Diff for /imach/src/imach.c between versions 1.7 and 1.127

version 1.7, 2001/05/02 17:50:24 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
 static int cptcov;  
 int cptcovn, cptcovage=0, cptcoveff=0;    Revision 1.117  2006/03/14 17:16:22  brouard
 int npar=NPARMAX;    (Module): varevsij Comments added explaining the second
 int nlstate=2; /* Number of live states */    table of variances if popbased=1 .
 int ndeath=1; /* Number of dead states */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): Function pstamp added
     (Module): Version 0.98d
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of 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 **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.115  2006/02/27 12:17:45  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): One freematrix added in mlikeli! 0.98c
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Revision 1.114  2006/02/26 12:57:58  brouard
 FILE *ficreseij;    (Module): Some improvements in processing parameter
   char filerese[FILENAMELENGTH];    filename with strsep.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.113  2006/02/24 14:20:24  brouard
  FILE  *ficresvpl;    (Module): Memory leaks checks with valgrind and:
   char fileresvpl[FILENAMELENGTH];    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.112  2006/01/30 09:55:26  brouard
 #define FTOL 1.0e-10    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 #define NRANSI    Revision 1.111  2006/01/25 20:38:18  brouard
 #define ITMAX 200    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 #define TOL 2.0e-4    can be a simple dot '.'.
   
 #define CGOLD 0.3819660    Revision 1.110  2006/01/25 00:51:50  brouard
 #define ZEPS 1.0e-10    (Module): Lots of cleaning and bugs added (Gompertz)
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.109  2006/01/24 19:37:15  brouard
 #define GOLD 1.618034    (Module): Comments (lines starting with a #) are allowed in data.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 static double maxarg1,maxarg2;    To be fixed
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.107  2006/01/19 16:20:37  brouard
      Test existence of gnuplot in imach path
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.105  2006/01/05 20:23:19  lievre
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    *** empty log message ***
   
 int imx;    Revision 1.104  2005/09/30 16:11:43  lievre
 int stepm;    (Module): sump fixed, loop imx fixed, and simplifications.
 /* Stepm, step in month: minimum step interpolation*/    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 int m,nb;    (instead of missing=-1 in earlier versions) and his/her
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    contributions to the likelihood is 1 - Prob of dying from last
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double **pmmij;    the healthy state at last known wave). Version is 0.98
   
 double *weight;    Revision 1.103  2005/09/30 15:54:49  lievre
 int **s; /* Status */    (Module): sump fixed, loop imx fixed, and simplifications.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    Revision 1.100  2004/07/12 18:29:06  brouard
 {    Add version for Mac OS X. Just define UNIX in Makefile
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.98  2004/05/16 15:05:56  brouard
    s = strrchr( path, '\\' );           /* find last / */    New version 0.97 . First attempt to estimate force of mortality
    if ( s == NULL ) {                   /* no directory, so use current */    directly from the data i.e. without the need of knowing the health
 #if     defined(__bsd__)                /* get current working directory */    state at each age, but using a Gompertz model: log u =a + b*age .
       extern char       *getwd( );    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
       if ( getwd( dirc ) == NULL ) {    cross-longitudinal survey is different from the mortality estimated
 #else    from other sources like vital statistic data.
       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 ) {  
 #endif    Agnès, who wrote this part of the code, tried to keep most of the
          return( GLOCK_ERROR_GETCWD );    former routines in order to include the new code within the former code.
       }  
       strcpy( name, path );             /* we've got it */    The output is very simple: only an estimate of the intercept and of
    } else {                             /* strip direcotry from path */    the slope with 95% confident intervals.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Current limitations:
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    A) Even if you enter covariates, i.e. with the
       strcpy( name, s );                /* save file name */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    B) There is no computation of Life Expectancy nor Life Table.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.97  2004/02/20 13:25:42  lievre
    l1 = strlen( dirc );                 /* length of directory */    Version 0.96d. Population forecasting command line is (temporarily)
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    suppressed.
    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
 void replace(char *s, char*t)    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   int i;    matrix (cov(a12,c31) instead of numbers.
   int lg=20;  
   i=0;    Revision 1.94  2003/06/27 13:00:02  brouard
   lg=strlen(t);    Just cleaning
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.93  2003/06/25 16:33:55  brouard
     if (t[i]== '\\') s[i]='/';    (Module): On windows (cygwin) function asctime_r doesn't
   }    exist so I changed back to asctime which exists.
