 month. Version 0.98f
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.120  2006/03/16 15:10:38  lievre
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): refinements in the computation of lli if
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.119  2006/03/15 17:42:26  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): Bug if status = -2, the loglikelihood was
 #define NCOVMAX 8 /* Maximum number of covariates */    computed as likelihood omitting the logarithm. Version O.98e
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.118  2006/03/14 18:20:07  brouard
 #define AGESUP 130    (Module): varevsij Comments added explaining the second
 #define AGEBASE 40    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 int nvar;    (Module): Version 0.98d
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.117  2006/03/14 17:16:22  brouard
 int nlstate=2; /* Number of live states */    (Module): varevsij Comments added explaining the second
 int ndeath=1; /* Number of dead states */    table of variances if popbased=1 .
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Version 0.98d
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.116  2006/03/06 10:29:27  brouard
 int mle, weightopt;    (Module): Variance-covariance wrong links and
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    varian-covariance of ej. is needed (Saito).
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.115  2006/02/27 12:17:45  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): One freematrix added in mlikeli! 0.98c
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Revision 1.114  2006/02/26 12:57:58  brouard
 FILE *ficgp, *fichtm;    (Module): Some improvements in processing parameter
 FILE *ficreseij;    filename with strsep.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.113  2006/02/24 14:20:24  brouard
   char fileresv[FILENAMELENGTH];    (Module): Memory leaks checks with valgrind and:
  FILE  *ficresvpl;    datafile was not closed, some imatrix were not freed and on matrix
   char fileresvpl[FILENAMELENGTH];    allocation too.
   
 #define NR_END 1    Revision 1.112  2006/01/30 09:55:26  brouard
 #define FREE_ARG char*    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define FTOL 1.0e-10  
     Revision 1.111  2006/01/25 20:38:18  brouard
 #define NRANSI    (Module): Lots of cleaning and bugs added (Gompertz)
 #define ITMAX 200    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 #define TOL 2.0e-4  
     Revision 1.110  2006/01/25 00:51:50  brouard
 #define CGOLD 0.3819660    (Module): Lots of cleaning and bugs added (Gompertz)
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.108  2006/01/19 18:05:42  lievre
 #define TINY 1.0e-20    Gnuplot problem appeared...
     To be fixed
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.107  2006/01/19 16:20:37  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Test existence of gnuplot in imach path
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.106  2006/01/19 13:24:36  brouard
 #define rint(a) floor(a+0.5)    Some cleaning and links added in html output
   
 static double sqrarg;    Revision 1.105  2006/01/05 20:23:19  lievre
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    *** empty log message ***
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.104  2005/09/30 16:11:43  lievre
 int imx;    (Module): sump fixed, loop imx fixed, and simplifications.
 int stepm;    (Module): If the status is missing at the last wave but we know
 /* Stepm, step in month: minimum step interpolation*/    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 int m,nb;    contributions to the likelihood is 1 - Prob of dying from last
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    the healthy state at last known wave). Version is 0.98
 double **pmmij;  
     Revision 1.103  2005/09/30 15:54:49  lievre
 double *weight;    (Module): sump fixed, loop imx fixed, and simplifications.
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.102  2004/09/15 17:31:30  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Add the possibility to read data file including tab characters.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.101  2004/09/15 10:38:38  brouard
 double ftolhess; /* Tolerance for computing hessian */    Fix on curr_time
   
 /**************** split *************************/    Revision 1.100  2004/07/12 18:29:06  brouard
 static  int split( char *path, char *dirc, char *name )    Add version for Mac OS X. Just define UNIX in Makefile
 {  
    char *s;                             /* pointer */    Revision 1.99  2004/06/05 08:57:40  brouard
    int  l1, l2;                         /* length counters */    *** empty log message ***
   
    l1 = strlen( path );                 /* length of path */    Revision 1.98  2004/05/16 15:05:56  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    New version 0.97 . First attempt to estimate force of mortality
    s = strrchr( path, '\\' );           /* find last / */    directly from the data i.e. without the need of knowing the health
    if ( s == NULL ) {                   /* no directory, so use current */    state at each age, but using a Gompertz model: log u =a + b*age .
 #if     defined(__bsd__)                /* get current working directory */    This is the basic analysis of mortality and should be done before any
       extern char       *getwd( );    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
       if ( getwd( dirc ) == NULL ) {    from other sources like vital statistic data.
 #else  
       extern char       *getcwd( );    The same imach parameter file can be used but the option for mle should be -3.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Agnès, who wrote this part of the code, tried to keep most of the
 #endif    former routines in order to include the new code within the former code.
          return( GLOCK_ERROR_GETCWD );  
       }    The output is very simple: only an estimate of the intercept and of
       strcpy( name, path );             /* we've got it */    the slope with 95% confident intervals.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Current limitations:
       l2 = strlen( s );                 /* length of filename */    A) Even if you enter covariates, i.e. with the
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
       strcpy( name, s );                /* save file name */    B) There is no computation of Life Expectancy nor Life Table.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.97  2004/02/20 13:25:42  lievre
    }    Version 0.96d. Population forecasting command line is (temporarily)
    l1 = strlen( dirc );                 /* length of directory */    suppressed.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */    Revision 1.96  2003/07/15 15:38:55  brouard
 }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
   
 /******************************************/    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 void replace(char *s, char*t)    (Repository): Using imachwizard code to output a more meaningful covariance
 {    matrix (cov(a12,c31) instead of numbers.
   int i;  
   int lg=20;    Revision 1.94  2003/06/27 13:00:02  brouard
   i=0;    Just cleaning
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.93  2003/06/25 16:33:55  brouard
     (s[i] = t[i]);    (Module): On windows (cygwin) function asctime_r doesn't
     if (t[i]== '\\') s[i]='/';    exist so I changed back to asctime which exists.
   }    (Module): Version 0.96b
 }  
     Revision 1.92  2003/06/25 16:30:45  brouard
 int nbocc(char *s, char occ)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int i,j=0;  
   int lg=20;    Revision 1.91  2003/06/25 15:30:29  brouard
   i=0;    * imach.c (Repository): Duplicated warning errors corrected.
   lg=strlen(s);    (Repository): Elapsed time after each iteration is now output. It
   for(i=0; i<= lg; i++) {    helps to forecast when convergence will be reached. Elapsed time
   if  (s[i] == occ ) j++;    is stamped in powell.  We created a new html file for the graphs
   }    concerning matrix of covariance. It has extension -cov.htm.
   return j;  
 }    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 void cutv(char *u,char *v, char*t, char occ)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int i,lg,j,p=0;  
   i=0;    Revision 1.89  2003/06/24 12:30:52  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Some bugs corrected for windows. Also, when
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
   
   lg=strlen(t);    Revision 1.88  2003/06/23 17:54:56  brouard
   for(j=0; j<p; j++) {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
     (u[j] = t[j]);  
   }    Revision 1.87  2003/06/18 12:26:01  brouard
      u[p]='\0';    Version 0.96
   
    for(j=0; j<= lg; j++) {    Revision 1.86  2003/06/17 20:04:08  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Module): Change position of html and gnuplot routines and added
   }    routine fileappend.
 }  
     Revision 1.85  2003/06/17 13:12:43  brouard
 /********************** nrerror ********************/    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 void nrerror(char error_text[])    prior to the death. In this case, dh was negative and likelihood
 {    was wrong (infinity). We still send an "Error" but patch by
   fprintf(stderr,"ERREUR ...\n");    assuming that the date of death was just one stepm after the
   fprintf(stderr,"%s\n",error_text);    interview.
   exit(1);    (Repository): Because some people have very long ID (first column)
 }    we changed int to long in num[] and we added a new lvector for
 /*********************** vector *******************/    memory allocation. But we also truncated to 8 characters (left
 double *vector(int nl, int nh)    truncation)
 {    (Repository): No more line truncation errors.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.84  2003/06/13 21:44:43  brouard
   if (!v) nrerror("allocation failure in vector");    * imach.c (Repository): Replace "freqsummary" at a correct
   return v-nl+NR_END;    place. It differs from routine "prevalence" which may be called
 }    many times. Probs is memory consuming and must be used with
     parcimony.
 /************************ free vector ******************/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.83  2003/06/10 13:39:11  lievre
   free((FREE_ARG)(v+nl-NR_END));    *** empty log message ***
 }  
     Revision 1.82  2003/06/05 15:57:20  brouard
 /************************ivector *******************************/    Add log in  imach.c and  fullversion number is now printed.
 int *ivector(long nl,long nh)  
 {  */
   int *v;  /*
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));     Interpolated Markov Chain
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Short summary of the programme:
 }    
     This program computes Healthy Life Expectancies from
 /******************free ivector **************************/    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 void free_ivector(int *v, long nl, long nh)    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   free((FREE_ARG)(v+nl-NR_END));    case of a health survey which is our main interest) -2- at least a
 }    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 /******************* imatrix *******************************/    computed from the time spent in each health state according to a
 int **imatrix(long nrl, long nrh, long ncl, long nch)    model. More health states you consider, more time is necessary to reach the
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Maximum Likelihood of the parameters involved in the model.  The
 {    simplest model is the multinomial logistic model where pij is the
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    probability to be observed in state j at the second wave
   int **m;    conditional to be observed in state i at the first wave. Therefore
      the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   /* allocate pointers to rows */    'age' is age and 'sex' is a covariate. If you want to have a more
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    complex model than "constant and age", you should modify the program
   if (!m) nrerror("allocation failure 1 in matrix()");    where the markup *Covariates have to be included here again* invites
   m += NR_END;    you to do it.  More covariates you add, slower the
   m -= nrl;    convergence.
    
