Diff for /imach/src/imach.c between versions 1.12 and 1.127

version 1.12, 2002/02/20 16:57:00 version 1.127, 2006/04/28 18:11:50
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      /* $Id$
 /*********************** 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()");
     /*ps[3][2]=1;*/    m[nrl] += NR_END;
     m[nrl] -= ncl;
   for(i=1; i<= nlstate; i++){  
      s1=0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=1; j<i; j++)    return m;
       s1+=exp(ps[i][j]);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     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++)  /*************************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)
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    free((FREE_ARG)(m+nrl-NR_END));
   } /* end i */  }
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  /******************* ma3x *******************************/
     for(jj=1; jj<= nlstate+ndeath; jj++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       ps[ii][jj]=0;  {
       ps[ii][ii]=1;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
   }  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    m += NR_END;
     for(jj=1; jj<= nlstate+ndeath; jj++){    m -= nrl;
      printf("%lf ",ps[ii][jj]);  
    }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     printf("\n ");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     printf("\n ");printf("%lf ",cov[2]);*/    m[nrl] -= ncl;
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   goto end;*/  
     return ps;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
 /**************** Product of 2 matrices ******************/    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      m[nrl][j]=m[nrl][j-1]+nlay;
 {    
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    for (i=nrl+1; i<=nrh; i++) {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   /* in, b, out are matrice of pointers which should have been initialized      for (j=ncl+1; j<=nch; j++) 
      before: only the contents of out is modified. The function returns        m[i][j]=m[i][j-1]+nlay;
      a pointer to pointers identical to out */    }
   long i, j, k;    return m; 
   for(i=nrl; i<= nrh; i++)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for(k=ncolol; k<=ncoloh; k++)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    */
         out[i][k] +=in[i][j]*b[j][k];  }
   
   return out;  /*************************free ma3x ************************/
 }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 /************* Higher Matrix Product ***************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  }
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*************** function subdirf ***********/
      duration (i.e. until  char *subdirf(char fileres[])
      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    /* Caution optionfilefiname is hidden */
      (typically every 2 years instead of every month which is too big).    strcpy(tmpout,optionfilefiname);
      Model is determined by parameters x and covariates have to be    strcat(tmpout,"/"); /* Add to the right */
      included manually here.    strcat(tmpout,fileres);
     return tmpout;
      */  }
   
   int i, j, d, h, k;  /*************** function subdirf2 ***********/
   double **out, cov[NCOVMAX];  char *subdirf2(char fileres[], char *preop)
   double **newm;  {
     
   /* Hstepm could be zero and should return the unit matrix */    /* Caution optionfilefiname is hidden */
   for (i=1;i<=nlstate+ndeath;i++)    strcpy(tmpout,optionfilefiname);
     for (j=1;j<=nlstate+ndeath;j++){    strcat(tmpout,"/");
       oldm[i][j]=(i==j ? 1.0 : 0.0);    strcat(tmpout,preop);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    strcat(tmpout,fileres);
     }    return tmpout;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  /*************** function subdirf3 ***********/
       newm=savm;  char *subdirf3(char fileres[], char *preop, char *preop2)
       /* Covariates have to be included here again */  {
       cov[1]=1.;    
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    strcpy(tmpout,optionfilefiname);
       for (k=1; k<=cptcovage;k++)    strcat(tmpout,"/");
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcat(tmpout,preop);
       for (k=1; k<=cptcovprod;k++)    strcat(tmpout,preop2);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,fileres);
     return tmpout;
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /***************** f1dim *************************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  extern int ncom; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  extern double *pcom,*xicom;
       savm=oldm;  extern double (*nrfunc)(double []); 
       oldm=newm;   
     }  double f1dim(double x) 
     for(i=1; i<=nlstate+ndeath; i++)  { 
       for(j=1;j<=nlstate+ndeath;j++) {    int j; 
         po[i][j][h]=newm[i][j];    double f;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double *xt; 
          */   
       }    xt=vector(1,ncom); 
   } /* end h */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   return po;    f=(*nrfunc)(xt); 
 }    free_vector(xt,1,ncom); 
     return f; 
   } 
 /*************** log-likelihood *************/  
 double func( double *x)  /*****************brent *************************/
 {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   int i, ii, j, k, mi, d, kk;  { 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    int iter; 
   double **out;    double a,b,d,etemp;
   double sw; /* Sum of weights */    double fu,fv,fw,fx;
   double lli; /* Individual log likelihood */    double ftemp;
   long ipmx;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   /*extern weight */    double e=0.0; 
   /* We are differentiating ll according to initial status */   
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    a=(ax < cx ? ax : cx); 
   /*for(i=1;i<imx;i++)    b=(ax > cx ? ax : cx); 
     printf(" %d\n",s[4][i]);    x=w=v=bx; 
   */    fw=fv=fx=(*f)(x); 
   cov[1]=1.;    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      printf(".");fflush(stdout);
     for(mi=1; mi<= wav[i]-1; mi++){      fprintf(ficlog,".");fflush(ficlog);
       for (ii=1;ii<=nlstate+ndeath;ii++)  #ifdef DEBUG
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      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);
       for(d=0; d<dh[mi][i]; d++){      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);
         newm=savm;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  #endif
         for (kk=1; kk<=cptcovage;kk++) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        *xmin=x; 
         }        return fx; 
              } 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      ftemp=fu;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      if (fabs(e) > tol1) { 
         savm=oldm;        r=(x-w)*(fx-fv); 
         oldm=newm;        q=(x-v)*(fx-fw); 
                p=(x-v)*q-(x-w)*r; 
                q=2.0*(q-r); 
       } /* end mult */        if (q > 0.0) p = -p; 
              q=fabs(q); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        etemp=e; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        e=d; 
       ipmx +=1;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       sw += weight[i];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        else { 
     } /* end of wave */          d=p/q; 
   } /* end of individual */          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];            d=SIGN(tol1,xm-x); 
   /* 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 */      } else { 
   return -l;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 }      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 /*********** Maximum Likelihood Estimation ***************/      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        SHFT(v,w,x,u) 
 {          SHFT(fv,fw,fx,fu) 
   int i,j, iter;          } else { 
   double **xi,*delti;            if (u < x) a=u; else b=u; 
   double fret;            if (fu <= fw || w == x) { 
   xi=matrix(1,npar,1,npar);              v=w; 
   for (i=1;i<=npar;i++)              w=u; 
     for (j=1;j<=npar;j++)              fv=fw; 
       xi[i][j]=(i==j ? 1.0 : 0.0);              fw=fu; 
   printf("Powell\n");            } else if (fu <= fv || v == x || v == w) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);              v=u; 
               fv=fu; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));            } 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));          } 
     } 
 }    nrerror("Too many iterations in brent"); 
     *xmin=x; 
 /**** Computes Hessian and covariance matrix ***/    return fx; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  } 
 {  
   double  **a,**y,*x,pd;  /****************** mnbrak ***********************/
   double **hess;  
   int i, j,jk;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   int *indx;              double (*func)(double)) 
   { 
   double hessii(double p[], double delta, int theta, double delti[]);    double ulim,u,r,q, dum;
   double hessij(double p[], double delti[], int i, int j);    double fu; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;   
   void ludcmp(double **a, int npar, int *indx, double *d) ;    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
   hess=matrix(1,npar,1,npar);    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
   printf("\nCalculation of the hessian matrix. Wait...\n");        SHFT(dum,*fb,*fa,dum) 
   for (i=1;i<=npar;i++){        } 
     printf("%d",i);fflush(stdout);    *cx=(*bx)+GOLD*(*bx-*ax); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    *fc=(*func)(*cx); 
     /*printf(" %f ",p[i]);*/    while (*fb > *fc) { 
     /*printf(" %lf ",hess[i][i]);*/      r=(*bx-*ax)*(*fb-*fc); 
   }      q=(*bx-*cx)*(*fb-*fa); 
        u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for (i=1;i<=npar;i++) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for (j=1;j<=npar;j++)  {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if (j>i) {      if ((*bx-u)*(u-*cx) > 0.0) { 
         printf(".%d%d",i,j);fflush(stdout);        fu=(*func)(u); 
         hess[i][j]=hessij(p,delti,i,j);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         hess[j][i]=hess[i][j];            fu=(*func)(u); 
         /*printf(" %lf ",hess[i][j]);*/        if (fu < *fc) { 
       }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }            SHFT(*fb,*fc,fu,(*func)(u)) 
   }            } 
   printf("\n");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        fu=(*func)(u); 
        } else { 
   a=matrix(1,npar,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
   y=matrix(1,npar,1,npar);        fu=(*func)(u); 
   x=vector(1,npar);      } 
   indx=ivector(1,npar);      SHFT(*ax,*bx,*cx,u) 
   for (i=1;i<=npar;i++)        SHFT(*fa,*fb,*fc,fu) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        } 
   ludcmp(a,npar,indx,&pd);  } 
   
   for (j=1;j<=npar;j++) {  /*************** linmin ************************/
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  int ncom; 
     lubksb(a,npar,indx,x);  double *pcom,*xicom;
     for (i=1;i<=npar;i++){  double (*nrfunc)(double []); 
       matcov[i][j]=x[i];   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   }  { 
     double brent(double ax, double bx, double cx, 
   printf("\n#Hessian matrix#\n");                 double (*f)(double), double tol, double *xmin); 
   for (i=1;i<=npar;i++) {    double f1dim(double x); 
     for (j=1;j<=npar;j++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       printf("%.3e ",hess[i][j]);                double *fc, double (*func)(double)); 
     }    int j; 
     printf("\n");    double xx,xmin,bx,ax; 
   }    double fx,fb,fa;
    