 }    (Module): Version 0.96b
   
 int nbocc(char *s, char occ)    Revision 1.92  2003/06/25 16:30:45  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   int i,j=0;    exist so I changed back to asctime which exists.
   int lg=20;  
   i=0;    Revision 1.91  2003/06/25 15:30:29  brouard
   lg=strlen(s);    * imach.c (Repository): Duplicated warning errors corrected.
   for(i=0; i<= lg; i++) {    (Repository): Elapsed time after each iteration is now output. It
   if  (s[i] == occ ) j++;    helps to forecast when convergence will be reached. Elapsed time
   }    is stamped in powell.  We created a new html file for the graphs
   return j;    concerning matrix of covariance. It has extension -cov.htm.
 }  
     Revision 1.90  2003/06/24 12:34:15  brouard
 void cutv(char *u,char *v, char*t, char occ)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   int i,lg,j,p=0;    of the covariance matrix to be input.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.89  2003/06/24 12:30:52  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Some bugs corrected for windows. Also, when
   }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.88  2003/06/23 17:54:56  brouard
     (u[j] = t[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[p]='\0';    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.86  2003/06/17 20:04:08  brouard
   }    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 /********************** nrerror ********************/    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 void nrerror(char error_text[])    current date of interview. It may happen when the death was just
 {    prior to the death. In this case, dh was negative and likelihood
   fprintf(stderr,"ERREUR ...\n");    was wrong (infinity). We still send an "Error" but patch by
   fprintf(stderr,"%s\n",error_text);    assuming that the date of death was just one stepm after the
   exit(1);    interview.
 }    (Repository): Because some people have very long ID (first column)
 /*********************** vector *******************/    we changed int to long in num[] and we added a new lvector for
 double *vector(int nl, int nh)    memory allocation. But we also truncated to 8 characters (left
 {    truncation)
   double *v;    (Repository): No more line truncation errors.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.84  2003/06/13 21:44:43  brouard
   return v-nl+NR_END;    * imach.c (Repository): Replace "freqsummary" at a correct
 }    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 /************************ free vector ******************/    parcimony.
 void free_vector(double*v, int nl, int nh)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /************************ivector *******************************/    Revision 1.82  2003/06/05 15:57:20  brouard
 int *ivector(long nl,long nh)    Add log in  imach.c and  fullversion number is now printed.
 {  
   int *v;  */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  /*
   if (!v) nrerror("allocation failure in ivector");     Interpolated Markov Chain
   return v-nl+NR_END;  
 }    Short summary of the programme:
     
 /******************free ivector **************************/    This program computes Healthy Life Expectancies from
 void free_ivector(int *v, long nl, long nh)    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 {    first survey ("cross") where individuals from different ages are
   free((FREE_ARG)(v+nl-NR_END));    interviewed on their health status or degree of disability (in the
 }    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 /******************* imatrix *******************************/    (if any) in individual health status.  Health expectancies are
 int **imatrix(long nrl, long nrh, long ncl, long nch)    computed from the time spent in each health state according to a
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    model. More health states you consider, more time is necessary to reach the
 {    Maximum Likelihood of the parameters involved in the model.  The
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    simplest model is the multinomial logistic model where pij is the
   int **m;    probability to be observed in state j at the second wave
      conditional to be observed in state i at the first wave. Therefore
   /* allocate pointers to rows */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    'age' is age and 'sex' is a covariate. If you want to have a more
   if (!m) nrerror("allocation failure 1 in matrix()");    complex model than "constant and age", you should modify the program
   m += NR_END;    where the markup *Covariates have to be included here again* invites
   m -= nrl;    you to do it.  More covariates you add, slower the
      convergence.
    
   /* allocate rows and set pointers to them */    The advantage of this computer programme, compared to a simple
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    multinomial logistic model, is clear when the delay between waves is not
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    identical for each individual. Also, if a individual missed an
   m[nrl] += NR_END;    intermediate interview, the information is lost, but taken into
   m[nrl] -= ncl;    account using an interpolation or extrapolation.  