      The advantage of this computer programme, compared to a simple
   /* allocate rows and set pointers to them */    multinomial logistic model, is clear when the delay between waves is not
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    identical for each individual. Also, if a individual missed an
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    intermediate interview, the information is lost, but taken into
   m[nrl] += NR_END;    account using an interpolation or extrapolation.  
   m[nrl] -= ncl;  
      hPijx is the probability to be observed in state i at age x+h
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    conditional to the observed state i at age x. The delay 'h' can be
      split into an exact number (nh*stepm) of unobserved intermediate
   /* return pointer to array of pointers to rows */    states. This elementary transition (by month, quarter,
   return m;    semester or year) is modelled as a multinomial logistic.  The hPx
 }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 /****************** free_imatrix *************************/    hPijx.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Also this programme outputs the covariance matrix of the parameters but also
       long nch,ncl,nrh,nrl;    of the life expectancies. It also computes the period (stable) prevalence. 
      /* free an int matrix allocated by imatrix() */    
 {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   free((FREE_ARG) (m[nrl]+ncl-NR_END));             Institut national d'études démographiques, Paris.
   free((FREE_ARG) (m+nrl-NR_END));    This software have been partly granted by Euro-REVES, a concerted action
 }    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 /******************* matrix *******************************/    software can be distributed freely for non commercial use. Latest version
 double **matrix(long nrl, long nrh, long ncl, long nch)    can be accessed at http://euroreves.ined.fr/imach .
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   double **m;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    **********************************************************************/
   if (!m) nrerror("allocation failure 1 in matrix()");  /*
   m += NR_END;    main
   m -= nrl;    read parameterfile
     read datafile
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    concatwav
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    freqsummary
   m[nrl] += NR_END;    if (mle >= 1)
   m[nrl] -= ncl;      mlikeli
     print results files
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    if mle==1 
   return m;       computes hessian
 }    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 /*************************free matrix ************************/    open gnuplot file
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    open html file
 {    period (stable) prevalence
   free((FREE_ARG)(m[nrl]+ncl-NR_END));     for age prevalim()
   free((FREE_ARG)(m+nrl-NR_END));    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /******************* ma3x *******************************/    health expectancies
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Variance-covariance of DFLE
 {    prevalence()
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;     movingaverage()
   double ***m;    varevsij() 
     if popbased==1 varevsij(,popbased)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    total life expectancies
   if (!m) nrerror("allocation failure 1 in matrix()");    Variance of period (stable) prevalence
   m += NR_END;   end
   m -= nrl;  */
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;   
   m[nrl] -= ncl;  #include <math.h>
   #include <stdio.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <stdlib.h>
   #include <string.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #include <unistd.h>
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  #include <limits.h>
   m[nrl][ncl] -= nll;  #include <sys/types.h>
   for (j=ncl+1; j<=nch; j++)  #include <sys/stat.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #include <errno.h>
    extern int errno;
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /* #include <sys/time.h> */
     for (j=ncl+1; j<=nch; j++)  #include <time.h>
       m[i][j]=m[i][j-1]+nlay;  #include "timeval.h"
   }  
   return m;  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 /*************************free ma3x ************************/  #define MAXLINE 256
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #define GNUPLOTPROGRAM "gnuplot"
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define FILENAMELENGTH 132
   free((FREE_ARG)(m+nrl-NR_END));  
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 /***************** f1dim *************************/  
 extern int ncom;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 extern double *pcom,*xicom;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 extern double (*nrfunc)(double []);  
    #define NINTERVMAX 8
 double f1dim(double x)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   int j;  #define NCOVMAX 8 /* Maximum number of covariates */
   double f;  #define MAXN 20000
   double *xt;  #define YEARM 12. /* Number of months per year */
    #define AGESUP 130
   xt=vector(1,ncom);  #define AGEBASE 40
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   f=(*nrfunc)(xt);  #ifdef UNIX
   free_vector(xt,1,ncom);  #define DIRSEPARATOR '/'
   return f;  #define CHARSEPARATOR "/"
 }  #define ODIRSEPARATOR '\\'
   #else
 /*****************brent *************************/  #define DIRSEPARATOR '\\'
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define CHARSEPARATOR "\\"
 {  #define ODIRSEPARATOR '/'
   int iter;  #endif
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /* $Id$ */
   double ftemp;  /* $State$ */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
    char fullversion[]="$Revision$ $Date$"; 
   a=(ax < cx ? ax : cx);  char strstart[80];
   b=(ax > cx ? ax : cx);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   x=w=v=bx;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   fw=fv=fx=(*f)(x);  int nvar;
   for (iter=1;iter<=ITMAX;iter++) {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
     xm=0.5*(a+b);  int npar=NPARMAX;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int nlstate=2; /* Number of live states */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int ndeath=1; /* Number of dead states */
     printf(".");fflush(stdout);  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #ifdef DEBUG  int popbased=0;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int *wav; /* Number of waves for this individuual 0 is possible */
 #endif  int maxwav; /* Maxim number of waves */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int jmin, jmax; /* min, max spacing between 2 waves */
       *xmin=x;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
       return fx;  int gipmx, gsw; /* Global variables on the number of contributions 
     }                     to the likelihood and the sum of weights (done by funcone)*/
     ftemp=fu;  int mle, weightopt;
     if (fabs(e) > tol1) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       r=(x-w)*(fx-fv);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       q=(x-v)*(fx-fw);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       p=(x-v)*q-(x-w)*r;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       q=2.0*(q-r);  double jmean; /* Mean space between 2 waves */
       if (q > 0.0) p = -p;  double **oldm, **newm, **savm; /* Working pointers to matrices */
       q=fabs(q);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       etemp=e;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       e=d;  FILE *ficlog, *ficrespow;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int globpr; /* Global variable for printing or not */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  double fretone; /* Only one call to likelihood */
       else {  long ipmx; /* Number of contributions */
         d=p/q;  double sw; /* Sum of weights */
         u=x+d;  char filerespow[FILENAMELENGTH];
         if (u-a < tol2 || b-u < tol2)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
           d=SIGN(tol1,xm-x);  FILE *ficresilk;
       }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     } else {  FILE *ficresprobmorprev;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *fichtm, *fichtmcov; /* Html File */
     }  FILE *ficreseij;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char filerese[FILENAMELENGTH];
     fu=(*f)(u);  FILE *ficresstdeij;
     if (fu <= fx) {  char fileresstde[FILENAMELENGTH];
       if (u >= x) a=x; else b=x;  FILE *ficrescveij;
       SHFT(v,w,x,u)  char filerescve[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  FILE  *ficresvij;
         } else {  char fileresv[FILENAMELENGTH];
           if (u < x) a=u; else b=u;  FILE  *ficresvpl;
           if (fu <= fw || w == x) {  char fileresvpl[FILENAMELENGTH];
             v=w;  char title[MAXLINE];
             w=u;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
             fv=fw;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
             fw=fu;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
           } else if (fu <= fv || v == x || v == w) {  char command[FILENAMELENGTH];
             v=u;  int  outcmd=0;
             fv=fu;  
           }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         }  
   }  char filelog[FILENAMELENGTH]; /* Log file */
   nrerror("Too many iterations in brent");  char filerest[FILENAMELENGTH];
   *xmin=x;  char fileregp[FILENAMELENGTH];
   return fx;  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /****************** mnbrak ***********************/  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  struct timezone tzp;
             double (*func)(double))  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double ulim,u,r,q, dum;  long time_value;
   double fu;  extern long time();
    char strcurr[80], strfor[80];
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  char *endptr;
   if (*fb > *fa) {  long lval;
     SHFT(dum,*ax,*bx,dum)  double dval;
       SHFT(dum,*fb,*fa,dum)  
       }  #define NR_END 1
   *cx=(*bx)+GOLD*(*bx-*ax);  #define FREE_ARG char*
   *fc=(*func)(*cx);  #define FTOL 1.0e-10
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  #define NRANSI 
     q=(*bx-*cx)*(*fb-*fa);  #define ITMAX 200 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define TOL 2.0e-4 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  #define CGOLD 0.3819660 
       fu=(*func)(u);  #define ZEPS 1.0e-10 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       fu=(*func)(u);  
       if (fu < *fc) {  #define GOLD 1.618034 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define GLIMIT 100.0 
           SHFT(*fb,*fc,fu,(*func)(u))  #define TINY 1.0e-20 
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  static double maxarg1,maxarg2;
       u=ulim;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       fu=(*func)(u);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     } else {    
       u=(*cx)+GOLD*(*cx-*bx);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       fu=(*func)(u);  #define rint(a) floor(a+0.5)
     }  
     SHFT(*ax,*bx,*cx,u)  static double sqrarg;
       SHFT(*fa,*fb,*fc,fu)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
 /*************** linmin ************************/  int imx; 
   int stepm=1;
 int ncom;  /* Stepm, step in month: minimum step interpolation*/
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  int m,nb;
   double brent(double ax, double bx, double cx,  long *num;
                double (*f)(double), double tol, double *xmin);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double f1dim(double x);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double **pmmij, ***probs;
               double *fc, double (*func)(double));  double *ageexmed,*agecens;
   int j;  double dateintmean=0;
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  double *weight;
    int **s; /* Status */
   ncom=n;  double *agedc, **covar, idx;
   pcom=vector(1,n);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   xicom=vector(1,n);  double *lsurv, *lpop, *tpop;
   nrfunc=func;  
   for (j=1;j<=n;j++) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     pcom[j]=p[j];  double ftolhess; /* Tolerance for computing hessian */
     xicom[j]=xi[j];  
   }  /**************** split *************************/
   ax=0.0;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   xx=1.0;  {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 #ifdef DEBUG    */ 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    char  *ss;                            /* pointer */
 #endif    int   l1, l2;                         /* length counters */
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;    l1 = strlen(path );                   /* length of path */
     p[j] += xi[j];    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   free_vector(xicom,1,n);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   free_vector(pcom,1,n);      strcpy( name, path );               /* we got the fullname name because no directory */
 }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 /*************** powell ************************/      /* get current working directory */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      /*    extern  char* getcwd ( char *buf , int len);*/
             double (*func)(double []))      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   void linmin(double p[], double xi[], int n, double *fret,      }
               double (*func)(double []));      /* got dirc from getcwd*/
   int i,ibig,j;      printf(" DIRC = %s \n",dirc);
   double del,t,*pt,*ptt,*xit;    } else {                              /* strip direcotry from path */
   double fp,fptt;      ss++;                               /* after this, the filename */
   double *xits;      l2 = strlen( ss );                  /* length of filename */
   pt=vector(1,n);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   ptt=vector(1,n);      strcpy( name, ss );         /* save file name */
   xit=vector(1,n);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   xits=vector(1,n);      dirc[l1-l2] = 0;                    /* add zero */
   *fret=(*func)(p);      printf(" DIRC2 = %s \n",dirc);
   for (j=1;j<=n;j++) pt[j]=p[j];    }
   for (*iter=1;;++(*iter)) {    /* We add a separator at the end of dirc if not exists */
     fp=(*fret);    l1 = strlen( dirc );                  /* length of directory */
     ibig=0;    if( dirc[l1-1] != DIRSEPARATOR ){
     del=0.0;      dirc[l1] =  DIRSEPARATOR;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      dirc[l1+1] = 0; 
     for (i=1;i<=n;i++)      printf(" DIRC3 = %s \n",dirc);
       printf(" %d %.12f",i, p[i]);    }
     printf("\n");    ss = strrchr( name, '.' );            /* find last / */
     for (i=1;i<=n;i++) {    if (ss >0){
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      ss++;
       fptt=(*fret);      strcpy(ext,ss);                     /* save extension */
 #ifdef DEBUG      l1= strlen( name);
       printf("fret=%lf \n",*fret);      l2= strlen(ss)+1;
 #endif      strncpy( finame, name, l1-l2);
       printf("%d",i);fflush(stdout);      finame[l1-l2]= 0;
       linmin(p,xit,n,fret,func);    }
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));    return( 0 );                          /* we're done */
         ibig=i;  }
       }  
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  /******************************************/
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  void replace_back_to_slash(char *s, char*t)
         printf(" x(%d)=%.12e",j,xit[j]);  {
       }    int i;
       for(j=1;j<=n;j++)    int lg=0;
         printf(" p=%.12e",p[j]);    i=0;
       printf("\n");    lg=strlen(t);
 #endif    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      if (t[i]== '\\') s[i]='/';
 #ifdef DEBUG    }
       int k[2],l;  }
       k[0]=1;  
       k[1]=-1;  int nbocc(char *s, char occ)
       printf("Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++)    int i,j=0;
         printf(" %.12e",p[j]);    int lg=20;
       printf("\n");    i=0;
       for(l=0;l<=1;l++) {    lg=strlen(s);
         for (j=1;j<=n;j++) {    for(i=0; i<= lg; i++) {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    if  (s[i] == occ ) j++;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    }
         }    return j;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  }
       }  
 #endif  void cutv(char *u,char *v, char*t, char occ)
   {
     /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       free_vector(xit,1,n);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       free_vector(xits,1,n);       gives u="abcedf" and v="ghi2j" */
       free_vector(ptt,1,n);    int i,lg,j,p=0;
       free_vector(pt,1,n);    i=0;
       return;    for(j=0; j<=strlen(t)-1; j++) {
     }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    }
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];    lg=strlen(t);
       xit[j]=p[j]-pt[j];    for(j=0; j<p; j++) {
       pt[j]=p[j];      (u[j] = t[j]);
     }    }
     fptt=(*func)(ptt);       u[p]='\0';
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);     for(j=0; j<= lg; j++) {
       if (t < 0.0) {      if (j>=(p+1))(v[j-p-1] = t[j]);
         linmin(p,xit,n,fret,func);    }
         for (j=1;j<=n;j++) {  }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /********************** nrerror ********************/
         }  
 #ifdef DEBUG  void nrerror(char error_text[])
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++)    fprintf(stderr,"ERREUR ...\n");
           printf(" %.12e",xit[j]);    fprintf(stderr,"%s\n",error_text);
         printf("\n");    exit(EXIT_FAILURE);
 #endif  }
       }  /*********************** vector *******************/
     }  double *vector(int nl, int nh)
   }  {
 }    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 /**** Prevalence limit ****************/    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  }
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /************************ free vector ******************/
      matrix by transitions matrix until convergence is reached */  void free_vector(double*v, int nl, int nh)
   {
   int i, ii,j,k;    free((FREE_ARG)(v+nl-NR_END));
   double min, max, maxmin, maxmax,sumnew=0.;  }
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /************************ivector *******************************/
   double **newm;  int *ivector(long nl,long nh)
   double agefin, delaymax=50 ; /* Max number of years to converge */  {
     int *v;
   for (ii=1;ii<=nlstate+ndeath;ii++)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     for (j=1;j<=nlstate+ndeath;j++){    if (!v) nrerror("allocation failure in ivector");
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return v-nl+NR_END;
     }  }
   
    cov[1]=1.;  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    free((FREE_ARG)(v+nl-NR_END));
     newm=savm;  }
     /* Covariates have to be included here again */  
      cov[2]=agefin;  /************************lvector *******************************/
    long *lvector(long nl,long nh)
       for (k=1; k<=cptcovn;k++) {  {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    long *v;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       }    if (!v) nrerror("allocation failure in ivector");
       for (k=1; k<=cptcovage;k++)    return v-nl+NR_END;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  }
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    free((FREE_ARG)(v+nl-NR_END));
   }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   /******************* imatrix *******************************/
     savm=oldm;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     oldm=newm;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     maxmax=0.;  { 
     for(j=1;j<=nlstate;j++){    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       min=1.;    int **m; 
       max=0.;    
       for(i=1; i<=nlstate; i++) {    /* allocate pointers to rows */ 
         sumnew=0;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    if (!m) nrerror("allocation failure 1 in matrix()"); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    m += NR_END; 
         max=FMAX(max,prlim[i][j]);    m -= nrl; 
         min=FMIN(min,prlim[i][j]);    
       }    
       maxmin=max-min;    /* allocate rows and set pointers to them */ 
       maxmax=FMAX(maxmax,maxmin);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     if(maxmax < ftolpl){    m[nrl] += NR_END; 
       return prlim;    m[nrl] -= ncl; 
     }    
   }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 }    
     /* return pointer to array of pointers to rows */ 
 /*************** transition probabilities **********/    return m; 
   } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /****************** free_imatrix *************************/
   double s1, s2;  void free_imatrix(m,nrl,nrh,ncl,nch)
   /*double t34;*/        int **m;
   int i,j,j1, nc, ii, jj;        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
     for(i=1; i<= nlstate; i++){  { 
     for(j=1; j<i;j++){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free((FREE_ARG) (m+nrl-NR_END)); 
         /*s2 += param[i][j][nc]*cov[nc];*/  } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!m) nrerror("allocation failure 1 in matrix()");
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    m += NR_END;
       }    m -= nrl;
       ps[i][j]=s2;  
     }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(i=1; i<= nlstate; i++){    m[nrl] += NR_END;
      s1=0;    m[nrl] -= ncl;
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=i+1; j<=nlstate+ndeath; j++)    return m;
       s1+=exp(ps[i][j]);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     ps[i][i]=1./(s1+1.);     */
     for(j=1; j<i; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************************free matrix ************************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  {
   } /* end i */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /******************* ma3x *******************************/
       ps[ii][ii]=1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
   }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      printf("%lf ",ps[ii][jj]);    if (!m) nrerror("allocation failure 1 in matrix()");
    }    m += NR_END;
     printf("\n ");    m -= nrl;
     }  
     printf("\n ");printf("%lf ",cov[2]);*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /*    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    m[nrl] += NR_END;
   goto end;*/    m[nrl] -= ncl;
     return ps;  
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
 /**************** Product of 2 matrices ******************/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    m[nrl][ncl] += NR_END;
 {    m[nrl][ncl] -= nll;
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    for (j=ncl+1; j<=nch; j++) 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      m[nrl][j]=m[nrl][j-1]+nlay;
   /* in, b, out are matrice of pointers which should have been initialized    
      before: only the contents of out is modified. The function returns    for (i=nrl+1; i<=nrh; i++) {
      a pointer to pointers identical to out */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   long i, j, k;      for (j=ncl+1; j<=nch; j++) 
   for(i=nrl; i<= nrh; i++)        m[i][j]=m[i][j-1]+nlay;
     for(k=ncolol; k<=ncoloh; k++)    }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    return m; 
         out[i][k] +=in[i][j]*b[j][k];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   return out;    */
 }  }
   