   /* Recompute Inverse */    ncom=n; 
   for (i=1;i<=npar;i++)    pcom=vector(1,n); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    xicom=vector(1,n); 
   ludcmp(a,npar,indx,&pd);    nrfunc=func; 
     for (j=1;j<=n;j++) { 
   /*  printf("\n#Hessian matrix recomputed#\n");      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   for (j=1;j<=npar;j++) {    } 
     for (i=1;i<=npar;i++) x[i]=0;    ax=0.0; 
     x[j]=1;    xx=1.0; 
     lubksb(a,npar,indx,x);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for (i=1;i<=npar;i++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       y[i][j]=x[i];  #ifdef DEBUG
       printf("%.3e ",y[i][j]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\n");  #endif
   }    for (j=1;j<=n;j++) { 
   */      xi[j] *= xmin; 
       p[j] += xi[j]; 
   free_matrix(a,1,npar,1,npar);    } 
   free_matrix(y,1,npar,1,npar);    free_vector(xicom,1,n); 
   free_vector(x,1,npar);    free_vector(pcom,1,n); 
   free_ivector(indx,1,npar);  } 
   free_matrix(hess,1,npar,1,npar);  
   char *asc_diff_time(long time_sec, char ascdiff[])
   {
 }    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
 /*************** hessian matrix ****************/    sec_left = (time_sec) % (60*60*24);
 double hessii( double x[], double delta, int theta, double delti[])    hours = (sec_left) / (60*60) ;
 {    sec_left = (sec_left) %(60*60);
   int i;    minutes = (sec_left) /60;
   int l=1, lmax=20;    sec_left = (sec_left) % (60);
   double k1,k2;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double p2[NPARMAX+1];    return ascdiff;
   double res;  }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;  /*************** powell ************************/
   int k=0,kmax=10;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double l1;              double (*func)(double [])) 
   { 
   fx=func(x);    void linmin(double p[], double xi[], int n, double *fret, 
   for (i=1;i<=npar;i++) p2[i]=x[i];                double (*func)(double [])); 
   for(l=0 ; l <=lmax; l++){    int i,ibig,j; 
     l1=pow(10,l);    double del,t,*pt,*ptt,*xit;
     delts=delt;    double fp,fptt;
     for(k=1 ; k <kmax; k=k+1){    double *xits;
       delt = delta*(l1*k);    int niterf, itmp;
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;    pt=vector(1,n); 
       p2[theta]=x[theta]-delt;    ptt=vector(1,n); 
       k2=func(p2)-fx;    xit=vector(1,n); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    xits=vector(1,n); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    *fret=(*func)(p); 
          for (j=1;j<=n;j++) pt[j]=p[j]; 
 #ifdef DEBUG    for (*iter=1;;++(*iter)) { 
       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);      fp=(*fret); 
 #endif      ibig=0; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      del=0.0; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      last_time=curr_time;
         k=kmax;      (void) gettimeofday(&curr_time,&tzp);
       }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      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);
         k=kmax; l=lmax*10.;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       }     for (i=1;i<=n;i++) {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        printf(" %d %.12f",i, p[i]);
         delts=delt;        fprintf(ficlog," %d %.12lf",i, p[i]);
       }        fprintf(ficrespow," %.12lf", p[i]);
     }      }
   }      printf("\n");
   delti[theta]=delts;      fprintf(ficlog,"\n");
   return res;      fprintf(ficrespow,"\n");fflush(ficrespow);
        if(*iter <=3){
 }        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
 double hessij( double x[], double delti[], int thetai,int thetaj)  /*       asctime_r(&tm,strcurr); */
 {        forecast_time=curr_time; 
   int i;        itmp = strlen(strcurr);
   int l=1, l1, lmax=20;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double k1,k2,k3,k4,res,fx;          strcurr[itmp-1]='\0';
   double p2[NPARMAX+1];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int k;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   fx=func(x);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (k=1; k<=2; k++) {          tmf = *localtime(&forecast_time.tv_sec);
     for (i=1;i<=npar;i++) p2[i]=x[i];  /*      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);
     k1=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);
     k2=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]; 
     k3=func(p2)-fx;        fptt=(*fret); 
    #ifdef DEBUG
     p2[thetai]=x[thetai]-delti[thetai]/k;        printf("fret=%lf \n",*fret);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fprintf(ficlog,"fret=%lf \n",*fret);
     k4=func(p2)-fx;  #endif
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        printf("%d",i);fflush(stdout);
 #ifdef DEBUG        fprintf(ficlog,"%d",i);fflush(ficlog);
     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);        linmin(p,xit,n,fret,func); 
 #endif        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
   return res;          ibig=i; 
 }        } 
   #ifdef DEBUG
 /************** Inverse of matrix **************/        printf("%d %.12e",i,(*fret));
 void ludcmp(double **a, int n, int *indx, double *d)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   int i,imax,j,k;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double big,dum,sum,temp;          printf(" x(%d)=%.12e",j,xit[j]);
   double *vv;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
          }
   vv=vector(1,n);        for(j=1;j<=n;j++) {
   *d=1.0;          printf(" p=%.12e",p[j]);
   for (i=1;i<=n;i++) {          fprintf(ficlog," p=%.12e",p[j]);
     big=0.0;        }
     for (j=1;j<=n;j++)        printf("\n");
       if ((temp=fabs(a[i][j])) > big) big=temp;        fprintf(ficlog,"\n");
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  #endif
     vv[i]=1.0/big;      } 
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for (j=1;j<=n;j++) {  #ifdef DEBUG
     for (i=1;i<j;i++) {        int k[2],l;
       sum=a[i][j];        k[0]=1;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        k[1]=-1;
       a[i][j]=sum;        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     big=0.0;        for (j=1;j<=n;j++) {
     for (i=j;i<=n;i++) {          printf(" %.12e",p[j]);
       sum=a[i][j];          fprintf(ficlog," %.12e",p[j]);
       for (k=1;k<j;k++)        }
         sum -= a[i][k]*a[k][j];        printf("\n");
       a[i][j]=sum;        fprintf(ficlog,"\n");
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(l=0;l<=1;l++) {
         big=dum;          for (j=1;j<=n;j++) {
         imax=i;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     if (j != imax) {          }
       for (k=1;k<=n;k++) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         dum=a[imax][k];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;  #endif
       }  
       *d = -(*d);  
       vv[imax]=vv[j];        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
     indx[j]=imax;        free_vector(ptt,1,n); 
     if (a[j][j] == 0.0) a[j][j]=TINY;        free_vector(pt,1,n); 
     if (j != n) {        return; 
       dum=1.0/(a[j][j]);      } 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { 
   }        ptt[j]=2.0*p[j]-pt[j]; 
   free_vector(vv,1,n);  /* Doesn't work */        xit[j]=p[j]-pt[j]; 
 ;        pt[j]=p[j]; 
 }      } 
       fptt=(*func)(ptt); 
 void lubksb(double **a, int n, int *indx, double b[])      if (fptt < fp) { 
 {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   int i,ii=0,ip,j;        if (t < 0.0) { 
   double sum;          linmin(p,xit,n,fret,func); 
            for (j=1;j<=n;j++) { 
   for (i=1;i<=n;i++) {            xi[j][ibig]=xi[j][n]; 
     ip=indx[i];            xi[j][n]=xit[j]; 
     sum=b[ip];          }
     b[ip]=b[i];  #ifdef DEBUG
     if (ii)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     else if (sum) ii=i;          for(j=1;j<=n;j++){
     b[i]=sum;            printf(" %.12e",xit[j]);
   }            fprintf(ficlog," %.12e",xit[j]);
   for (i=n;i>=1;i--) {          }
     sum=b[i];          printf("\n");
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          fprintf(ficlog,"\n");
     b[i]=sum/a[i][i];  #endif
   }        }
 }      } 
     } 
 /************ Frequencies ********************/  } 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  
 {  /* Some frequencies */  /**** Prevalence limit (stable or period prevalence)  ****************/
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double ***freq; /* Frequencies */  {
   double *pp;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   double pos;       matrix by transitions matrix until convergence is reached */
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   pp=vector(1,nlstate);    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   strcpy(fileresp,"p");    double **newm;
   strcat(fileresp,fileres);    double agefin, delaymax=50 ; /* Max number of years to converge */
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);    for (ii=1;ii<=nlstate+ndeath;ii++)
     exit(0);      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      }
   j1=0;  
      cov[1]=1.;
   j=cptcoveff;   
   if (cptcovn<1) {j=1;ncodemax[1]=1;}   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for(k1=1; k1<=j;k1++){      newm=savm;
    for(i1=1; i1<=ncodemax[k1];i1++){      /* Covariates have to be included here again */
        j1++;       cov[2]=agefin;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    
          scanf("%d", i);*/        for (k=1; k<=cptcovn;k++) {
         for (i=-1; i<=nlstate+ndeath; i++)            cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          for (jk=-1; jk<=nlstate+ndeath; jk++)            /*      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]]);*/
            for(m=agemin; m <= agemax+3; m++)        }
              freq[i][jk][m]=0;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                for (k=1; k<=cptcovprod;k++)
        for (i=1; i<=imx; i++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          bool=1;  
          if  (cptcovn>0) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
            for (z1=1; z1<=cptcoveff; z1++)        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
                bool=0;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
          }  
           if (bool==1) {      savm=oldm;
            for(m=firstpass; m<=lastpass-1; m++){      oldm=newm;
              if(agev[m][i]==0) agev[m][i]=agemax+1;      maxmax=0.;
              if(agev[m][i]==1) agev[m][i]=agemax+2;      for(j=1;j<=nlstate;j++){
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        min=1.;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        max=0.;
            }        for(i=1; i<=nlstate; i++) {
          }          sumnew=0;
        }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         if  (cptcovn>0) {          prlim[i][j]= newm[i][j]/(1-sumnew);
          fprintf(ficresp, "\n#********** Variable ");          max=FMAX(max,prlim[i][j]);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          min=FMIN(min,prlim[i][j]);
        fprintf(ficresp, "**********\n#");        }
         }        maxmin=max-min;
        for(i=1; i<=nlstate;i++)        maxmax=FMAX(maxmax,maxmin);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
        fprintf(ficresp, "\n");      if(maxmax < ftolpl){
                return prlim;
   for(i=(int)agemin; i <= (int)agemax+3; i++){      }
     if(i==(int)agemax+3)    }
       printf("Total");  }
     else  
       printf("Age %d", i);  /*************** transition probabilities ***************/ 
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         pp[jk] += freq[jk][m][i];  {
     }    double s1, s2;
     for(jk=1; jk <=nlstate ; jk++){    /*double t34;*/
       for(m=-1, pos=0; m <=0 ; m++)    int i,j,j1, nc, ii, jj;
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)      for(i=1; i<= nlstate; i++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for(j=1; j<i;j++){
       else          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            /*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; jk <=nlstate ; jk++){  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)          }
         pp[jk] += freq[jk][m][i];          ps[i][j]=s2;
     }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     for(jk=1,pos=0; jk <=nlstate ; jk++)        }
       pos += pp[jk];        for(j=i+1; j<=nlstate+ndeath;j++){
     for(jk=1; jk <=nlstate ; jk++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       if(pos>=1.e-5)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       else          }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          ps[i][j]=s2;
       if( i <= (int) agemax){        }
         if(pos>=1.e-5)      }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      /*ps[3][2]=1;*/
       else      
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      for(i=1; i<= nlstate; i++){
       }        s1=0;
     }        for(j=1; j<i; j++)
     for(jk=-1; jk <=nlstate+ndeath; jk++)          s1+=exp(ps[i][j]);
       for(m=-1; m <=nlstate+ndeath; m++)        for(j=i+1; j<=nlstate+ndeath; j++)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          s1+=exp(ps[i][j]);
     if(i <= (int) agemax)        ps[i][i]=1./(s1+1.);
       fprintf(ficresp,"\n");        for(j=1; j<i; j++)
     printf("\n");          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        for(j=i+1; j<=nlstate+ndeath; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
  }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        } /* end i */
   fclose(ficresp);      
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   free_vector(pp,1,nlstate);        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
 }  /* End of Freq */          ps[ii][ii]=1;
         }
 /************* Waves Concatenation ***************/      }
       