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    hPijx is the probability to be observed in state i at age x+h
      conditional to the observed state i at age x. The delay 'h' can be
   /* return pointer to array of pointers to rows */    split into an exact number (nh*stepm) of unobserved intermediate
   return m;    states. This elementary transition (by month, quarter,
 }    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 /****************** free_imatrix *************************/    and the contribution of each individual to the likelihood is simply
 void free_imatrix(m,nrl,nrh,ncl,nch)    hPijx.
       int **m;  
       long nch,ncl,nrh,nrl;    Also this programme outputs the covariance matrix of the parameters but also
      /* free an int matrix allocated by imatrix() */    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   free((FREE_ARG) (m+nrl-NR_END));             Institut national d'études démographiques, Paris.
 }    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 /******************* matrix *******************************/    It is copyrighted identically to a GNU software product, ie programme and
 double **matrix(long nrl, long nrh, long ncl, long nch)    software can be distributed freely for non commercial use. Latest version
 {    can be accessed at http://euroreves.ined.fr/imach .
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     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;  /*
   m -= nrl;    main
     read parameterfile
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    read datafile
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    concatwav
   m[nrl] += NR_END;    freqsummary
   m[nrl] -= ncl;    if (mle >= 1)
       mlikeli
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    print results files
   return m;    if mle==1 
 }       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 /*************************free matrix ************************/        begin-prev-date,...
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    open gnuplot file
 {    open html file
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    period (stable) prevalence
   free((FREE_ARG)(m+nrl-NR_END));     for age prevalim()
 }    h Pij x
     variance of p varprob
 /******************* ma3x *******************************/    forecasting if prevfcast==1 prevforecast call prevalence()
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    health expectancies
 {    Variance-covariance of DFLE
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    prevalence()
   double ***m;     movingaverage()
     varevsij() 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if popbased==1 varevsij(,popbased)
   if (!m) nrerror("allocation failure 1 in matrix()");    total life expectancies
   m += NR_END;    Variance of period (stable) prevalence
   m -= nrl;   end
   */
   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>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <stdio.h>
   #include <stdlib.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #include <string.h>
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #include <unistd.h>
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  #include <limits.h>
   for (j=ncl+1; j<=nch; j++)  #include <sys/types.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #include <sys/stat.h>
    #include <errno.h>
   for (i=nrl+1; i<=nrh; i++) {  extern int errno;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /* #include <sys/time.h> */
       m[i][j]=m[i][j-1]+nlay;  #include <time.h>
   }  #include "timeval.h"
   return m;  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define MAXLINE 256
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define GNUPLOTPROGRAM "gnuplot"
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free((FREE_ARG)(m+nrl-NR_END));  #define FILENAMELENGTH 132
 }  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /***************** f1dim *************************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 extern int ncom;  
 extern double *pcom,*xicom;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 extern double (*nrfunc)(double []);  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    
 double f1dim(double x)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   int j;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   double f;  #define NCOVMAX 8 /* Maximum number of covariates */
   double *xt;  #define MAXN 20000
    #define YEARM 12. /* Number of months per year */
   xt=vector(1,ncom);  #define AGESUP 130
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define AGEBASE 40
   f=(*nrfunc)(xt);  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   free_vector(xt,1,ncom);  #ifdef UNIX
   return f;  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /*****************brent *************************/  #else
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   int iter;  #define ODIRSEPARATOR '/'
   double a,b,d,etemp;  #endif
   double fu,fv,fw,fx;  
   double ftemp;  /* $Id$ */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /* $State$ */
   double e=0.0;  
    char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
   a=(ax < cx ? ax : cx);  char fullversion[]="$Revision$ $Date$"; 
   b=(ax > cx ? ax : cx);  char strstart[80];