   /*************************free ma3x ************************/
 /************* Higher Matrix Product ***************/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    free((FREE_ARG)(m+nrl-NR_END));
      duration (i.e. until  }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /*************** function subdirf ***********/
      (typically every 2 years instead of every month which is too big).  char *subdirf(char fileres[])
      Model is determined by parameters x and covariates have to be  {
      included manually here.    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
      */    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
   int i, j, d, h, k;    return tmpout;
   double **out, cov[NCOVMAX];  }
   double **newm;  
   /*************** function subdirf2 ***********/
   /* Hstepm could be zero and should return the unit matrix */  char *subdirf2(char fileres[], char *preop)
   for (i=1;i<=nlstate+ndeath;i++)  {
     for (j=1;j<=nlstate+ndeath;j++){    
       oldm[i][j]=(i==j ? 1.0 : 0.0);    /* Caution optionfilefiname is hidden */
       po[i][j][0]=(i==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,preop);
   for(h=1; h <=nhstepm; h++){    strcat(tmpout,fileres);
     for(d=1; d <=hstepm; d++){    return tmpout;
       newm=savm;  }
       /* Covariates have to be included here again */  
       cov[1]=1.;  /*************** function subdirf3 ***********/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
 for (k=1; k<=cptcovage;k++)    
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* Caution optionfilefiname is hidden */
    for (k=1; k<=cptcovprod;k++)    strcpy(tmpout,optionfilefiname);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,preop2);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    strcat(tmpout,fileres);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    return tmpout;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  /***************** f1dim *************************/
       oldm=newm;  extern int ncom; 
     }  extern double *pcom,*xicom;
     for(i=1; i<=nlstate+ndeath; i++)  extern double (*nrfunc)(double []); 
       for(j=1;j<=nlstate+ndeath;j++) {   
         po[i][j][h]=newm[i][j];  double f1dim(double x) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  { 
          */    int j; 
       }    double f;
   } /* end h */    double *xt; 
   return po;   
 }    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 /*************** log-likelihood *************/    free_vector(xt,1,ncom); 
 double func( double *x)    return f; 
 {  } 
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*****************brent *************************/
   double **out;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double sw; /* Sum of weights */  { 
   double lli; /* Individual log likelihood */    int iter; 
   long ipmx;    double a,b,d,etemp;
   /*extern weight */    double fu,fv,fw,fx;
   /* We are differentiating ll according to initial status */    double ftemp;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   /*for(i=1;i<imx;i++)    double e=0.0; 
     printf(" %d\n",s[4][i]);   
   */    a=(ax < cx ? ax : cx); 
   cov[1]=1.;    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    fw=fv=fx=(*f)(x); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (iter=1;iter<=ITMAX;iter++) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      xm=0.5*(a+b); 
     for(mi=1; mi<= wav[i]-1; mi++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       for (ii=1;ii<=nlstate+ndeath;ii++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf(".");fflush(stdout);
       for(d=0; d<dh[mi][i]; d++){      fprintf(ficlog,".");fflush(ficlog);
         newm=savm;  #ifdef DEBUG
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         for (kk=1; kk<=cptcovage;kk++) {      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         }  #endif
              if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        *xmin=x; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        return fx; 
         savm=oldm;      } 
         oldm=newm;      ftemp=fu;
              if (fabs(e) > tol1) { 
                r=(x-w)*(fx-fv); 
       } /* end mult */        q=(x-v)*(fx-fw); 
              p=(x-v)*q-(x-w)*r; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        q=2.0*(q-r); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        if (q > 0.0) p = -p; 
       ipmx +=1;        q=fabs(q); 
       sw += weight[i];        etemp=e; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        e=d; 
     } /* end of wave */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   } /* end of individual */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          d=p/q; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          u=x+d; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          if (u-a < tol2 || b-u < tol2) 
   return -l;            d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 /*********** Maximum Likelihood Estimation ***************/      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      fu=(*f)(u); 
 {      if (fu <= fx) { 
   int i,j, iter;        if (u >= x) a=x; else b=x; 
   double **xi,*delti;        SHFT(v,w,x,u) 
   double fret;          SHFT(fv,fw,fx,fu) 
   xi=matrix(1,npar,1,npar);          } else { 
   for (i=1;i<=npar;i++)            if (u < x) a=u; else b=u; 
     for (j=1;j<=npar;j++)            if (fu <= fw || w == x) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);              v=w; 
   printf("Powell\n");              w=u; 
   powell(p,xi,npar,ftol,&iter,&fret,func);              fv=fw; 
               fw=fu; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));            } else if (fu <= fv || v == x || v == w) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));              v=u; 
               fv=fu; 
 }            } 
           } 
 /**** Computes Hessian and covariance matrix ***/    } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    nrerror("Too many iterations in brent"); 
 {    *xmin=x; 
   double  **a,**y,*x,pd;    return fx; 
   double **hess;  } 
   int i, j,jk;  
   int *indx;  /****************** mnbrak ***********************/
   
   double hessii(double p[], double delta, int theta, double delti[]);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double hessij(double p[], double delti[], int i, int j);              double (*func)(double)) 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double ulim,u,r,q, dum;
     double fu; 
    
   hess=matrix(1,npar,1,npar);    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
   printf("\nCalculation of the hessian matrix. Wait...\n");    if (*fb > *fa) { 
   for (i=1;i<=npar;i++){      SHFT(dum,*ax,*bx,dum) 
     printf("%d",i);fflush(stdout);        SHFT(dum,*fb,*fa,dum) 
     hess[i][i]=hessii(p,ftolhess,i,delti);        } 
     /*printf(" %f ",p[i]);*/    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
   for (i=1;i<=npar;i++) {      r=(*bx-*ax)*(*fb-*fc); 
     for (j=1;j<=npar;j++)  {      q=(*bx-*cx)*(*fb-*fa); 
       if (j>i) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         printf(".%d%d",i,j);fflush(stdout);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         hess[i][j]=hessij(p,delti,i,j);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         hess[j][i]=hess[i][j];      if ((*bx-u)*(u-*cx) > 0.0) { 
       }        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   }        fu=(*func)(u); 
   printf("\n");        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   a=matrix(1,npar,1,npar);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   y=matrix(1,npar,1,npar);        u=ulim; 
   x=vector(1,npar);        fu=(*func)(u); 
   indx=ivector(1,npar);      } else { 
   for (i=1;i<=npar;i++)        u=(*cx)+GOLD*(*cx-*bx); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fu=(*func)(u); 
   ludcmp(a,npar,indx,&pd);      } 
       SHFT(*ax,*bx,*cx,u) 
   for (j=1;j<=npar;j++) {        SHFT(*fa,*fb,*fc,fu) 
     for (i=1;i<=npar;i++) x[i]=0;        } 
     x[j]=1;  } 
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /*************** linmin ************************/
       matcov[i][j]=x[i];  
     }  int ncom; 
   }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   printf("\n#Hessian matrix#\n");   
   for (i=1;i<=npar;i++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for (j=1;j<=npar;j++) {  { 
       printf("%.3e ",hess[i][j]);    double brent(double ax, double bx, double cx, 
     }                 double (*f)(double), double tol, double *xmin); 
     printf("\n");    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   /* Recompute Inverse */    int j; 
   for (i=1;i<=npar;i++)    double xx,xmin,bx,ax; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double fx,fb,fa;
   ludcmp(a,npar,indx,&pd);   
     ncom=n; 
   /*  printf("\n#Hessian matrix recomputed#\n");    pcom=vector(1,n); 
     xicom=vector(1,n); 
   for (j=1;j<=npar;j++) {    nrfunc=func; 
     for (i=1;i<=npar;i++) x[i]=0;    for (j=1;j<=n;j++) { 
     x[j]=1;      pcom[j]=p[j]; 
     lubksb(a,npar,indx,x);      xicom[j]=xi[j]; 
     for (i=1;i<=npar;i++){    } 
       y[i][j]=x[i];    ax=0.0; 
       printf("%.3e ",y[i][j]);    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     printf("\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   }  #ifdef DEBUG
   */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_matrix(a,1,npar,1,npar);  #endif
   free_matrix(y,1,npar,1,npar);    for (j=1;j<=n;j++) { 
   free_vector(x,1,npar);      xi[j] *= xmin; 
   free_ivector(indx,1,npar);      p[j] += xi[j]; 
   free_matrix(hess,1,npar,1,npar);    } 
     free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 }  } 
   
 /*************** hessian matrix ****************/  char *asc_diff_time(long time_sec, char ascdiff[])
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    long sec_left, days, hours, minutes;
   int i;    days = (time_sec) / (60*60*24);
   int l=1, lmax=20;    sec_left = (time_sec) % (60*60*24);
   double k1,k2;    hours = (sec_left) / (60*60) ;
   double p2[NPARMAX+1];    sec_left = (sec_left) %(60*60);
   double res;    minutes = (sec_left) /60;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    sec_left = (sec_left) % (60);
   double fx;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   int k=0,kmax=10;    return ascdiff;
   double l1;  }
   