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
      Death is a valid wave (if date is known).  /*         printf("ddd %lf ",ps[ii][jj]); */
      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]  /*       printf("\n "); */
      and mw[mi+1][i]. dh depends on stepm.  /*        } */
      */  /*        printf("\n ");printf("%lf ",cov[2]); */
          /*
   int i, mi, m;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        goto end;*/
      double sum=0., jmean=0.;*/      return ps;
   }
   int j, k=0,jk, ju, jl;  
   double sum=0.;  /**************** Product of 2 matrices ******************/
   jmin=1e+5;  
   jmax=-1;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   jmean=0.;  {
   for(i=1; i<=imx; i++){    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     mi=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     m=firstpass;    /* in, b, out are matrice of pointers which should have been initialized 
     while(s[m][i] <= nlstate){       before: only the contents of out is modified. The function returns
       if(s[m][i]>=1)       a pointer to pointers identical to out */
         mw[++mi][i]=m;    long i, j, k;
       if(m >=lastpass)    for(i=nrl; i<= nrh; i++)
         break;      for(k=ncolol; k<=ncoloh; k++)
       else        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         m++;          out[i][k] +=in[i][j]*b[j][k];
     }/* end while */  
     if (s[m][i] > nlstate){    return out;
       mi++;     /* Death is another wave */  }
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */  
       mw[mi][i]=m;  /************* Higher Matrix Product ***************/
     }  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     wav[i]=mi;  {
     if(mi==0)    /* Computes the transition matrix starting at age 'age' over 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);       'nhstepm*hstepm*stepm' months (i.e. until
   }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
   for(i=1; i<=imx; i++){       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for(mi=1; mi<wav[i];mi++){       (typically every 2 years instead of every month which is too big 
       if (stepm <=0)       for the memory).
         dh[mi][i]=1;       Model is determined by parameters x and covariates have to be 
       else{       included manually here. 
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {       */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */    int i, j, d, h, k;
           k=k+1;    double **out, cov[NCOVMAX];
           if (j >= jmax) jmax=j;    double **newm;
           if (j <= jmin) jmin=j;  
           sum=sum+j;    /* Hstepm could be zero and should return the unit matrix */
           /* if (j<10) printf("j=%d num=%d ",j,i); */    for (i=1;i<=nlstate+ndeath;i++)
           }      for (j=1;j<=nlstate+ndeath;j++){
         }        oldm[i][j]=(i==j ? 1.0 : 0.0);
         else{        po[i][j][0]=(i==j ? 1.0 : 0.0);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      }
           k=k+1;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           if (j >= jmax) jmax=j;    for(h=1; h <=nhstepm; h++){
           else if (j <= jmin)jmin=j;      for(d=1; d <=hstepm; d++){
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        newm=savm;
           sum=sum+j;        /* Covariates have to be included here again */
         }        cov[1]=1.;
         jk= j/stepm;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         jl= j -jk*stepm;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         ju= j -(jk+1)*stepm;        for (k=1; k<=cptcovage;k++)
         if(jl <= -ju)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           dh[mi][i]=jk;        for (k=1; k<=cptcovprod;k++)
         else          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmean=sum/k;        savm=oldm;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        oldm=newm;
  }      }
 /*********** Tricode ****************************/      for(i=1; i<=nlstate+ndeath; i++)
 void tricode(int *Tvar, int **nbcode, int imx)        for(j=1;j<=nlstate+ndeath;j++) {
 {          po[i][j][h]=newm[i][j];
   int Ndum[20],ij=1, k, j, i;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   int cptcode=0;           */
   cptcoveff=0;        }
      } /* end h */
   for (k=0; k<19; k++) Ndum[k]=0;    return po;
   for (k=1; k<=7; k++) ncodemax[k]=0;  }
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  /*************** log-likelihood *************/
       ij=(int)(covar[Tvar[j]][i]);  double func( double *x)
       Ndum[ij]++;  {
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    int i, ii, j, k, mi, d, kk;
       if (ij > cptcode) cptcode=ij;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     }    double **out;
     double sw; /* Sum of weights */
     for (i=0; i<=cptcode; i++) {    double lli; /* Individual log likelihood */
       if(Ndum[i]!=0) ncodemax[j]++;    int s1, s2;
     }    double bbh, survp;
     ij=1;    long ipmx;
     /*extern weight */
     /* We are differentiating ll according to initial status */
     for (i=1; i<=ncodemax[j]; i++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for (k=0; k<=19; k++) {    /*for(i=1;i<imx;i++) 
         if (Ndum[k] != 0) {      printf(" %d\n",s[4][i]);
           nbcode[Tvar[j]][ij]=k;    */
           ij++;    cov[1]=1.;
         }  
         if (ij > ncodemax[j]) break;    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }    
     }    if(mle==1){
   }        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  for (k=0; k<19; k++) Ndum[k]=0;        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
  for (i=1; i<=ncovmodel-2; i++) {            for (j=1;j<=nlstate+ndeath;j++){
       ij=Tvar[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       Ndum[ij]++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
           for(d=0; d<dh[mi][i]; d++){
  ij=1;            newm=savm;
  for (i=1; i<=10; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    if((Ndum[i]!=0) && (i<=ncov)){            for (kk=1; kk<=cptcovage;kk++) {
      Tvaraff[ij]=i;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      ij++;            }
    }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
     cptcoveff=ij-1;            oldm=newm;
 }          } /* end mult */
         