   x=w=v=bx;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   fw=fv=fx=(*f)(x);  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   for (iter=1;iter<=ITMAX;iter++) {  int nvar;
     xm=0.5*(a+b);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int npar=NPARMAX;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int nlstate=2; /* Number of live states */
     printf(".");fflush(stdout);  int ndeath=1; /* Number of dead states */
 #ifdef DEBUG  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     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);  int popbased=0;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  int *wav; /* Number of waves for this individuual 0 is possible */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int maxwav; /* Maxim number of waves */
       *xmin=x;  int jmin, jmax; /* min, max spacing between 2 waves */
       return fx;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
     }  int gipmx, gsw; /* Global variables on the number of contributions 
     ftemp=fu;                     to the likelihood and the sum of weights (done by funcone)*/
     if (fabs(e) > tol1) {  int mle, weightopt;
       r=(x-w)*(fx-fv);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       q=(x-v)*(fx-fw);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       p=(x-v)*q-(x-w)*r;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       q=2.0*(q-r);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       if (q > 0.0) p = -p;  double jmean; /* Mean space between 2 waves */
       q=fabs(q);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       etemp=e;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       e=d;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  FILE *ficlog, *ficrespow;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int globpr; /* Global variable for printing or not */
       else {  double fretone; /* Only one call to likelihood */
         d=p/q;  long ipmx; /* Number of contributions */
         u=x+d;  double sw; /* Sum of weights */
         if (u-a < tol2 || b-u < tol2)  char filerespow[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       }  FILE *ficresilk;
     } else {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficresprobmorprev;
     }  FILE *fichtm, *fichtmcov; /* Html File */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  FILE *ficreseij;
     fu=(*f)(u);  char filerese[FILENAMELENGTH];
     if (fu <= fx) {  FILE *ficresstdeij;
       if (u >= x) a=x; else b=x;  char fileresstde[FILENAMELENGTH];
       SHFT(v,w,x,u)  FILE *ficrescveij;
         SHFT(fv,fw,fx,fu)  char filerescve[FILENAMELENGTH];
         } else {  FILE  *ficresvij;
           if (u < x) a=u; else b=u;  char fileresv[FILENAMELENGTH];
           if (fu <= fw || w == x) {  FILE  *ficresvpl;
             v=w;  char fileresvpl[FILENAMELENGTH];
             w=u;  char title[MAXLINE];
             fv=fw;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
             fw=fu;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
           } else if (fu <= fv || v == x || v == w) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
             v=u;  char command[FILENAMELENGTH];
             fv=fu;  int  outcmd=0;
           }  
         }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  
   nrerror("Too many iterations in brent");  char filelog[FILENAMELENGTH]; /* Log file */
   *xmin=x;  char filerest[FILENAMELENGTH];
   return fx;  char fileregp[FILENAMELENGTH];
 }  char popfile[FILENAMELENGTH];
   
 /****************** mnbrak ***********************/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
             double (*func)(double))  struct timezone tzp;
 {  extern int gettimeofday();
   double ulim,u,r,q, dum;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double fu;  long time_value;
    extern long time();
   *fa=(*func)(*ax);  char strcurr[80], strfor[80];
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  char *endptr;
     SHFT(dum,*ax,*bx,dum)  long lval;
       SHFT(dum,*fb,*fa,dum)  double dval;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  #define NR_END 1
   *fc=(*func)(*cx);  #define FREE_ARG char*
   while (*fb > *fc) {  #define FTOL 1.0e-10
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  #define NRANSI 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define ITMAX 200 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define TOL 2.0e-4 
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  #define CGOLD 0.3819660 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define ZEPS 1.0e-10 
       fu=(*func)(u);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define GOLD 1.618034 
           SHFT(*fb,*fc,fu,(*func)(u))  #define GLIMIT 100.0 
           }  #define TINY 1.0e-20 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  static double maxarg1,maxarg2;
       fu=(*func)(u);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     } else {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       u=(*cx)+GOLD*(*cx-*bx);    
       fu=(*func)(u);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     }  #define rint(a) floor(a+0.5)
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  static double sqrarg;
       }  #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 ncom;  int stepm=1;
 double *pcom,*xicom;  /* Stepm, step in month: minimum step interpolation*/
 double (*nrfunc)(double []);  