   fx=func(x);  /*************** powell ************************/
   for (i=1;i<=npar;i++) p2[i]=x[i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for(l=0 ; l <=lmax; l++){              double (*func)(double [])) 
     l1=pow(10,l);  { 
     delts=delt;    void linmin(double p[], double xi[], int n, double *fret, 
     for(k=1 ; k <kmax; k=k+1){                double (*func)(double [])); 
       delt = delta*(l1*k);    int i,ibig,j; 
       p2[theta]=x[theta] +delt;    double del,t,*pt,*ptt,*xit;
       k1=func(p2)-fx;    double fp,fptt;
       p2[theta]=x[theta]-delt;    double *xits;
       k2=func(p2)-fx;    int niterf, itmp;
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    pt=vector(1,n); 
          ptt=vector(1,n); 
 #ifdef DEBUG    xit=vector(1,n); 
       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);    xits=vector(1,n); 
 #endif    *fret=(*func)(p); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (*iter=1;;++(*iter)) { 
         k=kmax;      fp=(*fret); 
       }      ibig=0; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      del=0.0; 
         k=kmax; l=lmax*10.;      last_time=curr_time;
       }      (void) gettimeofday(&curr_time,&tzp);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      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);
         delts=delt;      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); */
     }     for (i=1;i<=n;i++) {
   }        printf(" %d %.12f",i, p[i]);
   delti[theta]=delts;        fprintf(ficlog," %d %.12lf",i, p[i]);
   return res;        fprintf(ficrespow," %.12lf", p[i]);
        }
 }      printf("\n");
       fprintf(ficlog,"\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)      fprintf(ficrespow,"\n");fflush(ficrespow);
 {      if(*iter <=3){
   int i;        tm = *localtime(&curr_time.tv_sec);
   int l=1, l1, lmax=20;        strcpy(strcurr,asctime(&tm));
   double k1,k2,k3,k4,res,fx;  /*       asctime_r(&tm,strcurr); */
   double p2[NPARMAX+1];        forecast_time=curr_time; 
   int k;        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   fx=func(x);          strcurr[itmp-1]='\0';
   for (k=1; k<=2; k++) {        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (i=1;i<=npar;i++) p2[i]=x[i];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(niterf=10;niterf<=30;niterf+=10){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     k1=func(p2)-fx;          tmf = *localtime(&forecast_time.tv_sec);
    /*      asctime_r(&tmf,strfor); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          strcpy(strfor,asctime(&tmf));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          itmp = strlen(strfor);
     k2=func(p2)-fx;          if(strfor[itmp-1]=='\n')
            strfor[itmp-1]='\0';
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     k3=func(p2)-fx;        }
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (i=1;i<=n;i++) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     k4=func(p2)-fx;        fptt=(*fret); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #ifdef DEBUG
 #ifdef DEBUG        printf("fret=%lf \n",*fret);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        fprintf(ficlog,"fret=%lf \n",*fret);
 #endif  #endif
   }        printf("%d",i);fflush(stdout);
   return res;        fprintf(ficlog,"%d",i);fflush(ficlog);
 }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 /************** Inverse of matrix **************/          del=fabs(fptt-(*fret)); 
 void ludcmp(double **a, int n, int *indx, double *d)          ibig=i; 
 {        } 
   int i,imax,j,k;  #ifdef DEBUG
   double big,dum,sum,temp;        printf("%d %.12e",i,(*fret));
   double *vv;        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
   vv=vector(1,n);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   *d=1.0;          printf(" x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=n;i++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     big=0.0;        }
     for (j=1;j<=n;j++)        for(j=1;j<=n;j++) {
       if ((temp=fabs(a[i][j])) > big) big=temp;          printf(" p=%.12e",p[j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          fprintf(ficlog," p=%.12e",p[j]);
     vv[i]=1.0/big;        }
   }        printf("\n");
   for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
     for (i=1;i<j;i++) {  #endif
       sum=a[i][j];      } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       a[i][j]=sum;  #ifdef DEBUG
     }        int k[2],l;
     big=0.0;        k[0]=1;
     for (i=j;i<=n;i++) {        k[1]=-1;
       sum=a[i][j];        printf("Max: %.12e",(*func)(p));
       for (k=1;k<j;k++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         sum -= a[i][k]*a[k][j];        for (j=1;j<=n;j++) {
       a[i][j]=sum;          printf(" %.12e",p[j]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          fprintf(ficlog," %.12e",p[j]);
         big=dum;        }
         imax=i;        printf("\n");
       }        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
     if (j != imax) {          for (j=1;j<=n;j++) {
       for (k=1;k<=n;k++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         dum=a[imax][k];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[imax][k]=a[j][k];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[j][k]=dum;          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       *d = -(*d);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       vv[imax]=vv[j];        }
     }  #endif
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {        free_vector(xit,1,n); 
       dum=1.0/(a[j][j]);        free_vector(xits,1,n); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
   }        return; 
   free_vector(vv,1,n);  /* Doesn't work */      } 
 ;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 void lubksb(double **a, int n, int *indx, double b[])        xit[j]=p[j]-pt[j]; 
 {        pt[j]=p[j]; 
   int i,ii=0,ip,j;      } 
   double sum;      fptt=(*func)(ptt); 
        if (fptt < fp) { 
   for (i=1;i<=n;i++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     ip=indx[i];        if (t < 0.0) { 
     sum=b[ip];          linmin(p,xit,n,fret,func); 
     b[ip]=b[i];          for (j=1;j<=n;j++) { 
     if (ii)            xi[j][ibig]=xi[j][n]; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            xi[j][n]=xit[j]; 
     else if (sum) ii=i;          }
     b[i]=sum;  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=n;i>=1;i--) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     sum=b[i];          for(j=1;j<=n;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            printf(" %.12e",xit[j]);
     b[i]=sum/a[i][i];            fprintf(ficlog," %.12e",xit[j]);
   }          }
 }          printf("\n");
           fprintf(ficlog,"\n");
 /************ Frequencies ********************/  #endif
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)        }
 {  /* Some frequencies */      } 
      } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  } 
   double ***freq; /* Frequencies */  
   double *pp;  /**** Prevalence limit (stable or period prevalence)  ****************/
   double pos;  
   FILE *ficresp;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   char fileresp[FILENAMELENGTH];  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   pp=vector(1,nlstate);       matrix by transitions matrix until convergence is reached */
   
   strcpy(fileresp,"p");    int i, ii,j,k;
   strcat(fileresp,fileres);    double min, max, maxmin, maxmax,sumnew=0.;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double **matprod2();
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double **out, cov[NCOVMAX], **pmij();
     exit(0);    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   j=cptcoveff;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
   
   for(k1=1; k1<=j;k1++){     cov[1]=1.;
    for(i1=1; i1<=ncodemax[k1];i1++){   
        j1++;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
          scanf("%d", i);*/      newm=savm;
         for (i=-1; i<=nlstate+ndeath; i++)        /* Covariates have to be included here again */
          for (jk=-1; jk<=nlstate+ndeath; jk++)         cov[2]=agefin;
            for(m=agemin; m <= agemax+3; m++)    
              freq[i][jk][m]=0;        for (k=1; k<=cptcovn;k++) {
                  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        for (i=1; i<=imx; i++) {          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
          bool=1;        }
          if  (cptcovn>0) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
            for (z1=1; z1<=cptcoveff; z1++)        for (k=1; k<=cptcovprod;k++)
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                bool=0;  
          }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
           if (bool==1) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
            for(m=firstpass; m<=lastpass-1; m++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
              if(agev[m][i]==0) agev[m][i]=agemax+1;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
              if(agev[m][i]==1) agev[m][i]=agemax+2;  
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      savm=oldm;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      oldm=newm;
            }      maxmax=0.;
          }      for(j=1;j<=nlstate;j++){
        }        min=1.;
         if  (cptcovn>0) {        max=0.;
          fprintf(ficresp, "\n#********** Variable ");        for(i=1; i<=nlstate; i++) {
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          sumnew=0;
        fprintf(ficresp, "**********\n#");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         }          prlim[i][j]= newm[i][j]/(1-sumnew);
        for(i=1; i<=nlstate;i++)          max=FMAX(max,prlim[i][j]);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          min=FMIN(min,prlim[i][j]);
        fprintf(ficresp, "\n");        }
                maxmin=max-min;
   for(i=(int)agemin; i <= (int)agemax+3; i++){        maxmax=FMAX(maxmax,maxmin);
     if(i==(int)agemax+3)      }
       printf("Total");      if(maxmax < ftolpl){
     else        return prlim;
       printf("Age %d", i);      }
     for(jk=1; jk <=nlstate ; jk++){    }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
         pp[jk] += freq[jk][m][i];  
     }  /*************** transition probabilities ***************/ 
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         pos += freq[jk][m][i];  {
       if(pp[jk]>=1.e-10)    double s1, s2;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /*double t34;*/
       else    int i,j,j1, nc, ii, jj;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
     }      for(i=1; i<= nlstate; i++){
     for(jk=1; jk <=nlstate ; jk++){        for(j=1; j<i;j++){
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         pp[jk] += freq[jk][m][i];            /*s2 += param[i][j][nc]*cov[nc];*/
     }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for(jk=1,pos=0; jk <=nlstate ; jk++)  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       pos += pp[jk];          }
     for(jk=1; jk <=nlstate ; jk++){          ps[i][j]=s2;
       if(pos>=1.e-5)  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        }
       else        for(j=i+1; j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       if( i <= (int) agemax){            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         if(pos>=1.e-5)  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          }
       else          ps[i][j]=s2;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        }
       }      }
     }      /*ps[3][2]=1;*/
     for(jk=-1; jk <=nlstate+ndeath; jk++)      
       for(m=-1; m <=nlstate+ndeath; m++)      for(i=1; i<= nlstate; i++){
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        s1=0;
     if(i <= (int) agemax)        for(j=1; j<i; j++)
       fprintf(ficresp,"\n");          s1+=exp(ps[i][j]);
     printf("\n");        for(j=i+1; j<=nlstate+ndeath; j++)
     }          s1+=exp(ps[i][j]);
     }        ps[i][i]=1./(s1+1.);
  }        for(j=1; j<i; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
   fclose(ficresp);        for(j=i+1; j<=nlstate+ndeath; j++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   free_vector(pp,1,nlstate);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
 }  /* End of Freq */      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 /************* Waves Concatenation ***************/        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          ps[ii][ii]=1;
 {        }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      }
      Death is a valid wave (if date is known).      
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
      and mw[mi+1][i]. dh depends on stepm.  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
      */  /*         printf("ddd %lf ",ps[ii][jj]); */
   /*       } */
   int i, mi, m;  /*       printf("\n "); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  /*        } */
      double sum=0., jmean=0.;*/  /*        printf("\n ");printf("%lf ",cov[2]); */
          /*
 int j, k=0,jk, ju, jl;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
      double sum=0.;        goto end;*/
 jmin=1e+5;      return ps;
  jmax=-1;  }
 jmean=0.;  
   for(i=1; i<=imx; i++){  /**************** Product of 2 matrices ******************/
     mi=0;  
     m=firstpass;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     while(s[m][i] <= nlstate){  {
       if(s[m][i]>=1)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         mw[++mi][i]=m;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       if(m >=lastpass)    /* in, b, out are matrice of pointers which should have been initialized 
         break;       before: only the contents of out is modified. The function returns
       else       a pointer to pointers identical to out */
         m++;    long i, j, k;
     }/* end while */    for(i=nrl; i<= nrh; i++)
     if (s[m][i] > nlstate){      for(k=ncolol; k<=ncoloh; k++)
       mi++;     /* Death is another wave */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       /* if(mi==0)  never been interviewed correctly before death */          out[i][k] +=in[i][j]*b[j][k];
          /* Only death is a correct wave */  
       mw[mi][i]=m;    return out;
     }  }
   