 /*********** Health Expectancies ****************/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 {           * (in months) between two waves is not a multiple of stepm, we rounded to 
   /* Health expectancies */           * the nearest (and in case of equal distance, to the lowest) interval but now
   int i, j, nhstepm, hstepm, h;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double age, agelim,hf;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double ***p3mat;           * probability in order to take into account the bias as a fraction of the way
             * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   fprintf(ficreseij,"# Health expectancies\n");           * -stepm/2 to stepm/2 .
   fprintf(ficreseij,"# Age");           * For stepm=1 the results are the same as for previous versions of Imach.
   for(i=1; i<=nlstate;i++)           * For stepm > 1 the results are less biased than in previous versions. 
     for(j=1; j<=nlstate;j++)           */
       fprintf(ficreseij," %1d-%1d",i,j);          s1=s[mw[mi][i]][i];
   fprintf(ficreseij,"\n");          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   hstepm=1*YEARM; /*  Every j years of age (in month) */          /* bias bh is positive if real duration
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */           * is higher than the multiple of stepm and negative otherwise.
            */
   agelim=AGESUP;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          if( s2 > nlstate){ 
     /* nhstepm age range expressed in number of stepm */            /* i.e. if s2 is a death state and if the date of death is known 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);               then the contribution to the likelihood is the probability to 
     /* Typically if 20 years = 20*12/6=40 stepm */               die between last step unit time and current  step unit time, 
     if (stepm >= YEARM) hstepm=1;               which is also equal to probability to die before dh 
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */               minus probability to die before dh-stepm . 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               In version up to 0.92 likelihood was computed
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          as if date of death was unknown. Death was treated as any other
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          health state: the date of the interview describes the actual state
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            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
     for(i=1; i<=nlstate;i++)          introduced the exact date of death then we should have modified
       for(j=1; j<=nlstate;j++)          the contribution of an exact death to the likelihood. This new
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          contribution is smaller and very dependent of the step unit
           eij[i][j][(int)age] +=p3mat[i][j][h];          stepm. It is no more the probability to die between last interview
         }          and month of death but the probability to survive from last
              interview up to one month before death multiplied by the
     hf=1;          probability to die within a month. Thanks to Chris
     if (stepm >= YEARM) hf=stepm/YEARM;          Jackson for correcting this bug.  Former versions increased
     fprintf(ficreseij,"%.0f",age );          mortality artificially. The bad side is that we add another loop
     for(i=1; i<=nlstate;i++)          which slows down the processing. The difference can be up to 10%
       for(j=1; j<=nlstate;j++){          lower mortality.
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            */
       }            lli=log(out[s1][s2] - savm[s1][s2]);
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }          } else if  (s2==-2) {
 }            for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /************ Variance ******************/            /*survp += out[s1][j]; */
 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)            lli= log(survp);
 {          }
   /* Variance of health expectancies */          
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          else if  (s2==-4) { 
   double **newm;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double **dnewm,**doldm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int i, j, nhstepm, hstepm, h;            lli= log(survp); 
   int k, cptcode;          } 
   double *xp;  
   double **gp, **gm;          else if  (s2==-5) { 
   double ***gradg, ***trgradg;            for (j=1,survp=0. ; j<=2; 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{
   fprintf(ficresvij,"# Age");            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for(i=1; 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 */
     for(j=1; j<=nlstate;j++)          } 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fprintf(ficresvij,"\n");          /*if(lli ==000.0)*/
           /*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); */
   xp=vector(1,npar);          ipmx +=1;
   dnewm=matrix(1,nlstate,1,npar);          sw += weight[i];
   doldm=matrix(1,nlstate,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   hstepm=1*YEARM; /* Every year of age */      } /* end of individual */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    }  else if(mle==2){
   agelim = AGESUP;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) hstepm=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (j=1;j<=nlstate+ndeath;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gp=matrix(0,nhstepm,1,nlstate);            }
     gm=matrix(0,nhstepm,1,nlstate);          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
     for(theta=1; theta <=npar; theta++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (kk=1; kk<=cptcovage;kk++) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<= nlstate; j++){            savm=oldm;
         for(h=0; h<=nhstepm; h++){            oldm=newm;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          } /* end mult */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
       for(i=1; i<=npar; i++) /* Computes gradient */          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 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ipmx +=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            sw += weight[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          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 */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      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(j=1; j<= nlstate; j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(h=0; h<=nhstepm; h++){            for (j=1;j<=nlstate+ndeath;j++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     } /* End theta */            }
           for(d=0; d<dh[mi][i]; d++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(h=0; h<=nhstepm; h++)            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<=nlstate;j++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(theta=1; theta <=npar; theta++)            }
           trgradg[h][j][theta]=gradg[h][theta][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1;i<=nlstate;i++)            savm=oldm;
       for(j=1;j<=nlstate;j++)            oldm=newm;
         vareij[i][j][(int)age] =0.;          } /* end mult */
     for(h=0;h<=nhstepm;h++){        
       for(k=0;k<=nhstepm;k++){          s1=s[mw[mi][i]][i];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          s2=s[mw[mi+1][i]][i];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          bbh=(double)bh[mi][i]/(double)stepm; 
         for(i=1;i<=nlstate;i++)          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 */
           for(j=1;j<=nlstate;j++)          ipmx +=1;
             vareij[i][j][(int)age] += doldm[i][j];          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     h=1;      } /* end of individual */
     if (stepm >= YEARM) h=stepm/YEARM;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     fprintf(ficresvij,"%.0f ",age );      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(j=1; j<=nlstate;j++){        for(mi=1; mi<= wav[i]-1; mi++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresvij,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gp,0,nhstepm,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gm,0,nhstepm,1,nlstate);            }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            newm=savm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   } /* End age */            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);          
   free_matrix(dnewm,1,nlstate,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /************ Variance of prevlim ******************/          } /* end mult */
 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)        
 {          s1=s[mw[mi][i]][i];
   /* Variance of prevalence limit */          s2=s[mw[mi+1][i]][i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          if( s2 > nlstate){ 
   double **newm;            lli=log(out[s1][s2] - savm[s1][s2]);
   double **dnewm,**doldm;          }else{
   int i, j, nhstepm, hstepm;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   int k, cptcode;          }
   double *xp;          ipmx +=1;
   double *gp, *gm;          sw += weight[i];
   double **gradg, **trgradg;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim;  /*      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]); */
   int theta;        } /* end of wave */
          } /* end of individual */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   fprintf(ficresvpl,"# Age");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresvpl," %1d-%1d",i,i);        for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficresvpl,"\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   xp=vector(1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewm=matrix(1,nlstate,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate,1,nlstate);            }
            for(d=0; d<dh[mi][i]; d++){
   hstepm=1*YEARM; /* Every year of age */            newm=savm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   agelim = AGESUP;            for (kk=1; kk<=cptcovage;kk++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     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 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gradg=matrix(1,npar,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gp=vector(1,nlstate);            savm=oldm;
     gm=vector(1,nlstate);            oldm=newm;
           } /* end mult */
     for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++){ /* Computes gradient */          s1=s[mw[mi][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s2=s[mw[mi+1][i]][i];
       }          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];
         gp[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<=npar; i++) /* Computes gradient */        } /* end of wave */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      } /* end of individual */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } /* End of if */
       for(i=1;i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         gm[i] = prlim[i][i];    /* 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(i=1;i<=nlstate;i++)    return -l;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  }
     } /* End theta */  
   /*************** log-likelihood *************/
     trgradg =matrix(1,nlstate,1,npar);  double funcone( double *x)
   {
     for(j=1; j<=nlstate;j++)    /* Same as likeli but slower because of a lot of printf and if */
       for(theta=1; theta <=npar; theta++)    int i, ii, j, k, mi, d, kk;
         trgradg[j][theta]=gradg[theta][j];    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
     for(i=1;i<=nlstate;i++)    double lli; /* Individual log likelihood */
       varpl[i][(int)age] =0.;    double llt;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    int s1, s2;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    double bbh, survp;
     for(i=1;i<=nlstate;i++)    /*extern weight */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     fprintf(ficresvpl,"%.0f ",age );    /*for(i=1;i<imx;i++) 
     for(i=1; i<=nlstate;i++)      printf(" %d\n",s[4][i]);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    */
     fprintf(ficresvpl,"\n");    cov[1]=1.;
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   } /* End age */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
   free_vector(xp,1,npar);        for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(doldm,1,nlstate,1,npar);          for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(dnewm,1,nlstate,1,nlstate);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }          }
         for(d=0; d<dh[mi][i]; d++){
           newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /***********************************************/          for (kk=1; kk<=cptcovage;kk++) {
 /**************** Main Program *****************/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /***********************************************/          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /*int main(int argc, char *argv[])*/                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 int main()          savm=oldm;
 {          oldm=newm;
         } /* end mult */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        
   double agedeb, agefin,hf;        s1=s[mw[mi][i]][i];
   double agemin=1.e20, agemax=-1.e20;        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
   double fret;        /* bias is positive if real duration
   double **xi,tmp,delta;         * is higher than the multiple of stepm and negative otherwise.
          */
   double dum; /* Dummy variable */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   double ***p3mat;          lli=log(out[s1][s2] - savm[s1][s2]);
   int *indx;        } else if  (s2==-2) {
   char line[MAXLINE], linepar[MAXLINE];          for (j=1,survp=0. ; j<=nlstate; j++) 
   char title[MAXLINE];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];          lli= log(survp);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];        }else if (mle==1){
   char filerest[FILENAMELENGTH];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   char fileregp[FILENAMELENGTH];        } else if(mle==2){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          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 */
   int firstobs=1, lastobs=10;        } else if(mle==3){  /* exponential inter-extrapolation */
   int sdeb, sfin; /* Status at beginning and end */          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 */
   int c,  h , cpt,l;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   int ju,jl, mi;          lli=log(out[s1][s2]); /* Original formula */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          lli=log(out[s1][s2]); /* Original formula */
          } /* End of if */
   int hstepm, nhstepm;        ipmx +=1;
   double bage, fage, age, agelim, agebase;        sw += weight[i];
   double ftolpl=FTOL;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **prlim;  /*       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 *severity;        if(globpr){
   double ***param; /* Matrix of parameters */          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   double  *p;   %11.6f %11.6f %11.6f ", \
   double **matcov; /* Matrix of covariance */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double ***delti3; /* Scale */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double *delti; /* Scale */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double ***eij, ***vareij;            llt +=ll[k]*gipmx/gsw;
   double **varpl; /* Variances of prevalence limits by age */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double *epj, vepp;          }
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";          fprintf(ficresilk," %10.6f\n", -llt);
   char *alph[]={"a","a","b","c","d","e"}, str[4];        }
       } /* end of wave */
   char z[1]="c", occ;    } /* end of individual */
 #include <sys/time.h>    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 #include <time.h>    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /* long total_usecs;    if(globpr==0){ /* First time we count the contributions and weights */
   struct timeval start_time, end_time;      gipmx=ipmx;
        gsw=sw;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    }
     return -l;
   }
   printf("\nIMACH, Version 0.64b");  
   printf("\nEnter the parameter file name: ");  
   /*************** function likelione ***********/
 #ifdef windows  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   scanf("%s",pathtot);  {
   getcwd(pathcd, size);    /* This routine should help understanding what is done with 
   /*cygwin_split_path(pathtot,path,optionfile);       the selection of individuals/waves and
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       to check the exact contribution to the likelihood.
   /* cutv(path,optionfile,pathtot,'\\');*/       Plotting could be done.
      */
 split(pathtot, path,optionfile);    int k;
   chdir(path);  
   replace(pathc,path);    if(*globpri !=0){ /* Just counts and sums, no printings */
 #endif      strcpy(fileresilk,"ilk"); 
 #ifdef unix      strcat(fileresilk,fileres);
   scanf("%s",optionfile);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 #endif        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 /*-------- arguments in the command line --------*/      }
       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");
   strcpy(fileres,"r");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   strcat(fileres, optionfile);      /*  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++) 
   /*---------arguments file --------*/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    *fretone=(*funcone)(p);
   }    if(*globpri !=0){
       fclose(ficresilk);
   strcpy(filereso,"o");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   strcat(filereso,fileres);      fflush(fichtm); 
   if((ficparo=fopen(filereso,"w"))==NULL) {    } 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    return;
   }  }
   