     wav[i]=mi;  
     if(mi==0)  /************* Higher Matrix Product ***************/
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
   for(i=1; i<=imx; i++){    /* Computes the transition matrix starting at age 'age' over 
     for(mi=1; mi<wav[i];mi++){       'nhstepm*hstepm*stepm' months (i.e. until
       if (stepm <=0)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         dh[mi][i]=1;       nhstepm*hstepm matrices. 
       else{       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         if (s[mw[mi+1][i]][i] > nlstate) {       (typically every 2 years instead of every month which is too big 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       for the memory).
           /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/       Model is determined by parameters x and covariates have to be 
           if(j==0) j=1;  /* Survives at least one month after exam */       included manually here. 
           k=k+1;  
           if (j >= jmax) jmax=j;       */
           else if (j <= jmin)jmin=j;  
           sum=sum+j;    int i, j, d, h, k;
         }    double **out, cov[NCOVMAX];
         else{    double **newm;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/    /* Hstepm could be zero and should return the unit matrix */
           k=k+1;    for (i=1;i<=nlstate+ndeath;i++)
           if (j >= jmax) jmax=j;      for (j=1;j<=nlstate+ndeath;j++){
           else if (j <= jmin)jmin=j;        oldm[i][j]=(i==j ? 1.0 : 0.0);
           sum=sum+j;        po[i][j][0]=(i==j ? 1.0 : 0.0);
         }      }
         jk= j/stepm;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         jl= j -jk*stepm;    for(h=1; h <=nhstepm; h++){
         ju= j -(jk+1)*stepm;      for(d=1; d <=hstepm; d++){
         if(jl <= -ju)        newm=savm;
           dh[mi][i]=jk;        /* Covariates have to be included here again */
         else        cov[1]=1.;
           dh[mi][i]=jk+1;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         if(dh[mi][i]==0)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           dh[mi][i]=1; /* At least one step */        for (k=1; k<=cptcovage;k++)
       }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
   }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
 }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 /*********** Tricode ****************************/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 void tricode(int *Tvar, int **nbcode, int imx)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int Ndum[20],ij=1, k, j, i;        savm=oldm;
   int cptcode=0;        oldm=newm;
   cptcoveff=0;      }
        for(i=1; i<=nlstate+ndeath; i++)
   for (k=0; k<19; k++) Ndum[k]=0;        for(j=1;j<=nlstate+ndeath;j++) {
   for (k=1; k<=7; k++) ncodemax[k]=0;          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]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {           */
     for (i=1; i<=imx; i++) {        }
       ij=(int)(covar[Tvar[j]][i]);    } /* end h */
       Ndum[ij]++;    return po;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  }
       if (ij > cptcode) cptcode=ij;  
     }  
   /*************** log-likelihood *************/
     for (i=0; i<=cptcode; i++) {  double func( double *x)
       if(Ndum[i]!=0) ncodemax[j]++;  {
     }    int i, ii, j, k, mi, d, kk;
     ij=1;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
     double sw; /* Sum of weights */
     for (i=1; i<=ncodemax[j]; i++) {    double lli; /* Individual log likelihood */
       for (k=0; k<=19; k++) {    int s1, s2;
         if (Ndum[k] != 0) {    double bbh, survp;
           nbcode[Tvar[j]][ij]=k;    long ipmx;
           ij++;    /*extern weight */
         }    /* We are differentiating ll according to initial status */
         if (ij > ncodemax[j]) break;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }      /*for(i=1;i<imx;i++) 
     }      printf(" %d\n",s[4][i]);
   }      */
     cov[1]=1.;
  for (k=0; k<19; k++) Ndum[k]=0;  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
  for (i=1; i<=ncovmodel; i++) {  
       ij=Tvar[i];    if(mle==1){
       Ndum[ij]++;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
  ij=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
  for (i=1; i<=10; i++) {            for (j=1;j<=nlstate+ndeath;j++){
    if((Ndum[i]!=0) && (i<=ncov)){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      Tvaraff[ij]=i;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      ij++;            }
    }          for(d=0; d<dh[mi][i]; d++){
  }            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     cptcoveff=ij-1;            for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /*********** Health Expectancies ****************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            savm=oldm;
 {            oldm=newm;
   /* Health expectancies */          } /* end mult */
   int i, j, nhstepm, hstepm, h;        
   double age, agelim,hf;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double ***p3mat;          /* But now since version 0.9 we anticipate for bias at large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   fprintf(ficreseij,"# Health expectancies\n");           * (in months) between two waves is not a multiple of stepm, we rounded to 
   fprintf(ficreseij,"# Age");           * the nearest (and in case of equal distance, to the lowest) interval but now
   for(i=1; i<=nlstate;i++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for(j=1; j<=nlstate;j++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       fprintf(ficreseij," %1d-%1d",i,j);           * probability in order to take into account the bias as a fraction of the way
   fprintf(ficreseij,"\n");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   hstepm=1*YEARM; /*  Every j years of age (in month) */           * For stepm=1 the results are the same as for previous versions of Imach.
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */           * For stepm > 1 the results are less biased than in previous versions. 
            */
   agelim=AGESUP;          s1=s[mw[mi][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          s2=s[mw[mi+1][i]][i];
     /* nhstepm age range expressed in number of stepm */          bbh=(double)bh[mi][i]/(double)stepm; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          /* bias bh is positive if real duration
     /* Typically if 20 years = 20*12/6=40 stepm */           * is higher than the multiple of stepm and negative otherwise.
     if (stepm >= YEARM) hstepm=1;           */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if( s2 > nlstate){ 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            /* i.e. if s2 is a death state and if the date of death is known 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */               then the contribution to the likelihood is the probability to 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                 die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
     for(i=1; i<=nlstate;i++)               In version up to 0.92 likelihood was computed
       for(j=1; j<=nlstate;j++)          as if date of death was unknown. Death was treated as any other
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          health state: the date of the interview describes the actual state
           eij[i][j][(int)age] +=p3mat[i][j][h];          and not the date of a change in health state. The former idea was
         }          to consider that at each interview the state was recorded
              (healthy, disable or death) and IMaCh was corrected; but when we
     hf=1;          introduced the exact date of death then we should have modified
     if (stepm >= YEARM) hf=stepm/YEARM;          the contribution of an exact death to the likelihood. This new
     fprintf(ficreseij,"%.0f",age );          contribution is smaller and very dependent of the step unit
     for(i=1; i<=nlstate;i++)          stepm. It is no more the probability to die between last interview
       for(j=1; j<=nlstate;j++){          and month of death but the probability to survive from last
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          interview up to one month before death multiplied by the
       }          probability to die within a month. Thanks to Chris
     fprintf(ficreseij,"\n");          Jackson for correcting this bug.  Former versions increased
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          mortality artificially. The bad side is that we add another loop
   }          which slows down the processing. The difference can be up to 10%
 }          lower mortality.
             */
 /************ Variance ******************/            lli=log(out[s1][s2] - savm[s1][s2]);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {  
   /* Variance of health expectancies */          } else if  (s2==-2) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (j=1,survp=0. ; j<=nlstate; j++) 
   double **newm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double **dnewm,**doldm;            /*survp += out[s1][j]; */
   int i, j, nhstepm, hstepm, h;            lli= log(survp);
   int k, cptcode;          }
    double *xp;          
   double **gp, **gm;          else if  (s2==-4) { 
   double ***gradg, ***trgradg;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double ***p3mat;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double age,agelim;            lli= log(survp); 
   int theta;          } 
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");          else if  (s2==-5) { 
   fprintf(ficresvij,"# Age");            for (j=1,survp=0. ; j<=2; j++)  
   for(i=1; i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(j=1; j<=nlstate;j++)            lli= log(survp); 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          } 
   fprintf(ficresvij,"\n");          
           else{
   xp=vector(1,npar);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   dnewm=matrix(1,nlstate,1,npar);            /*  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 */
   doldm=matrix(1,nlstate,1,nlstate);          } 
            /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   hstepm=1*YEARM; /* Every year of age */          /*if(lli ==000.0)*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   agelim = AGESUP;          ipmx +=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          sw += weight[i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (stepm >= YEARM) hstepm=1;        } /* end of wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } /* end of individual */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }  else if(mle==2){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gp=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gm=matrix(0,nhstepm,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){ /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<=dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
       for(j=1; j<= nlstate; j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(h=0; h<=nhstepm; h++){            for (kk=1; kk<=cptcovage;kk++) {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       for(i=1; i<=npar; i++) /* Computes gradient */            oldm=newm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          } /* end mult */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          s1=s[mw[mi][i]][i];
       for(j=1; j<= nlstate; j++){          s2=s[mw[mi+1][i]][i];
         for(h=0; h<=nhstepm; h++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          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 */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          ipmx +=1;
         }          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<= nlstate; j++)        } /* end of wave */
         for(h=0; h<=nhstepm; h++){      } /* end of individual */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    }  else if(mle==3){  /* exponential inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     } /* End theta */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     for(h=0; h<=nhstepm; h++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(theta=1; theta <=npar; theta++)            }
           trgradg[h][j][theta]=gradg[h][theta][j];          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for(i=1;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1;j<=nlstate;j++)            for (kk=1; kk<=cptcovage;kk++) {
         vareij[i][j][(int)age] =0.;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(h=0;h<=nhstepm;h++){            }
       for(k=0;k<=nhstepm;k++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            savm=oldm;
         for(i=1;i<=nlstate;i++)            oldm=newm;
           for(j=1;j<=nlstate;j++)          } /* end mult */
             vareij[i][j][(int)age] += doldm[i][j];        
       }          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
     h=1;          bbh=(double)bh[mi][i]/(double)stepm; 
     if (stepm >= YEARM) h=stepm/YEARM;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     fprintf(ficresvij,"%.0f ",age );          ipmx +=1;
     for(i=1; i<=nlstate;i++)          sw += weight[i];
       for(j=1; j<=nlstate;j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        } /* end of wave */
       }      } /* end of individual */
     fprintf(ficresvij,"\n");    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     free_matrix(gp,0,nhstepm,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_matrix(gm,0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (j=1;j<=nlstate+ndeath;j++){
   } /* End age */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);          for(d=0; d<dh[mi][i]; d++){
   free_matrix(dnewm,1,nlstate,1,nlstate);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /************ Variance of prevlim ******************/            }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Variance of prevalence limit */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            savm=oldm;
   double **newm;            oldm=newm;
   double **dnewm,**doldm;          } /* end mult */
   int i, j, nhstepm, hstepm;        
   int k, cptcode;          s1=s[mw[mi][i]][i];
   double *xp;          s2=s[mw[mi+1][i]][i];
   double *gp, *gm;          if( s2 > nlstate){ 
   double **gradg, **trgradg;            lli=log(out[s1][s2] - savm[s1][s2]);
   double age,agelim;          }else{
   int theta;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
              }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          ipmx +=1;
   fprintf(ficresvpl,"# Age");          sw += weight[i];
   for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresvpl," %1d-%1d",i,i);  /*      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]); */
   fprintf(ficresvpl,"\n");        } /* end of wave */
       } /* end of individual */
   xp=vector(1,npar);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   dnewm=matrix(1,nlstate,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   doldm=matrix(1,nlstate,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   hstepm=1*YEARM; /* Every year of age */          for (ii=1;ii<=nlstate+ndeath;ii++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (j=1;j<=nlstate+ndeath;j++){
   agelim = AGESUP;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            }
     if (stepm >= YEARM) hstepm=1;          for(d=0; d<dh[mi][i]; d++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            newm=savm;
     gradg=matrix(1,npar,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     gp=vector(1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
     gm=vector(1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
     for(theta=1; theta <=npar; theta++){          
       for(i=1; i<=npar; i++){ /* Computes gradient */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            oldm=newm;
       for(i=1;i<=nlstate;i++)          } /* end mult */
         gp[i] = prlim[i][i];        
              s1=s[mw[mi][i]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */          s2=s[mw[mi+1][i]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ipmx +=1;
       for(i=1;i<=nlstate;i++)          sw += weight[i];
         gm[i] = prlim[i][i];          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]);*/
       for(i=1;i<=nlstate;i++)        } /* end of wave */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      } /* end of individual */
     } /* End theta */    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     trgradg =matrix(1,nlstate,1,npar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(j=1; j<=nlstate;j++)    return -l;
       for(theta=1; theta <=npar; theta++)  }
         trgradg[j][theta]=gradg[theta][j];  
   /*************** log-likelihood *************/
     for(i=1;i<=nlstate;i++)  double funcone( double *x)
       varpl[i][(int)age] =0.;  {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    /* Same as likeli but slower because of a lot of printf and if */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    int i, ii, j, k, mi, d, kk;
     for(i=1;i<=nlstate;i++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double **out;
     double lli; /* Individual log likelihood */
     fprintf(ficresvpl,"%.0f ",age );    double llt;
     for(i=1; i<=nlstate;i++)    int s1, s2;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    double bbh, survp;
     fprintf(ficresvpl,"\n");    /*extern weight */
     free_vector(gp,1,nlstate);    /* We are differentiating ll according to initial status */
     free_vector(gm,1,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     free_matrix(gradg,1,npar,1,nlstate);    /*for(i=1;i<imx;i++) 
     free_matrix(trgradg,1,nlstate,1,npar);      printf(" %d\n",s[4][i]);
   } /* End age */    */
     cov[1]=1.;
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
 /***********************************************/            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /**************** Main Program *****************/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /***********************************************/          }
         for(d=0; d<dh[mi][i]; d++){
 /*int main(int argc, char *argv[])*/          newm=savm;
 int main()          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          }
   double agedeb, agefin,hf;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double agemin=1.e20, agemax=-1.e20;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
   double fret;          oldm=newm;
   double **xi,tmp,delta;        } /* end mult */
         
   double dum; /* Dummy variable */        s1=s[mw[mi][i]][i];
   double ***p3mat;        s2=s[mw[mi+1][i]][i];
   int *indx;        bbh=(double)bh[mi][i]/(double)stepm; 
   char line[MAXLINE], linepar[MAXLINE];        /* bias is positive if real duration
   char title[MAXLINE];         * is higher than the multiple of stepm and negative otherwise.
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];         */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   char filerest[FILENAMELENGTH];          lli=log(out[s1][s2] - savm[s1][s2]);
   char fileregp[FILENAMELENGTH];        } else if  (s2==-2) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          for (j=1,survp=0. ; j<=nlstate; j++) 
   int firstobs=1, lastobs=10;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int sdeb, sfin; /* Status at beginning and end */          lli= log(survp);
   int c,  h , cpt,l;        }else if (mle==1){
   int ju,jl, mi;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        } else if(mle==2){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          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 */
          } else if(mle==3){  /* exponential inter-extrapolation */
   int hstepm, nhstepm;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double bage, fage, age, agelim, agebase;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double ftolpl=FTOL;          lli=log(out[s1][s2]); /* Original formula */
   double **prlim;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   double *severity;          lli=log(out[s1][s2]); /* Original formula */
   double ***param; /* Matrix of parameters */        } /* End of if */
   double  *p;        ipmx +=1;
   double **matcov; /* Matrix of covariance */        sw += weight[i];
   double ***delti3; /* Scale */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *delti; /* Scale */  /*       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]); */
   double ***eij, ***vareij;        if(globpr){
   double **varpl; /* Variances of prevalence limits by age */          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   double *epj, vepp;   %11.6f %11.6f %11.6f ", \
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   char *alph[]={"a","a","b","c","d","e"}, str[4];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   char z[1]="c", occ;            llt +=ll[k]*gipmx/gsw;
 #include <sys/time.h>            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
 #include <time.h>          }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          fprintf(ficresilk," %10.6f\n", -llt);
   /* long total_usecs;        }
   struct timeval start_time, end_time;      } /* end of wave */
      } /* end of individual */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   printf("\nIMACH, Version 0.64a");    if(globpr==0){ /* First time we count the contributions and weights */
   printf("\nEnter the parameter file name: ");      gipmx=ipmx;
       gsw=sw;
 #ifdef windows    }
   scanf("%s",pathtot);    return -l;
   getcwd(pathcd, size);  }
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 split(pathtot, path,optionfile);  {
   chdir(path);    /* This routine should help understanding what is done with 
   replace(pathc,path);       the selection of individuals/waves and
 #endif       to check the exact contribution to the likelihood.
 #ifdef unix       Plotting could be done.
   scanf("%s",optionfile);     */
 #endif    int k;
   
 /*-------- arguments in the command line --------*/    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   strcpy(fileres,"r");      strcat(fileresilk,fileres);
   strcat(fileres, optionfile);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
   /*---------arguments file --------*/        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     printf("Problem with optionfile %s\n",optionfile);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     goto end;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   }      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   strcpy(filereso,"o");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   strcat(filereso,fileres);    }
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    *fretone=(*funcone)(p);
   }    if(*globpri !=0){
       fclose(ficresilk);
   /* Reads comments: lines beginning with '#' */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   while((c=getc(ficpar))=='#' && c!= EOF){      fflush(fichtm); 
     ungetc(c,ficpar);    } 
     fgets(line, MAXLINE, ficpar);    return;
     puts(line);  }
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  /*********** Maximum Likelihood Estimation ***************/
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);  {
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    int i,j, iter;
     double **xi;
   covar=matrix(0,NCOVMAX,1,n);    double fret;
   cptcovn=0;    double fretone; /* Only one call to likelihood */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
   ncovmodel=2+cptcovn;    for (i=1;i<=npar;i++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      for (j=1;j<=npar;j++)
          xi[i][j]=(i==j ? 1.0 : 0.0);
   /* Read guess parameters */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   /* Reads comments: lines beginning with '#' */    strcpy(filerespow,"pow"); 
   while((c=getc(ficpar))=='#' && c!= EOF){    strcat(filerespow,fileres);
     ungetc(c,ficpar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);      printf("Problem with resultfile: %s\n", filerespow);
     puts(line);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     fputs(line,ficparo);    }
   }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   ungetc(c,ficpar);    for (i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate+ndeath;j++)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     for(i=1; i <=nlstate; i++)    fprintf(ficrespow,"\n");
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    powell(p,xi,npar,ftol,&iter,&fret,func);
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);    free_matrix(xi,1,npar,1,npar);
       for(k=1; k<=ncovmodel;k++){    fclose(ficrespow);
         fscanf(ficpar," %lf",&param[i][j][k]);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         printf(" %lf",param[i][j][k]);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         fprintf(ficparo," %lf",param[i][j][k]);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
       fscanf(ficpar,"\n");  }
       printf("\n");  
       fprintf(ficparo,"\n");  /**** Computes Hessian and covariance matrix ***/
     }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    double  **a,**y,*x,pd;
   p=param[1][1];    double **hess;
      int i, j,jk;
   /* Reads comments: lines beginning with '#' */    int *indx;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fgets(line, MAXLINE, ficpar);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     puts(line);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     fputs(line,ficparo);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   }    double gompertz(double p[]);
   ungetc(c,ficpar);    hess=matrix(1,npar,1,npar);
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    printf("\nCalculation of the hessian matrix. Wait...\n");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for(i=1; i <=nlstate; i++){    for (i=1;i<=npar;i++){
     for(j=1; j <=nlstate+ndeath-1; j++){      printf("%d",i);fflush(stdout);
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficlog,"%d",i);fflush(ficlog);
       printf("%1d%1d",i,j);     
       fprintf(ficparo,"%1d%1d",i1,j1);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(k=1; k<=ncovmodel;k++){      
         fscanf(ficpar,"%le",&delti3[i][j][k]);      /*  printf(" %f ",p[i]);
         printf(" %le",delti3[i][j][k]);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         fprintf(ficparo," %le",delti3[i][j][k]);    }
       }    
       fscanf(ficpar,"\n");    for (i=1;i<=npar;i++) {
       printf("\n");      for (j=1;j<=npar;j++)  {
       fprintf(ficparo,"\n");        if (j>i) { 
     }          printf(".%d%d",i,j);fflush(stdout);
   }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   delti=delti3[1][1];          hess[i][j]=hessij(p,delti,i,j,func,npar);
            
   /* Reads comments: lines beginning with '#' */          hess[j][i]=hess[i][j];    
   while((c=getc(ficpar))=='#' && c!= EOF){          /*printf(" %lf ",hess[i][j]);*/
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    }
     fputs(line,ficparo);    printf("\n");
   }    fprintf(ficlog,"\n");
   ungetc(c,ficpar);  
      printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   matcov=matrix(1,npar,1,npar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   for(i=1; i <=npar; i++){    
     fscanf(ficpar,"%s",&str);    a=matrix(1,npar,1,npar);
     printf("%s",str);    y=matrix(1,npar,1,npar);
     fprintf(ficparo,"%s",str);    x=vector(1,npar);
     for(j=1; j <=i; j++){    indx=ivector(1,npar);
       fscanf(ficpar," %le",&matcov[i][j]);    for (i=1;i<=npar;i++)
       printf(" %.5le",matcov[i][j]);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       fprintf(ficparo," %.5le",matcov[i][j]);    ludcmp(a,npar,indx,&pd);
     }  
     fscanf(ficpar,"\n");    for (j=1;j<=npar;j++) {
     printf("\n");      for (i=1;i<=npar;i++) x[i]=0;
     fprintf(ficparo,"\n");      x[j]=1;
   }      lubksb(a,npar,indx,x);
   for(i=1; i <=npar; i++)      for (i=1;i<=npar;i++){ 
     for(j=i+1;j<=npar;j++)        matcov[i][j]=x[i];
       matcov[i][j]=matcov[j][i];      }
        }
   printf("\n");  
     printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     /*-------- data file ----------*/    for (i=1;i<=npar;i++) { 
     if((ficres =fopen(fileres,"w"))==NULL) {      for (j=1;j<=npar;j++) { 
       printf("Problem with resultfile: %s\n", fileres);goto end;        printf("%.3e ",hess[i][j]);
     }        fprintf(ficlog,"%.3e ",hess[i][j]);
     fprintf(ficres,"#%s\n",version);      }
          printf("\n");
     if((fic=fopen(datafile,"r"))==NULL)    {      fprintf(ficlog,"\n");
       printf("Problem with datafile: %s\n", datafile);goto end;    }
     }  
     /* Recompute Inverse */
     n= lastobs;    for (i=1;i<=npar;i++)
     severity = vector(1,maxwav);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     outcome=imatrix(1,maxwav+1,1,n);    ludcmp(a,npar,indx,&pd);
     num=ivector(1,n);  
     moisnais=vector(1,n);    /*  printf("\n#Hessian matrix recomputed#\n");
     annais=vector(1,n);  
     moisdc=vector(1,n);    for (j=1;j<=npar;j++) {
     andc=vector(1,n);      for (i=1;i<=npar;i++) x[i]=0;
     agedc=vector(1,n);      x[j]=1;
     cod=ivector(1,n);      lubksb(a,npar,indx,x);
     weight=vector(1,n);      for (i=1;i<=npar;i++){ 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        y[i][j]=x[i];
     mint=matrix(1,maxwav,1,n);        printf("%.3e ",y[i][j]);
     anint=matrix(1,maxwav,1,n);        fprintf(ficlog,"%.3e ",y[i][j]);
     s=imatrix(1,maxwav+1,1,n);      }
     adl=imatrix(1,maxwav+1,1,n);          printf("\n");
     tab=ivector(1,NCOVMAX);      fprintf(ficlog,"\n");
     ncodemax=ivector(1,8);    }
     */
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {    free_matrix(a,1,npar,1,npar);
       if ((i >= firstobs) && (i <=lastobs)) {    free_matrix(y,1,npar,1,npar);
            free_vector(x,1,npar);
         for (j=maxwav;j>=1;j--){    free_ivector(indx,1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    free_matrix(hess,1,npar,1,npar);
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  }
         }  
          /*************** hessian matrix ****************/
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  {
     int i;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    int l=1, lmax=20;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double k1,k2;
     double p2[NPARMAX+1];
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    double res;
         for (j=ncov;j>=1;j--){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double fx;
         }    int k=0,kmax=10;
         num[i]=atol(stra);    double l1;
   
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
         i=i+1;    for(l=0 ; l <=lmax; l++){
       }      l1=pow(10,l);
     }      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
     /*scanf("%d",i);*/        delt = delta*(l1*k);
   imx=i-1; /* Number of individuals */        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
   /* Calculation of the number of parameter from char model*/        p2[theta]=x[theta]-delt;
   Tvar=ivector(1,15);        k2=func(p2)-fx;
   Tprod=ivector(1,15);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   Tvaraff=ivector(1,15);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   Tvard=imatrix(1,15,1,2);        
   Tage=ivector(1,15);        #ifdef DEBUG
            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);
   if (strlen(model) >1){        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);
     j=0, j1=0, k1=1, k2=1;  #endif
     j=nbocc(model,'+');        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     j1=nbocc(model,'*');        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     cptcovn=j+1;          k=kmax;
     cptcovprod=j1;        }
            else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
              k=kmax; l=lmax*10.;
     strcpy(modelsav,model);        }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       printf("Error. Non available option model=%s ",model);          delts=delt;
       goto end;        }
     }      }
        }
     for(i=(j+1); i>=1;i--){    delti[theta]=delts;
       cutv(stra,strb,modelsav,'+');    return res; 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  }
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         cutv(strd,strc,strb,'*');  {
         if (strcmp(strc,"age")==0) {    int i;
           cptcovprod--;    int l=1, l1, lmax=20;
           cutv(strb,stre,strd,'V');    double k1,k2,k3,k4,res,fx;
           Tvar[i]=atoi(stre);    double p2[NPARMAX+1];
           cptcovage++;    int k;
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/    fx=func(x);
         }    for (k=1; k<=2; k++) {
         else if (strcmp(strd,"age")==0) {      for (i=1;i<=npar;i++) p2[i]=x[i];
           cptcovprod--;      p2[thetai]=x[thetai]+delti[thetai]/k;
           cutv(strb,stre,strc,'V');      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           Tvar[i]=atoi(stre);      k1=func(p2)-fx;
           cptcovage++;    
           Tage[cptcovage]=i;      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         else {      k2=func(p2)-fx;
           cutv(strb,stre,strc,'V');    
           Tvar[i]=ncov+k1;      p2[thetai]=x[thetai]-delti[thetai]/k;
           cutv(strb,strc,strd,'V');      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           Tprod[k1]=i;      k3=func(p2)-fx;
           Tvard[k1][1]=atoi(strc);    
           Tvard[k1][2]=atoi(stre);      p2[thetai]=x[thetai]-delti[thetai]/k;
           Tvar[cptcovn+k2]=Tvard[k1][1];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      k4=func(p2)-fx;
           for (k=1; k<=lastobs;k++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  #ifdef DEBUG
           k1++;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
           k2=k2+2;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         }  #endif
       }    }
       else {    return res;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  }
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');  /************** Inverse of matrix **************/
       Tvar[i]=atoi(strc);  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
       strcpy(modelsav,stra);      int i,imax,j,k; 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    double big,dum,sum,temp; 
         scanf("%d",i);*/    double *vv; 
     }   
 }    vv=vector(1,n); 
      *d=1.0; 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    for (i=1;i<=n;i++) { 
   printf("cptcovprod=%d ", cptcovprod);      big=0.0; 
   scanf("%d ",i);*/      for (j=1;j<=n;j++) 
     fclose(fic);        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     /*  if(mle==1){*/      vv[i]=1.0/big; 
     if (weightopt != 1) { /* Maximisation without weights*/    } 
       for(i=1;i<=n;i++) weight[i]=1.0;    for (j=1;j<=n;j++) { 
     }      for (i=1;i<j;i++) { 
     /*-calculation of age at interview from date of interview and age at death -*/        sum=a[i][j]; 
     agev=matrix(1,maxwav,1,imx);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
     for (i=1; i<=imx; i++)  {      } 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      big=0.0; 
       for(m=1; (m<= maxwav); m++){      for (i=j;i<=n;i++) { 
         if(s[m][i] >0){        sum=a[i][j]; 
           if (s[m][i] == nlstate+1) {        for (k=1;k<j;k++) 
             if(agedc[i]>0)          sum -= a[i][k]*a[k][j]; 
               if(moisdc[i]!=99 && andc[i]!=9999)        a[i][j]=sum; 
               agev[m][i]=agedc[i];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
             else {          big=dum; 
               if (andc[i]!=9999){          imax=i; 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        } 
               agev[m][i]=-1;      } 
               }      if (j != imax) { 
             }        for (k=1;k<=n;k++) { 
           }          dum=a[imax][k]; 
           else if(s[m][i] !=9){ /* Should no more exist */          a[imax][k]=a[j][k]; 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          a[j][k]=dum; 
             if(mint[m][i]==99 || anint[m][i]==9999)        } 
               agev[m][i]=1;        *d = -(*d); 
             else if(agev[m][i] <agemin){        vv[imax]=vv[j]; 
               agemin=agev[m][i];      } 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      indx[j]=imax; 
             }      if (a[j][j] == 0.0) a[j][j]=TINY; 
             else if(agev[m][i] >agemax){      if (j != n) { 
               agemax=agev[m][i];        dum=1.0/(a[j][j]); 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
             }      } 
             /*agev[m][i]=anint[m][i]-annais[i];*/    } 
             /*   agev[m][i] = age[i]+2*m;*/    free_vector(vv,1,n);  /* Doesn't work */
           }  ;
           else { /* =9 */  } 
             agev[m][i]=1;  
             s[m][i]=-1;  void lubksb(double **a, int n, int *indx, double b[]) 
           }  { 
         }    int i,ii=0,ip,j; 
         else /*= 0 Unknown */    double sum; 
           agev[m][i]=1;   
       }    for (i=1;i<=n;i++) { 
          ip=indx[i]; 
     }      sum=b[ip]; 
     for (i=1; i<=imx; i++)  {      b[ip]=b[i]; 
       for(m=1; (m<= maxwav); m++){      if (ii) 
         if (s[m][i] > (nlstate+ndeath)) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           printf("Error: Wrong value in nlstate or ndeath\n");        else if (sum) ii=i; 
           goto end;      b[i]=sum; 
         }    } 
       }    for (i=n;i>=1;i--) { 
     }      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      b[i]=sum/a[i][i]; 
     } 
     free_vector(severity,1,maxwav);  } 
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);  void pstamp(FILE *fichier)
     free_vector(annais,1,n);  {
     free_matrix(mint,1,maxwav,1,n);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     free_matrix(anint,1,maxwav,1,n);  }
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);  /************ 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[])
      {  /* Some frequencies */
     wav=ivector(1,imx);    
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    int first;
        double ***freq; /* Frequencies */
     /* Concatenates waves */    double *pp, **prop;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
     