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /*********** Maximum Likelihood Estimation ***************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     puts(line);  {
     fputs(line,ficparo);    int i,j, iter;
   }    double **xi;
   ungetc(c,ficpar);    double fret;
     double fretone; /* Only one call to likelihood */
   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);    /*  char filerespow[FILENAMELENGTH];*/
   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);    xi=matrix(1,npar,1,npar);
   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);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   covar=matrix(0,NCOVMAX,1,n);        xi[i][j]=(i==j ? 1.0 : 0.0);
   cptcovn=0;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
   ncovmodel=2+cptcovn;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   /* Read guess parameters */    }
   /* Reads comments: lines beginning with '#' */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=nlstate;i++)
     ungetc(c,ficpar);      for(j=1;j<=nlstate+ndeath;j++)
     fgets(line, MAXLINE, ficpar);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     puts(line);    fprintf(ficrespow,"\n");
     fputs(line,ficparo);  
   }    powell(p,xi,npar,ftol,&iter,&fret,func);
   ungetc(c,ficpar);  
      free_matrix(xi,1,npar,1,npar);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fclose(ficrespow);
     for(i=1; i <=nlstate; i++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);  }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  /**** Computes Hessian and covariance matrix ***/
         printf(" %lf",param[i][j][k]);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         fprintf(ficparo," %lf",param[i][j][k]);  {
       }    double  **a,**y,*x,pd;
       fscanf(ficpar,"\n");    double **hess;
       printf("\n");    int i, j,jk;
       fprintf(ficparo,"\n");    int *indx;
     }  
      double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
   p=param[1][1];    void ludcmp(double **a, int npar, int *indx, double *d) ;
      double gompertz(double p[]);
   /* Reads comments: lines beginning with '#' */    hess=matrix(1,npar,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    printf("\nCalculation of the hessian matrix. Wait...\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     puts(line);    for (i=1;i<=npar;i++){
     fputs(line,ficparo);      printf("%d",i);fflush(stdout);
   }      fprintf(ficlog,"%d",i);fflush(ficlog);
   ungetc(c,ficpar);     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      /*  printf(" %f ",p[i]);
   for(i=1; i <=nlstate; i++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     for(j=1; j <=nlstate+ndeath-1; j++){    }
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       printf("%1d%1d",i,j);    for (i=1;i<=npar;i++) {
       fprintf(ficparo,"%1d%1d",i1,j1);      for (j=1;j<=npar;j++)  {
       for(k=1; k<=ncovmodel;k++){        if (j>i) { 
         fscanf(ficpar,"%le",&delti3[i][j][k]);          printf(".%d%d",i,j);fflush(stdout);
         printf(" %le",delti3[i][j][k]);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         fprintf(ficparo," %le",delti3[i][j][k]);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       }          
       fscanf(ficpar,"\n");          hess[j][i]=hess[i][j];    
       printf("\n");          /*printf(" %lf ",hess[i][j]);*/
       fprintf(ficparo,"\n");        }
     }      }
   }    }
   delti=delti3[1][1];    printf("\n");
      fprintf(ficlog,"\n");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     ungetc(c,ficpar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     fgets(line, MAXLINE, ficpar);    
     puts(line);    a=matrix(1,npar,1,npar);
     fputs(line,ficparo);    y=matrix(1,npar,1,npar);
   }    x=vector(1,npar);
   ungetc(c,ficpar);    indx=ivector(1,npar);
      for (i=1;i<=npar;i++)
   matcov=matrix(1,npar,1,npar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   for(i=1; i <=npar; i++){    ludcmp(a,npar,indx,&pd);
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);    for (j=1;j<=npar;j++) {
     fprintf(ficparo,"%s",str);      for (i=1;i<=npar;i++) x[i]=0;
     for(j=1; j <=i; j++){      x[j]=1;
       fscanf(ficpar," %le",&matcov[i][j]);      lubksb(a,npar,indx,x);
       printf(" %.5le",matcov[i][j]);      for (i=1;i<=npar;i++){ 
       fprintf(ficparo," %.5le",matcov[i][j]);        matcov[i][j]=x[i];
     }      }
     fscanf(ficpar,"\n");    }
     printf("\n");  
     fprintf(ficparo,"\n");    printf("\n#Hessian matrix#\n");
   }    fprintf(ficlog,"\n#Hessian matrix#\n");
   for(i=1; i <=npar; i++)    for (i=1;i<=npar;i++) { 
     for(j=i+1;j<=npar;j++)      for (j=1;j<=npar;j++) { 
       matcov[i][j]=matcov[j][i];        printf("%.3e ",hess[i][j]);
            fprintf(ficlog,"%.3e ",hess[i][j]);
   printf("\n");      }
       printf("\n");
       fprintf(ficlog,"\n");
     /*-------- data file ----------*/    }
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;    /* Recompute Inverse */
     }    for (i=1;i<=npar;i++)
     fprintf(ficres,"#%s\n",version);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
        ludcmp(a,npar,indx,&pd);
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;    /*  printf("\n#Hessian matrix recomputed#\n");
     }  
     for (j=1;j<=npar;j++) {
     n= lastobs;      for (i=1;i<=npar;i++) x[i]=0;
     severity = vector(1,maxwav);      x[j]=1;
     outcome=imatrix(1,maxwav+1,1,n);      lubksb(a,npar,indx,x);
     num=ivector(1,n);      for (i=1;i<=npar;i++){ 
     moisnais=vector(1,n);        y[i][j]=x[i];
     annais=vector(1,n);        printf("%.3e ",y[i][j]);
     moisdc=vector(1,n);        fprintf(ficlog,"%.3e ",y[i][j]);
     andc=vector(1,n);      }
     agedc=vector(1,n);      printf("\n");
     cod=ivector(1,n);      fprintf(ficlog,"\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);    free_matrix(a,1,npar,1,npar);
     s=imatrix(1,maxwav+1,1,n);    free_matrix(y,1,npar,1,npar);
     adl=imatrix(1,maxwav+1,1,n);        free_vector(x,1,npar);
     tab=ivector(1,NCOVMAX);    free_ivector(indx,1,npar);
     ncodemax=ivector(1,8);    free_matrix(hess,1,npar,1,npar);
   
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {  }
       if ((i >= firstobs) && (i <=lastobs)) {  
          /*************** hessian matrix ****************/
         for (j=maxwav;j>=1;j--){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  {
           strcpy(line,stra);    int i;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int l=1, lmax=20;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double k1,k2;
         }    double p2[NPARMAX+1];
            double res;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    double fx;
     int k=0,kmax=10;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    double l1;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
     fx=func(x);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=1;i<=npar;i++) p2[i]=x[i];
         for (j=ncov;j>=1;j--){    for(l=0 ; l <=lmax; l++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      l1=pow(10,l);
         }      delts=delt;
         num[i]=atol(stra);      for(k=1 ; k <kmax; k=k+1){
                delt = delta*(l1*k);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        p2[theta]=x[theta] +delt;
           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])); ij=ij+1;}*/        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
         i=i+1;        k2=func(p2)-fx;
       }        /*res= (k1-2.0*fx+k2)/delt/delt; */
     }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     /* printf("ii=%d", ij);        
        scanf("%d",i);*/  #ifdef DEBUG
   imx=i-1; /* Number of individuals */        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   /* for (i=1; i<=imx; i++){  #endif
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          k=kmax;
   }        }
   for (i=1; i<=imx; i++) 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]));*/        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   Tprod=ivector(1,15);          delts=delt;
   Tvaraff=ivector(1,15);        }
   Tvard=imatrix(1,15,1,2);      }
   Tage=ivector(1,15);          }
        delti[theta]=delts;
   if (strlen(model) >1){    return res; 
     j=0, j1=0, k1=1, k2=1;    
     j=nbocc(model,'+');  }
     j1=nbocc(model,'*');  
     cptcovn=j+1;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     cptcovprod=j1;  {
        int i;
        int l=1, l1, lmax=20;
     strcpy(modelsav,model);    double k1,k2,k3,k4,res,fx;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double p2[NPARMAX+1];
       printf("Error. Non available option model=%s ",model);    int k;
       goto end;  
     }    fx=func(x);
        for (k=1; k<=2; k++) {
     for(i=(j+1); i>=1;i--){      for (i=1;i<=npar;i++) p2[i]=x[i];
       cutv(stra,strb,modelsav,'+');      p2[thetai]=x[thetai]+delti[thetai]/k;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      k1=func(p2)-fx;
       /*scanf("%d",i);*/    
       if (strchr(strb,'*')) {      p2[thetai]=x[thetai]+delti[thetai]/k;
         cutv(strd,strc,strb,'*');      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         if (strcmp(strc,"age")==0) {      k2=func(p2)-fx;
           cptcovprod--;    
           cutv(strb,stre,strd,'V');      p2[thetai]=x[thetai]-delti[thetai]/k;
           Tvar[i]=atoi(stre);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           cptcovage++;      k3=func(p2)-fx;
             Tage[cptcovage]=i;    
             /*printf("stre=%s ", stre);*/      p2[thetai]=x[thetai]-delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         else if (strcmp(strd,"age")==0) {      k4=func(p2)-fx;
           cptcovprod--;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           cutv(strb,stre,strc,'V');  #ifdef DEBUG
           Tvar[i]=atoi(stre);      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);
           cptcovage++;      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);
           Tage[cptcovage]=i;  #endif
         }    }
         else {    return res;
           cutv(strb,stre,strc,'V');  }
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');  /************** Inverse of matrix **************/
           Tprod[k1]=i;  void ludcmp(double **a, int n, int *indx, double *d) 
           Tvard[k1][1]=atoi(strc);  { 
           Tvard[k1][2]=atoi(stre);    int i,imax,j,k; 
           Tvar[cptcovn+k2]=Tvard[k1][1];    double big,dum,sum,temp; 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    double *vv; 
           for (k=1; k<=lastobs;k++)   
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    vv=vector(1,n); 
           k1++;    *d=1.0; 
           k2=k2+2;    for (i=1;i<=n;i++) { 
         }      big=0.0; 
       }      for (j=1;j<=n;j++) 
       else {        if ((temp=fabs(a[i][j])) > big) big=temp; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        /*  scanf("%d",i);*/      vv[i]=1.0/big; 
       cutv(strd,strc,strb,'V');    } 
       Tvar[i]=atoi(strc);    for (j=1;j<=n;j++) { 
       }      for (i=1;i<j;i++) { 
       strcpy(modelsav,stra);          sum=a[i][j]; 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         scanf("%d",i);*/        a[i][j]=sum; 
     }      } 
 }      big=0.0; 
        for (i=j;i<=n;i++) { 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        sum=a[i][j]; 
   printf("cptcovprod=%d ", cptcovprod);        for (k=1;k<j;k++) 
   scanf("%d ",i);*/          sum -= a[i][k]*a[k][j]; 
     fclose(fic);        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     /*  if(mle==1){*/          big=dum; 
     if (weightopt != 1) { /* Maximisation without weights*/          imax=i; 
       for(i=1;i<=n;i++) weight[i]=1.0;        } 
     }      } 
     /*-calculation of age at interview from date of interview and age at death -*/      if (j != imax) { 
     agev=matrix(1,maxwav,1,imx);        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
    for (i=1; i<=imx; i++)          a[imax][k]=a[j][k]; 
      for(m=2; (m<= maxwav); m++)          a[j][k]=dum; 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        } 
          anint[m][i]=9999;        *d = -(*d); 
          s[m][i]=-1;        vv[imax]=vv[j]; 
        }      } 
          indx[j]=imax; 
     for (i=1; i<=imx; i++)  {      if (a[j][j] == 0.0) a[j][j]=TINY; 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      if (j != n) { 
       for(m=1; (m<= maxwav); m++){        dum=1.0/(a[j][j]); 
         if(s[m][i] >0){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           if (s[m][i] == nlstate+1) {      } 
             if(agedc[i]>0)    } 
               if(moisdc[i]!=99 && andc[i]!=9999)    free_vector(vv,1,n);  /* Doesn't work */
               agev[m][i]=agedc[i];  ;
             else {  } 
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  void lubksb(double **a, int n, int *indx, double b[]) 
               agev[m][i]=-1;  { 
               }    int i,ii=0,ip,j; 
             }    double sum; 
           }   
           else if(s[m][i] !=9){ /* Should no more exist */    for (i=1;i<=n;i++) { 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      ip=indx[i]; 
             if(mint[m][i]==99 || anint[m][i]==9999)      sum=b[ip]; 
               agev[m][i]=1;      b[ip]=b[i]; 
             else if(agev[m][i] <agemin){      if (ii) 
               agemin=agev[m][i];        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      else if (sum) ii=i; 
             }      b[i]=sum; 
             else if(agev[m][i] >agemax){    } 
               agemax=agev[m][i];    for (i=n;i>=1;i--) { 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      sum=b[i]; 
             }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
             /*agev[m][i]=anint[m][i]-annais[i];*/      b[i]=sum/a[i][i]; 
             /*   agev[m][i] = age[i]+2*m;*/    } 
           }  } 
           else { /* =9 */  
             agev[m][i]=1;  void pstamp(FILE *fichier)
             s[m][i]=-1;  {
           }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         }  }
         else /*= 0 Unknown */  
           agev[m][i]=1;  /************ 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 */
     }    
     for (i=1; i<=imx; i++)  {    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       for(m=1; (m<= maxwav); m++){    int first;
         if (s[m][i] > (nlstate+ndeath)) {    double ***freq; /* Frequencies */
           printf("Error: Wrong value in nlstate or ndeath\n");      double *pp, **prop;
           goto end;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         }    char fileresp[FILENAMELENGTH];
       }    
     }    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     free_vector(severity,1,maxwav);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     free_imatrix(outcome,1,maxwav+1,1,n);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     free_vector(moisnais,1,n);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     free_vector(annais,1,n);      exit(0);
     free_matrix(mint,1,maxwav,1,n);    }
     free_matrix(anint,1,maxwav,1,n);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     free_vector(moisdc,1,n);    j1=0;
     free_vector(andc,1,n);    
     j=cptcoveff;
        if (cptcovn<1) {j=1;ncodemax[1]=1;}
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    first=1;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
        for(k1=1; k1<=j;k1++){
     /* Concatenates waves */      for(i1=1; i1<=ncodemax[k1];i1++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
       Tcode=ivector(1,100);        for (i=-5; i<=nlstate+ndeath; i++)  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       ncodemax[1]=1;            for(m=iagemin; m <= iagemax+3; m++)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              freq[i][jk][m]=0;
        
    codtab=imatrix(1,100,1,10);      for (i=1; i<=nlstate; i++)  
    h=0;        for(m=iagemin; m <= iagemax+3; m++)
    m=pow(2,cptcoveff);          prop[i][m]=0;
          
    for(k=1;k<=cptcoveff; k++){        dateintsum=0;
      for(i=1; i <=(m/pow(2,k));i++){        k2cpt=0;
        for(j=1; j <= ncodemax[k]; j++){        for (i=1; i<=imx; i++) {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          bool=1;
            h++;          if  (cptcovn>0) {
            if (h>m) h=1;codtab[h][k]=j;            for (z1=1; z1<=cptcoveff; z1++) 
          }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        }                bool=0;
      }          }
    }          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
    /*for(i=1; i <=m ;i++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
      for(k=1; k <=cptcovn; k++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);                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];
      printf("\n");                if (m<lastpass) {
    }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    scanf("%d",i);*/                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                    }
    /* Calculates basic frequencies. Computes observed prevalence at single age                
        and prints on file fileres'p'. */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);                  dateintsum=dateintsum+k2;
                   k2cpt++;
     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]        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        pstamp(ficresp);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
     if(mle==1){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          fprintf(ficresp, "**********\n#");
     }        }
            for(i=1; i<=nlstate;i++) 
     /*--------- results files --------------*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     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);        fprintf(ficresp, "\n");
            
    jk=1;        for(i=iagemin; i <= iagemax+3; i++){
    fprintf(ficres,"# Parameters\n");          if(i==iagemax+3){
    printf("# Parameters\n");            fprintf(ficlog,"Total");
    for(i=1,jk=1; i <=nlstate; i++){          }else{
      for(k=1; k <=(nlstate+ndeath); k++){            if(first==1){
        if (k != i)              first=0;
          {              printf("See log file for details...\n");
            printf("%d%d ",i,k);            }
            fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficlog,"Age %d", i);
            for(j=1; j <=ncovmodel; j++){          }
              printf("%f ",p[jk]);          for(jk=1; jk <=nlstate ; jk++){
              fprintf(ficres,"%f ",p[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){
  if(mle==1){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     /* Computing hessian and covariance matrix */              }
     ftolhess=ftol; /* Usually correct */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     hesscov(matcov, p, npar, delti, ftolhess, func);            }else{
  }              if(first==1)
     fprintf(ficres,"# Scales\n");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("# Scales\n");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      for(i=1,jk=1; i <=nlstate; i++){            }
       for(j=1; j <=nlstate+ndeath; j++){          }
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);          for(jk=1; jk <=nlstate ; jk++){
           printf("%1d%1d",i,j);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           for(k=1; k<=ncovmodel;k++){              pp[jk] += freq[jk][m][i];
             printf(" %.5e",delti[jk]);          }       
             fprintf(ficres," %.5e",delti[jk]);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             jk++;            pos += pp[jk];
           }            posprop += prop[jk][i];
           printf("\n");          }
           fprintf(ficres,"\n");          for(jk=1; jk <=nlstate ; jk++){
         }            if(pos>=1.e-5){
       }              if(first==1)
       }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     k=1;            }else{
     fprintf(ficres,"# Covariance\n");              if(first==1)
     printf("# Covariance\n");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1;i<=npar;i++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       /*  if (k>nlstate) k=1;            }
       i1=(i-1)/(ncovmodel*nlstate)+1;            if( i <= iagemax){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              if(pos>=1.e-5){
       printf("%s%d%d",alph[k],i1,tab[i]);*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       fprintf(ficres,"%3d",i);                /*probs[i][jk][j1]= pp[jk]/pos;*/
       printf("%3d",i);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for(j=1; j<=i;j++){              }
         fprintf(ficres," %.5e",matcov[i][j]);              else
         printf(" %.5e",matcov[i][j]);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       }            }
       fprintf(ficres,"\n");          }
       printf("\n");          
       k++;          for(jk=-1; jk <=nlstate+ndeath; jk++)
     }            for(m=-1; m <=nlstate+ndeath; m++)
                  if(freq[jk][m][i] !=0 ) {
     while((c=getc(ficpar))=='#' && c!= EOF){              if(first==1)
       ungetc(c,ficpar);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       fgets(line, MAXLINE, ficpar);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       puts(line);              }
       fputs(line,ficparo);          if(i <= iagemax)
     }            fprintf(ficresp,"\n");
     ungetc(c,ficpar);          if(first==1)
              printf("Others in log...\n");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          fprintf(ficlog,"\n");
            }
     if (fage <= 2) {      }
       bage = agemin;    }
       fage = agemax;    dateintmean=dateintsum/k2cpt; 
     }   
     fclose(ficresp);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        /* End of Freq */
 /*------------ gnuplot -------------*/  }
 chdir(pathcd);  
   if((ficgp=fopen("graph.plt","w"))==NULL) {  /************ Prevalence ********************/
     printf("Problem with file graph.gp");goto end;  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)
   }  {  
 #ifdef windows    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   fprintf(ficgp,"cd \"%s\" \n",pathc);       in each health status at the date of interview (if between dateprev1 and dateprev2).
 #endif       We still use firstpass and lastpass as another selection.
 m=pow(2,cptcoveff);    */
     