       Tcode=ivector(1,100);    pp=vector(1,nlstate);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    prop=matrix(1,nlstate,iagemin,iagemax+3);
       ncodemax[1]=1;    strcpy(fileresp,"p");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    strcat(fileresp,fileres);
          if((ficresp=fopen(fileresp,"w"))==NULL) {
    codtab=imatrix(1,100,1,10);      printf("Problem with prevalence resultfile: %s\n", fileresp);
    h=0;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    m=pow(2,cptcoveff);      exit(0);
      }
    for(k=1;k<=cptcoveff; k++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      for(i=1; i <=(m/pow(2,k));i++){    j1=0;
        for(j=1; j <= ncodemax[k]; j++){    
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    j=cptcoveff;
            h++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
            if (h>m) h=1;codtab[h][k]=j;  
          }    first=1;
        }  
      }    for(k1=1; k1<=j;k1++){
    }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
    /*for(i=1; i <=m ;i++){          scanf("%d", i);*/
      for(k=1; k <=cptcovn; k++){        for (i=-5; i<=nlstate+ndeath; i++)  
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
      }            for(m=iagemin; m <= iagemax+3; m++)
      printf("\n");              freq[i][jk][m]=0;
    }  
    scanf("%d",i);*/      for (i=1; i<=nlstate; i++)  
            for(m=iagemin; m <= iagemax+3; m++)
    /* Calculates basic frequencies. Computes observed prevalence at single age          prop[i][m]=0;
        and prints on file fileres'p'. */        
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);        dateintsum=0;
         k2cpt=0;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i<=imx; i++) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          bool=1;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if  (cptcovn>0) {
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for (z1=1; z1<=cptcoveff; z1++) 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
     /* For Powell, parameters are in a vector p[] starting at p[1]          }
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          if (bool==1){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
     if(mle==1){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     /*--------- results files --------------*/                if (m<lastpass) {
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                      freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    jk=1;                }
    fprintf(ficres,"# Parameters\n");                
    printf("# Parameters\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
    for(i=1,jk=1; i <=nlstate; i++){                  dateintsum=dateintsum+k2;
      for(k=1; k <=(nlstate+ndeath); k++){                  k2cpt++;
        if (k != i)                }
          {                /*}*/
            printf("%d%d ",i,k);            }
            fprintf(ficres,"%1d%1d ",i,k);          }
            for(j=1; j <=ncovmodel; j++){        }
              printf("%f ",p[jk]);         
              fprintf(ficres,"%f ",p[jk]);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
              jk++;        pstamp(ficresp);
            }        if  (cptcovn>0) {
            printf("\n");          fprintf(ficresp, "\n#********** Variable "); 
            fprintf(ficres,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          }          fprintf(ficresp, "**********\n#");
      }        }
    }        for(i=1; i<=nlstate;i++) 
  if(mle==1){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     /* Computing hessian and covariance matrix */        fprintf(ficresp, "\n");
     ftolhess=ftol; /* Usually correct */        
     hesscov(matcov, p, npar, delti, ftolhess, func);        for(i=iagemin; i <= iagemax+3; i++){
  }          if(i==iagemax+3){
     fprintf(ficres,"# Scales\n");            fprintf(ficlog,"Total");
     printf("# Scales\n");          }else{
      for(i=1,jk=1; i <=nlstate; i++){            if(first==1){
       for(j=1; j <=nlstate+ndeath; j++){              first=0;
         if (j!=i) {              printf("See log file for details...\n");
           fprintf(ficres,"%1d%1d",i,j);            }
           printf("%1d%1d",i,j);            fprintf(ficlog,"Age %d", i);
           for(k=1; k<=ncovmodel;k++){          }
             printf(" %.5e",delti[jk]);          for(jk=1; jk <=nlstate ; jk++){
             fprintf(ficres," %.5e",delti[jk]);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             jk++;              pp[jk] += freq[jk][m][i]; 
           }          }
           printf("\n");          for(jk=1; jk <=nlstate ; jk++){
           fprintf(ficres,"\n");            for(m=-1, pos=0; m <=0 ; m++)
         }              pos += freq[jk][m][i];
       }            if(pp[jk]>=1.e-10){
       }              if(first==1){
                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     k=1;              }
     fprintf(ficres,"# Covariance\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     printf("# Covariance\n");            }else{
     for(i=1;i<=npar;i++){              if(first==1)
       /*  if (k>nlstate) k=1;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       i1=(i-1)/(ncovmodel*nlstate)+1;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            }
       printf("%s%d%d",alph[k],i1,tab[i]);*/          }
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);          for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<=i;j++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         fprintf(ficres," %.5e",matcov[i][j]);              pp[jk] += freq[jk][m][i];
         printf(" %.5e",matcov[i][j]);          }       
       }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       fprintf(ficres,"\n");            pos += pp[jk];
       printf("\n");            posprop += prop[jk][i];
       k++;          }
     }          for(jk=1; jk <=nlstate ; jk++){
                if(pos>=1.e-5){
     while((c=getc(ficpar))=='#' && c!= EOF){              if(first==1)
       ungetc(c,ficpar);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fgets(line, MAXLINE, ficpar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       puts(line);            }else{
       fputs(line,ficparo);              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
              }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            if( i <= iagemax){
                  if(pos>=1.e-5){
     if (fage <= 2) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       bage = agemin;                /*probs[i][jk][j1]= pp[jk]/pos;*/
       fage = agemax;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     }              }
               else
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            }
           }
              
 /*------------ gnuplot -------------*/          for(jk=-1; jk <=nlstate+ndeath; jk++)
 chdir(pathcd);            for(m=-1; m <=nlstate+ndeath; m++)
   if((ficgp=fopen("graph.plt","w"))==NULL) {              if(freq[jk][m][i] !=0 ) {
     printf("Problem with file graph.gp");goto end;              if(first==1)
   }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 #ifdef windows                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficgp,"cd \"%s\" \n",pathc);              }
 #endif          if(i <= iagemax)
 m=pow(2,cptcoveff);            fprintf(ficresp,"\n");
            if(first==1)
  /* 1eme*/            printf("Others in log...\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {          fprintf(ficlog,"\n");
    for (k1=1; k1<= m ; k1 ++) {        }
       }
 #ifdef windows    }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    dateintmean=dateintsum/k2cpt; 
 #endif   
 #ifdef unix    fclose(ficresp);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 #endif    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 for (i=1; i<= nlstate ; i ++) {    /* End of Freq */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  /************ Prevalence ********************/
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
     for (i=1; i<= nlstate ; i ++) {  {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   else fprintf(ficgp," \%%*lf (\%%*lf)");       in each health status at the date of interview (if between dateprev1 and dateprev2).
 }       We still use firstpass and lastpass as another selection.
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    */
      for (i=1; i<= nlstate ; i ++) {   
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***freq; /* Frequencies */
 }      double *pp, **prop;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    double pos,posprop; 
 #ifdef unix    double  y2; /* in fractional years */
 fprintf(ficgp,"\nset ter gif small size 400,300");    int iagemin, iagemax;
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    iagemin= (int) agemin;
    }    iagemax= (int) agemax;
   }    /*pp=vector(1,nlstate);*/
   /*2 eme*/    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   for (k1=1; k1<= m ; k1 ++) {    j1=0;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    
        j=cptcoveff;
     for (i=1; i<= nlstate+1 ; i ++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       k=2*i;    
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    for(k1=1; k1<=j;k1++){
       for (j=1; j<= nlstate+1 ; j ++) {      for(i1=1; i1<=ncodemax[k1];i1++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        j1++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        
 }          for (i=1; i<=nlstate; i++)  
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          for(m=iagemin; m <= iagemax+3; m++)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            prop[i][m]=0.0;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);       
       for (j=1; j<= nlstate+1 ; j ++) {        for (i=1; i<=imx; i++) { /* Each individual */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          bool=1;
         else fprintf(ficgp," \%%*lf (\%%*lf)");          if  (cptcovn>0) {
 }              for (z1=1; z1<=cptcoveff; z1++) 
       fprintf(ficgp,"\" t\"\" w l 0,");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                bool=0;
       for (j=1; j<= nlstate+1 ; j ++) {          } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (bool==1) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 }                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       else fprintf(ficgp,"\" t\"\" w l 0,");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                    /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   /*3eme*/                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
   for (k1=1; k1<= m ; k1 ++) {                } 
     for (cpt=1; cpt<= nlstate ; cpt ++) {              }
       k=2+nlstate*(cpt-1);            } /* end selection of waves */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          }
       for (i=1; i< nlstate ; i ++) {        }
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        for(i=iagemin; i <= iagemax+3; i++){  
       }          
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     }            posprop += prop[jk][i]; 
   }          } 
    