  /* 1eme*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double ***freq; /* Frequencies */
    for (k1=1; k1<= m ; k1 ++) {    double *pp, **prop;
     double pos,posprop; 
 #ifdef windows    double  y2; /* in fractional years */
     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);    int iagemin, iagemax;
 #endif  
 #ifdef unix    iagemin= (int) agemin;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    iagemax= (int) agemax;
 #endif    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
 for (i=1; i<= nlstate ; i ++) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    j1=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }    j=cptcoveff;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(k1=1; k1<=j;k1++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        
      for (i=1; i<= nlstate ; i ++) {        for (i=1; i<=nlstate; i++)  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(m=iagemin; m <= iagemax+3; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            prop[i][m]=0.0;
 }         
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        for (i=1; i<=imx; i++) { /* Each individual */
 #ifdef unix          bool=1;
 fprintf(ficgp,"\nset ter gif small size 400,300");          if  (cptcovn>0) {
 #endif            for (z1=1; z1<=cptcoveff; z1++) 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    }                bool=0;
   }          } 
   /*2 eme*/          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   for (k1=1; k1<= m ; k1 ++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for (i=1; i<= nlstate+1 ; i ++) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       k=2*i;                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); 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for (j=1; j<= nlstate+1 ; j ++) {                  /*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]]);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  prop[s[m][i]][iagemax+3] += weight[i]; 
 }                  } 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            } /* end selection of waves */
     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 ++) {        }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=iagemin; i <= iagemax+3; i++){  
         else fprintf(ficgp," \%%*lf (\%%*lf)");          
 }            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       fprintf(ficgp,"\" t\"\" w l 0,");            posprop += prop[jk][i]; 
      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 ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){     
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if( i <=  iagemax){ 
 }                if(posprop>=1.e-5){ 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                probs[i][jk][j1]= prop[jk][i]/posprop;
       else fprintf(ficgp,"\" t\"\" w l 0,");              } 
     }            } 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          }/* end jk */ 
   }        }/* end i */ 
        } /* end i1 */
   /*3eme*/    } /* end k1 */
     
   for (k1=1; k1<= m ; k1 ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {    /*free_vector(pp,1,nlstate);*/
       k=2+nlstate*(cpt-1);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       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);  }  /* End of prevalence */
       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);  /************* Waves Concatenation ***************/
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  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)
     }  {
   }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         Death is a valid wave (if date is known).
   /* CV preval stat */       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   for (k1=1; k1<= m ; k1 ++) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for (cpt=1; cpt<nlstate ; cpt ++) {       and mw[mi+1][i]. dh depends on stepm.
       k=3;       */
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)    int i, mi, m;
         fprintf(ficgp,"+$%d",k+i+1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);       double sum=0., jmean=0.;*/
          int first;
       l=3+(nlstate+ndeath)*cpt;    int j, k=0,jk, ju, jl;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double sum=0.;
       for (i=1; i< nlstate ; i ++) {    first=0;
         l=3+(nlstate+ndeath)*cpt;    jmin=1e+5;
         fprintf(ficgp,"+$%d",l+i+1);    jmax=-1;
       }    jmean=0.;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      for(i=1; i<=imx; i++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      mi=0;
     }      m=firstpass;
   }      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   /* proba elementaires */          mw[++mi][i]=m;
    for(i=1,jk=1; i <=nlstate; i++){        if(m >=lastpass)
     for(k=1; k <=(nlstate+ndeath); k++){          break;
       if (k != i) {        else
         for(j=1; j <=ncovmodel; j++){          m++;
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      }/* end while */
           /*fprintf(ficgp,"%s",alph[1]);*/      if (s[m][i] > nlstate){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        mi++;     /* Death is another wave */
           jk++;        /* if(mi==0)  never been interviewed correctly before death */
           fprintf(ficgp,"\n");           /* Only death is a correct wave */
         }        mw[mi][i]=m;
       }      }
     }  
     }      wav[i]=mi;
       if(mi==0){
   for(jk=1; jk <=m; jk++) {        nbwarn++;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        if(first==0){
    i=1;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
    for(k2=1; k2<=nlstate; k2++) {          first=1;
      k3=i;        }
      for(k=1; k<=(nlstate+ndeath); k++) {        if(first==1){
        if (k != k2){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        }
 ij=1;      } /* end mi==0 */
         for(j=3; j <=ncovmodel; j++) {    } /* End individuals */
           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]]]);    for(i=1; i<=imx; i++){
             ij++;      for(mi=1; mi<wav[i];mi++){
           }        if (stepm <=0)
           else          dh[mi][i]=1;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        else{
         }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           fprintf(ficgp,")/(1");            if (agedc[i] < 2*AGESUP) {
                      j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         for(k1=1; k1 <=nlstate; k1++){                if(j==0) j=1;  /* Survives at least one month after exam */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              else if(j<0){
 ij=1;                nberr++;
           for(j=3; j <=ncovmodel; j++){                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]);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                j=1; /* Temporary Dangerous patch */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                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);
             ij++;                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);
           else              }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              k=k+1;
           }              if (j >= jmax){
           fprintf(ficgp,")");                jmax=j;
         }                ijmax=i;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              if (j <= jmin){
         i=i+ncovmodel;                jmin=j;
        }                ijmin=i;
      }              }
    }              sum=sum+j;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              /*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);*/
                }
   fclose(ficgp);          }
              else{
 chdir(path);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     free_matrix(agev,1,maxwav,1,imx);  /*        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]); */
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            k=k+1;
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            if (j >= jmax) {
                  jmax=j;
     free_imatrix(s,1,maxwav+1,1,n);              ijmax=i;
                }
                else if (j <= jmin){
     free_ivector(num,1,n);              jmin=j;
     free_vector(agedc,1,n);              ijmin=i;
     free_vector(weight,1,n);            }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     fclose(ficparo);            /*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]);*/
     fclose(ficres);            if(j<0){
     /*  }*/              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]);
    /*________fin mle=1_________*/              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]);
                }
             sum=sum+j;
            }
     /* No more information from the sample is required now */          jk= j/stepm;
   /* Reads comments: lines beginning with '#' */          jl= j -jk*stepm;
   while((c=getc(ficpar))=='#' && c!= EOF){          ju= j -(jk+1)*stepm;
     ungetc(c,ficpar);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     fgets(line, MAXLINE, ficpar);            if(jl==0){
     puts(line);              dh[mi][i]=jk;
     fputs(line,ficparo);              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
   ungetc(c,ficpar);                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              bh[mi][i]=ju;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);            }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          }else{
 /*--------- index.htm --------*/            if(jl <= -ju){
               dh[mi][i]=jk;
   strcpy(optionfilehtm,optionfile);              bh[mi][i]=jl;       /* bias is positive if real duration
   strcat(optionfilehtm,".htm");                                   * is higher than the multiple of stepm and negative otherwise.
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                                   */
     printf("Problem with %s \n",optionfilehtm);goto end;            }
   }            else{
               dh[mi][i]=jk+1;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">              bh[mi][i]=ju;
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>            }
 Total number of observations=%d <br>            if(dh[mi][i]==0){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>              dh[mi][i]=1; /* At least one step */
 <hr  size=\"2\" color=\"#EC5E5E\">              bh[mi][i]=ju; /* At least one step */
 <li>Outputs files<br><br>\n              /*  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);*/
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          } /* end if mle */
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      } /* end wave */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    jmean=sum/k;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    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);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    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);
         - 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);   }
   
  fprintf(fichtm," <li>Graphs</li><p>");  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
  m=cptcoveff;  {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
  j1=0;    int cptcode=0;
  for(k1=1; k1<=m;k1++){    cptcoveff=0; 
    for(i1=1; i1<=ncodemax[k1];i1++){   
        j1++;    for (k=0; k<maxncov; k++) Ndum[k]=0;
        if (cptcovn > 0) {    for (k=1; k<=7; k++) ncodemax[k]=0;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                                 modality*/ 
        }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        Ndum[ij]++; /*store the modality */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
        for(cpt=1; cpt<nlstate;cpt++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>                                         Tvar[j]. If V=sex and male is 0 and 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                                         female is 1, then  cptcode=1.*/
        }      }
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for (i=0; i<=cptcode; i++) {
 interval) in state (%d): v%s%d%d.gif <br>        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 */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        }
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {      ij=1; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      for (i=1; i<=ncodemax[j]; i++) {
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for (k=0; k<= maxncov; k++) {
      }          if (Ndum[k] != 0) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            nbcode[Tvar[j]][ij]=k; 
 health expectancies in states (1) and (2): e%s%d.gif<br>            /* 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; */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            
 fprintf(fichtm,"\n</body>");            ij++;
    }          }
  }          if (ij > ncodemax[j]) break; 
 fclose(fichtm);        }  
       } 
   /*--------------- Prevalence limit --------------*/    }  
    
   strcpy(filerespl,"pl");   for (k=0; k< maxncov; k++) Ndum[k]=0;
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   for (i=1; i<=ncovmodel-2; i++) { 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   }     ij=Tvar[i];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);     Ndum[ij]++;
   fprintf(ficrespl,"#Prevalence limit\n");   }
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);   ij=1;
   fprintf(ficrespl,"\n");   for (i=1; i<= maxncov; i++) {
       if((Ndum[i]!=0) && (i<=ncovcol)){
   prlim=matrix(1,nlstate,1,nlstate);       Tvaraff[ij]=i; /*For printing */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       ij++;
   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 */   cptcoveff=ij-1; /*Number of simple covariates*/
   k=0;  }
   agebase=agemin;  
   agelim=agemax;  /*********** Health Expectancies ****************/
   ftolpl=1.e-10;  
   i1=cptcoveff;  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 (cptcovn < 1){i1=1;}  
   {
   for(cptcov=1;cptcov<=i1;cptcov++){    /* Health expectancies, no variances */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
         k=k+1;    int nhstepma, nstepma; /* Decreasing with age */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double age, agelim, hf;
         fprintf(ficrespl,"\n#******");    double ***p3mat;
         for(j=1;j<=cptcoveff;j++)    double eip;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");    pstamp(ficreseij);
            fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
         for (age=agebase; age<=agelim; age++){    fprintf(ficreseij,"# Age");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    for(i=1; i<=nlstate;i++){
           fprintf(ficrespl,"%.0f",age );      for(j=1; j<=nlstate;j++){
           for(i=1; i<=nlstate;i++)        fprintf(ficreseij," e%1d%1d ",i,j);
           fprintf(ficrespl," %.5f", prlim[i][i]);      }
           fprintf(ficrespl,"\n");      fprintf(ficreseij," e%1d. ",i);
         }    }
       }    fprintf(ficreseij,"\n");
     }  
   fclose(ficrespl);    
   /*------------- h Pij x at various ages ------------*/    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    else  hstepm=estepm;   
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * This is mainly to measure the difference between two models: for example
   printf("Computing pij: result on file '%s' \n", filerespij);     * if stepm=24 months pijx are given only every 2 years and by summing them
       * we are calculating an estimate of the Life Expectancy assuming a linear 
   stepsize=(int) (stepm+YEARM-1)/YEARM;     * progression in between and thus overestimating or underestimating according
   if (stepm<=24) stepsize=2;     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   agelim=AGESUP;     * to compare the new estimate of Life expectancy with the same linear 
   hstepm=stepsize*YEARM; /* Every year of age */     * hypothesis. A more precise result, taking into account a more precise
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */     * curvature will be obtained if estepm is as small as stepm. */
    
   k=0;    /* For example we decided to compute the life expectancy with the smallest unit */
   for(cptcov=1;cptcov<=i1;cptcov++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       nhstepm is the number of hstepm from age to agelim 
       k=k+1;       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
         for(j=1;j<=cptcoveff;j++)       and note for a fixed period like estepm months */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficrespij,"******\n");       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
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       results. So we changed our mind and took the option of the best precision.
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      agelim=AGESUP;
           fprintf(ficrespij,"# Age");    /* If stepm=6 months */
           for(i=1; i<=nlstate;i++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             for(j=1; j<=nlstate+ndeath;j++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
               fprintf(ficrespij," %1d-%1d",i,j);      
           fprintf(ficrespij,"\n");  /* nhstepm age range expressed in number of stepm */
           for (h=0; h<=nhstepm; h++){    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             for(i=1; i<=nlstate;i++)    /* if (stepm >= YEARM) hstepm=1;*/
               for(j=1; j<=nlstate+ndeath;j++)    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");  
           }    for (age=bage; age<=fage; age ++){ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           fprintf(ficrespij,"\n");      /* 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 */
   fclose(ficrespij);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   /*---------- Health expectancies and variances ------------*/      
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   strcpy(filerest,"t");      
   strcat(filerest,fileres);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficrest=fopen(filerest,"w"))==NULL) {      
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      printf("%d|",(int)age);fflush(stdout);
   }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   strcpy(filerese,"e");        for(j=1; j<=nlstate;j++)
   strcat(filerese,fileres);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   if((ficreseij=fopen(filerese,"w"))==NULL) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            
   }            /* 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]);*/
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
           }
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);      fprintf(ficreseij,"%3.0f",age );
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      for(i=1; i<=nlstate;i++){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        eip=0;
   }        for(j=1; j<=nlstate;j++){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficreseij,"%9.4f", eip );
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;      fprintf(ficreseij,"\n");
       fprintf(ficrest,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficrest,"******\n");    printf("\n");
     fprintf(ficlog,"\n");
       fprintf(ficreseij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)  }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
       fprintf(ficresvij,"\n#****** ");  {
       for(j=1;j<=cptcoveff;j++)    /* Covariances of health expectancies eij and of total life expectancies according
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);     to initial status i, ei. .
       fprintf(ficresvij,"******\n");    */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int nhstepma, nstepma; /* Decreasing with age */
       oldm=oldms;savm=savms;    double age, agelim, hf;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      double ***p3matp, ***p3matm, ***varhe;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double **dnewm,**doldm;
       oldm=oldms;savm=savms;    double *xp, *xm;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double **gp, **gm;
          double ***gradg, ***trgradg;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    int theta;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    double eip, vip;
          
       hf=1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       if (stepm >= YEARM) hf=stepm/YEARM;    xp=vector(1,npar);
       epj=vector(1,nlstate+1);    xm=vector(1,npar);
       for(age=bage; age <=fage ;age++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         fprintf(ficrest," %.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    pstamp(ficresstdeij);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    fprintf(ficresstdeij,"# Age");
           }    for(i=1; i<=nlstate;i++){
           epj[nlstate+1] +=epj[j];      for(j=1; j<=nlstate;j++)
         }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
         for(i=1, vepp=0.;i <=nlstate;i++)      fprintf(ficresstdeij," e%1d. ",i);
           for(j=1;j <=nlstate;j++)    }
             vepp += vareij[i][j][(int)age];    fprintf(ficresstdeij,"\n");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  
         for(j=1;j <=nlstate;j++){    pstamp(ficrescveij);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         }    fprintf(ficrescveij,"# Age");
         fprintf(ficrest,"\n");    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++){
  fclose(ficreseij);            cptj2= (j2-1)*nlstate+i2;
  fclose(ficresvij);            if(cptj2 <= cptj)
   fclose(ficrest);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   fclose(ficpar);          }
   free_vector(epj,1,nlstate+1);      }
   /*  scanf("%d ",i); */    fprintf(ficrescveij,"\n");
     
   /*------- Variance limit prevalence------*/      if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
 strcpy(fileresvpl,"vpl");    }
   strcat(fileresvpl,fileres);    else  hstepm=estepm;   
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    /* We compute the life expectancy from trapezoids spaced every estepm months
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     * This is mainly to measure the difference between two models: for example
     exit(0);     * if stepm=24 months pijx are given only every 2 years and by summing them
   }     * we are calculating an estimate of the Life Expectancy assuming a linear 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
  k=0;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
  for(cptcov=1;cptcov<=i1;cptcov++){     * to compare the new estimate of Life expectancy with the same linear 
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * hypothesis. A more precise result, taking into account a more precise
      k=k+1;     * curvature will be obtained if estepm is as small as stepm. */
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcoveff;j++)    /* For example we decided to compute the life expectancy with the smallest unit */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      fprintf(ficresvpl,"******\n");       nhstepm is the number of hstepm from age to agelim 
             nstepm is the number of stepm from age to agelin. 
      varpl=matrix(1,nlstate,(int) bage, (int) fage);       Look at hpijx to understand the reason of that which relies in memory size
      oldm=oldms;savm=savms;       and note for a fixed period like estepm months */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    }       survival function given by stepm (the optimization length). Unfortunately it
  }       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fclose(ficresvpl);       results. So we changed our mind and took the option of the best precision.
     */
   /*---------- End : free ----------------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      /* If stepm=6 months */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* nhstepm age range expressed in number of stepm */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    agelim=AGESUP;
      nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    /* if (stepm >= YEARM) hstepm=1;*/
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(matcov,1,npar,1,npar);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   free_vector(delti,1,npar);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   printf("End of Imach\n");    for (age=bage; age<=fage; age ++){ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /* 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);*/      /* if (stepm >= YEARM) hstepm=1;*/
   /*printf("Total time was %d uSec.\n", total_usecs);*/      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   /*------ End -----------*/  
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
  end:         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
 #ifdef windows      
  chdir(pathcd);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 #endif  
  /*system("wgnuplot graph.plt");*/      /* Computing  Variances of health expectancies */
  /*system("../gp37mgw/wgnuplot graph.plt");*/      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
  /*system("cd ../gp37mgw");*/         decrease memory allocation */
  system("..\\gp37mgw\\wgnuplot graph.plt");      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
 #ifdef windows          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   while (z[0] != 'q') {          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     chdir(pathcd);        }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     scanf("%s",z);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     if (z[0] == 'c') system("./imach");    
     else if (z[0] == 'e') {        for(j=1; j<= nlstate; j++){
       chdir(path);          for(i=1; i<=nlstate; i++){
       system(optionfilehtm);            for(h=0; h<=nhstepm-1; h++){
     }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     else if (z[0] == 'q') exit(0);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   }            }
 #endif          }
 }        }
        
         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.1.12  
changed lines
  Added in v.1.127


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