   /* CV preval stat */          for(jk=1; jk <=nlstate ; jk++){     
   for (k1=1; k1<= m ; k1 ++) {            if( i <=  iagemax){ 
     for (cpt=1; cpt<nlstate ; cpt ++) {              if(posprop>=1.e-5){ 
       k=3;                probs[i][jk][j1]= prop[jk][i]/posprop;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              } 
       for (i=1; i< nlstate ; i ++)            } 
         fprintf(ficgp,"+$%d",k+i+1);          }/* end jk */ 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        }/* end i */ 
            } /* end i1 */
       l=3+(nlstate+ndeath)*cpt;    } /* end k1 */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    
       for (i=1; i< nlstate ; i ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         l=3+(nlstate+ndeath)*cpt;    /*free_vector(pp,1,nlstate);*/
         fprintf(ficgp,"+$%d",l+i+1);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       }  }  /* End of prevalence */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  /************* Waves Concatenation ***************/
     }  
   }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
   /* proba elementaires */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
    for(i=1,jk=1; i <=nlstate; i++){       Death is a valid wave (if date is known).
     for(k=1; k <=(nlstate+ndeath); k++){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       if (k != i) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for(j=1; j <=ncovmodel; j++){       and mw[mi+1][i]. dh depends on stepm.
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/       */
           /*fprintf(ficgp,"%s",alph[1]);*/  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    int i, mi, m;
           jk++;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           fprintf(ficgp,"\n");       double sum=0., jmean=0.;*/
         }    int first;
       }    int j, k=0,jk, ju, jl;
     }    double sum=0.;
     }    first=0;
     jmin=1e+5;
   for(jk=1; jk <=m; jk++) {    jmax=-1;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    jmean=0.;
    i=1;    for(i=1; i<=imx; i++){
    for(k2=1; k2<=nlstate; k2++) {      mi=0;
      k3=i;      m=firstpass;
      for(k=1; k<=(nlstate+ndeath); k++) {      while(s[m][i] <= nlstate){
        if (k != k2){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          mw[++mi][i]=m;
 ij=1;        if(m >=lastpass)
         for(j=3; j <=ncovmodel; j++) {          break;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        else
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          m++;
             ij++;      }/* end while */
           }      if (s[m][i] > nlstate){
           else        mi++;     /* Death is another wave */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        /* if(mi==0)  never been interviewed correctly before death */
         }           /* Only death is a correct wave */
           fprintf(ficgp,")/(1");        mw[mi][i]=m;
              }
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      wav[i]=mi;
 ij=1;      if(mi==0){
           for(j=3; j <=ncovmodel; j++){        nbwarn++;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        if(first==0){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
             ij++;          first=1;
           }        }
           else        if(first==1){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           }        }
           fprintf(ficgp,")");      } /* end mi==0 */
         }    } /* End individuals */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    for(i=1; i<=imx; i++){
         i=i+ncovmodel;      for(mi=1; mi<wav[i];mi++){
        }        if (stepm <=0)
      }          dh[mi][i]=1;
    }        else{
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   }            if (agedc[i] < 2*AGESUP) {
                  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   fclose(ficgp);              if(j==0) j=1;  /* Survives at least one month after exam */
                  else if(j<0){
 chdir(path);                nberr++;
     free_matrix(agev,1,maxwav,1,imx);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     free_ivector(wav,1,imx);                j=1; /* Temporary Dangerous patch */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                    fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     free_imatrix(s,1,maxwav+1,1,n);              }
                  k=k+1;
                  if (j >= jmax){
     free_ivector(num,1,n);                jmax=j;
     free_vector(agedc,1,n);                ijmax=i;
     free_vector(weight,1,n);              }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/              if (j <= jmin){
     fclose(ficparo);                jmin=j;
     fclose(ficres);                ijmin=i;
     /*  }*/              }
                  sum=sum+j;
    /*________fin mle=1_________*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                  /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
            }
     /* No more information from the sample is required now */          else{
   /* Reads comments: lines beginning with '#' */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   while((c=getc(ficpar))=='#' && c!= EOF){  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);            k=k+1;
     puts(line);            if (j >= jmax) {
     fputs(line,ficparo);              jmax=j;
   }              ijmax=i;
   ungetc(c,ficpar);            }
              else if (j <= jmin){
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              jmin=j;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              ijmin=i;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            }
 /*--------- index.htm --------*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   if((fichtm=fopen("index.htm","w"))==NULL)    {            if(j<0){
     printf("Problem with index.htm \n");goto end;              nberr++;
   }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64a </font> <hr size=\"2\" color=\"#EC5E5E\">            }
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>            sum=sum+j;
 Total number of observations=%d <br>          }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          jk= j/stepm;
 <hr  size=\"2\" color=\"#EC5E5E\">          jl= j -jk*stepm;
 <li>Outputs files<br><br>\n          ju= j -(jk+1)*stepm;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            if(jl==0){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>              dh[mi][i]=jk;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>              bh[mi][i]=0;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            }else{ /* We want a negative bias in order to only have interpolation ie
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                    * at the price of an extra matrix product in likelihood */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              dh[mi][i]=jk+1;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              bh[mi][i]=ju;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            }
           }else{
  fprintf(fichtm," <li>Graphs</li><p>");            if(jl <= -ju){
               dh[mi][i]=jk;
  m=cptcoveff;              bh[mi][i]=jl;       /* bias is positive if real duration
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
  j1=0;            }
  for(k1=1; k1<=m;k1++){            else{
    for(i1=1; i1<=ncodemax[k1];i1++){              dh[mi][i]=jk+1;
        j1++;              bh[mi][i]=ju;
        if (cptcovn > 0) {            }
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            if(dh[mi][i]==0){
          for (cpt=1; cpt<=cptcoveff;cpt++)              dh[mi][i]=1; /* At least one step */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);              bh[mi][i]=ju; /* At least one step */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
        }            }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          } /* end if mle */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            }
        for(cpt=1; cpt<nlstate;cpt++){      } /* end wave */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    jmean=sum/k;
        }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     for(cpt=1; cpt<=nlstate;cpt++) {    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident   }
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    /*********** Tricode ****************************/
      }  void tricode(int *Tvar, int **nbcode, int imx)
      for(cpt=1; cpt<=nlstate;cpt++) {  {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    int Ndum[20],ij=1, k, j, i, maxncov=19;
      }    int cptcode=0;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    cptcoveff=0; 
 health expectancies in states (1) and (2): e%s%d.gif<br>   
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    for (k=0; k<maxncov; k++) Ndum[k]=0;
 fprintf(fichtm,"\n</body>");    for (k=1; k<=7; k++) ncodemax[k]=0;
    }  
  }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 fclose(fichtm);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   /*--------------- Prevalence limit --------------*/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
          Ndum[ij]++; /*store the modality */
   strcpy(filerespl,"pl");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   strcat(filerespl,fileres);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                                         Tvar[j]. If V=sex and male is 0 and 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                                         female is 1, then  cptcode=1.*/
   }      }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");      for (i=0; i<=cptcode; i++) {
   fprintf(ficrespl,"#Age ");        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 */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      }
   fprintf(ficrespl,"\n");  
        ij=1; 
   prlim=matrix(1,nlstate,1,nlstate);      for (i=1; i<=ncodemax[j]; i++) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (k=0; k<= maxncov; k++) {
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if (Ndum[k] != 0) {
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            nbcode[Tvar[j]][ij]=k; 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            /* 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; */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            
   k=0;            ij++;
   agebase=agemin;          }
   agelim=agemax;          if (ij > ncodemax[j]) break; 
   ftolpl=1.e-10;        }  
   i1=cptcoveff;      } 
   if (cptcovn < 1){i1=1;}    }  
   
   for(cptcov=1;cptcov<=i1;cptcov++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;   for (i=1; i<=ncovmodel-2; i++) { 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         fprintf(ficrespl,"\n#******");     ij=Tvar[i];
         for(j=1;j<=cptcoveff;j++)     Ndum[ij]++;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   }
         fprintf(ficrespl,"******\n");  
           ij=1;
         for (age=agebase; age<=agelim; age++){   for (i=1; i<= maxncov; i++) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     if((Ndum[i]!=0) && (i<=ncovcol)){
           fprintf(ficrespl,"%.0f",age );       Tvaraff[ij]=i; /*For printing */
           for(i=1; i<=nlstate;i++)       ij++;
           fprintf(ficrespl," %.5f", prlim[i][i]);     }
           fprintf(ficrespl,"\n");   }
         }   
       }   cptcoveff=ij-1; /*Number of simple covariates*/
     }  }
   fclose(ficrespl);  
   /*------------- h Pij x at various ages ------------*/  /*********** Health Expectancies ****************/
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  {
   }    /* Health expectancies, no variances */
   printf("Computing pij: result on file '%s' \n", filerespij);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
      int nhstepma, nstepma; /* Decreasing with age */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double age, agelim, hf;
   if (stepm<=24) stepsize=2;    double ***p3mat;
     double eip;
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    pstamp(ficreseij);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    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");
   k=0;    for(i=1; i<=nlstate;i++){
   for(cptcov=1;cptcov<=i1;cptcov++){      for(j=1; j<=nlstate;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficreseij," e%1d%1d ",i,j);
       k=k+1;      }
         fprintf(ficrespij,"\n#****** ");      fprintf(ficreseij," e%1d. ",i);
         for(j=1;j<=cptcoveff;j++)    }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficreseij,"\n");
         fprintf(ficrespij,"******\n");  
            
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    if(estepm < stepm){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf ("Problem %d lower than %d\n",estepm, stepm);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    else  hstepm=estepm;   
           oldm=oldms;savm=savms;    /* We compute the life expectancy from trapezoids spaced every estepm months
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * This is mainly to measure the difference between two models: for example
           fprintf(ficrespij,"# Age");     * if stepm=24 months pijx are given only every 2 years and by summing them
           for(i=1; i<=nlstate;i++)     * we are calculating an estimate of the Life Expectancy assuming a linear 
             for(j=1; j<=nlstate+ndeath;j++)     * progression in between and thus overestimating or underestimating according
               fprintf(ficrespij," %1d-%1d",i,j);     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficrespij,"\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           for (h=0; h<=nhstepm; h++){     * to compare the new estimate of Life expectancy with the same linear 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );     * hypothesis. A more precise result, taking into account a more precise
             for(i=1; i<=nlstate;i++)     * curvature will be obtained if estepm is as small as stepm. */
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    /* For example we decided to compute the life expectancy with the smallest unit */
             fprintf(ficrespij,"\n");    /* 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 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       nstepm is the number of stepm from age to agelin. 
           fprintf(ficrespij,"\n");       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
   fclose(ficrespij);       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.
   /*---------- Health expectancies and variances ------------*/    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    agelim=AGESUP;
   if((ficrest=fopen(filerest,"w"))==NULL) {    /* If stepm=6 months */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   strcpy(filerese,"e");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   strcat(filerese,fileres);    /* if (stepm >= YEARM) hstepm=1;*/
   if((ficreseij=fopen(filerese,"w"))==NULL) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  strcpy(fileresv,"v");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   strcat(fileresv,fileres);      /* if (stepm >= YEARM) hstepm=1;*/
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }      /* If stepm=6 months */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   k=0;      
   for(cptcov=1;cptcov<=i1;cptcov++){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      
       k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficrest,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)      printf("%d|",(int)age);fflush(stdout);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficrest,"******\n");      
       /* Computing expectancies */
       fprintf(ficreseij,"\n#****** ");      for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)        for(j=1; j<=nlstate;j++)
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficreseij,"******\n");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
       fprintf(ficresvij,"\n#****** ");            /* 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]);*/
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          }
       fprintf(ficresvij,"******\n");  
       fprintf(ficreseij,"%3.0f",age );
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(i=1; i<=nlstate;i++){
       oldm=oldms;savm=savms;        eip=0;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          for(j=1; j<=nlstate;j++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          eip +=eij[i][j][(int)age];
       oldm=oldms;savm=savms;          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }
              fprintf(ficreseij,"%9.4f", eip );
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      fprintf(ficreseij,"\n");
       fprintf(ficrest,"\n");      
            }
       hf=1;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (stepm >= YEARM) hf=stepm/YEARM;    printf("\n");
       epj=vector(1,nlstate+1);    fprintf(ficlog,"\n");
       for(age=bage; age <=fage ;age++){    
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  }
         fprintf(ficrest," %.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  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[] )
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  {
           }    /* Covariances of health expectancies eij and of total life expectancies according
           epj[nlstate+1] +=epj[j];     to initial status i, ei. .
         }    */
         for(i=1, vepp=0.;i <=nlstate;i++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           for(j=1;j <=nlstate;j++)    int nhstepma, nstepma; /* Decreasing with age */
             vepp += vareij[i][j][(int)age];    double age, agelim, hf;
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    double ***p3matp, ***p3matm, ***varhe;
         for(j=1;j <=nlstate;j++){    double **dnewm,**doldm;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    double *xp, *xm;
         }    double **gp, **gm;
         fprintf(ficrest,"\n");    double ***gradg, ***trgradg;
       }    int theta;
     }  
   }    double eip, vip;
          
  fclose(ficreseij);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
  fclose(ficresvij);    xp=vector(1,npar);
   fclose(ficrest);    xm=vector(1,npar);
   fclose(ficpar);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   free_vector(epj,1,nlstate+1);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   /*  scanf("%d ",i); */    
     pstamp(ficresstdeij);
   /*------- Variance limit prevalence------*/      fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
 strcpy(fileresvpl,"vpl");    for(i=1; i<=nlstate;i++){
   strcat(fileresvpl,fileres);      for(j=1; j<=nlstate;j++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      fprintf(ficresstdeij," e%1d. ",i);
     exit(0);    }
   }    fprintf(ficresstdeij,"\n");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
     pstamp(ficrescveij);
  k=0;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
  for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficrescveij,"# Age");
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(i=1; i<=nlstate;i++)
      k=k+1;      for(j=1; j<=nlstate;j++){
      fprintf(ficresvpl,"\n#****** ");        cptj= (j-1)*nlstate+i;
      for(j=1;j<=cptcoveff;j++)        for(i2=1; i2<=nlstate;i2++)
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(j2=1; j2<=nlstate;j2++){
      fprintf(ficresvpl,"******\n");            cptj2= (j2-1)*nlstate+i2;
                  if(cptj2 <= cptj)
      varpl=matrix(1,nlstate,(int) bage, (int) fage);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
      oldm=oldms;savm=savms;          }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      }
    }    fprintf(ficrescveij,"\n");
  }    
     if(estepm < stepm){
   fclose(ficresvpl);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   /*---------- End : free ----------------*/    else  hstepm=estepm;   
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);     * if stepm=24 months pijx are given only every 2 years and by summing them
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);     * 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 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     * to compare the new estimate of Life expectancy with the same linear 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);     * hypothesis. A more precise result, taking into account a more precise
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);     * curvature will be obtained if estepm is as small as stepm. */
    
   free_matrix(matcov,1,npar,1,npar);    /* For example we decided to compute the life expectancy with the smallest unit */
   free_vector(delti,1,npar);    /* 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 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   printf("End of Imach\n");       and note for a fixed period like estepm months */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /* 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
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/       means that if the survival funtion is printed only each two years of age and if
   /*printf("Total time was %d uSec.\n", total_usecs);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /*------ End -----------*/       results. So we changed our mind and took the option of the best precision.
     */
  end:    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #ifdef windows  
  chdir(pathcd);    /* If stepm=6 months */
 #endif    /* nhstepm age range expressed in number of stepm */
  /*system("wgnuplot graph.plt");*/    agelim=AGESUP;
  system("../gp37mgw/wgnuplot graph.plt");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 #ifdef windows    /* if (stepm >= YEARM) hstepm=1;*/
   while (z[0] != 'q') {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     chdir(pathcd);    
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     scanf("%s",z);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if (z[0] == 'c') system("./imach");    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     else if (z[0] == 'e') {    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       chdir(path);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
       system("index.htm");    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     }  
     else if (z[0] == 'q') exit(0);    for (age=bage; age<=fage; age ++){ 
   }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 #endif      /* 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 */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[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(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           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]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       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] += (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]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       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(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," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       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(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %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);
     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,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     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 in the population i.e cross-sectionally\n in each health state (popbased=1)");
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* 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 k years */
     /* 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 every 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;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,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*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* 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 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) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("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);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           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(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><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     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(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              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>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        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,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        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: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            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,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           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,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - 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), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <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 \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       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,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         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+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);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\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]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       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{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     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 ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             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);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%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);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s 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);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           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);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* 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); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     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\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     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\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <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\
    - Log file of the run: <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",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);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,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       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);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       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(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* 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);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("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");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           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);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,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(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,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(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     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);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     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(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      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);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.8  
changed lines
  Added in v.1.127


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>