    int estepm;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   double brent(double ax, double bx, double cx,  int m,nb;
                double (*f)(double), double tol, double *xmin);  long *num;
   double f1dim(double x);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
               double *fc, double (*func)(double));  double **pmmij, ***probs;
   int j;  double *ageexmed,*agecens;
   double xx,xmin,bx,ax;  double dateintmean=0;
   double fx,fb,fa;  
    double *weight;
   ncom=n;  int **s; /* Status */
   pcom=vector(1,n);  double *agedc, **covar, idx;
   xicom=vector(1,n);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   nrfunc=func;  double *lsurv, *lpop, *tpop;
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     xicom[j]=xi[j];  double ftolhess; /* Tolerance for computing hessian */
   }  
   ax=0.0;  /**************** split *************************/
   xx=1.0;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 #ifdef DEBUG       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    */ 
 #endif    char  *ss;                            /* pointer */
   for (j=1;j<=n;j++) {    int   l1, l2;                         /* length counters */
     xi[j] *= xmin;  
     p[j] += xi[j];    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   free_vector(xicom,1,n);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   free_vector(pcom,1,n);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
 }      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /*************** powell ************************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      /* get current working directory */
             double (*func)(double []))      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   void linmin(double p[], double xi[], int n, double *fret,        return( GLOCK_ERROR_GETCWD );
               double (*func)(double []));      }
   int i,ibig,j;      /* got dirc from getcwd*/
   double del,t,*pt,*ptt,*xit;      printf(" DIRC = %s \n",dirc);
   double fp,fptt;    } else {                              /* strip direcotry from path */
   double *xits;      ss++;                               /* after this, the filename */
   pt=vector(1,n);      l2 = strlen( ss );                  /* length of filename */
   ptt=vector(1,n);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   xit=vector(1,n);      strcpy( name, ss );         /* save file name */
   xits=vector(1,n);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   *fret=(*func)(p);      dirc[l1-l2] = 0;                    /* add zero */
   for (j=1;j<=n;j++) pt[j]=p[j];      printf(" DIRC2 = %s \n",dirc);
   for (*iter=1;;++(*iter)) {    }
     fp=(*fret);    /* We add a separator at the end of dirc if not exists */
     ibig=0;    l1 = strlen( dirc );                  /* length of directory */
     del=0.0;    if( dirc[l1-1] != DIRSEPARATOR ){
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      dirc[l1] =  DIRSEPARATOR;
     for (i=1;i<=n;i++)      dirc[l1+1] = 0; 
       printf(" %d %.12f",i, p[i]);      printf(" DIRC3 = %s \n",dirc);
     printf("\n");    }
     for (i=1;i<=n;i++) {    ss = strrchr( name, '.' );            /* find last / */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    if (ss >0){
       fptt=(*fret);      ss++;
 #ifdef DEBUG      strcpy(ext,ss);                     /* save extension */
       printf("fret=%lf \n",*fret);      l1= strlen( name);
 #endif      l2= strlen(ss)+1;
       printf("%d",i);fflush(stdout);      strncpy( finame, name, l1-l2);
       linmin(p,xit,n,fret,func);      finame[l1-l2]= 0;
       if (fabs(fptt-(*fret)) > del) {    }
         del=fabs(fptt-(*fret));  
         ibig=i;    return( 0 );                          /* we're done */
       }  }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  /******************************************/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  void replace_back_to_slash(char *s, char*t)
       }  {
       for(j=1;j<=n;j++)    int i;
         printf(" p=%.12e",p[j]);    int lg=0;
       printf("\n");    i=0;
 #endif    lg=strlen(t);
     }    for(i=0; i<= lg; i++) {
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      (s[i] = t[i]);
 #ifdef DEBUG      if (t[i]== '\\') s[i]='/';
       int k[2],l;    }
       k[0]=1;  }
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  int nbocc(char *s, char occ)
       for (j=1;j<=n;j++)  {
         printf(" %.12e",p[j]);    int i,j=0;
       printf("\n");    int lg=20;
       for(l=0;l<=1;l++) {    i=0;
         for (j=1;j<=n;j++) {    lg=strlen(s);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    for(i=0; i<= lg; i++) {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    if  (s[i] == occ ) j++;
         }    }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    return j;
       }  }
 #endif  
   void cutv(char *u,char *v, char*t, char occ)
   {
       free_vector(xit,1,n);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       free_vector(xits,1,n);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       free_vector(ptt,1,n);       gives u="abcedf" and v="ghi2j" */
       free_vector(pt,1,n);    int i,lg,j,p=0;
       return;    i=0;
     }    for(j=0; j<=strlen(t)-1; j++) {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     for (j=1;j<=n;j++) {    }
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];    lg=strlen(t);
       pt[j]=p[j];    for(j=0; j<p; j++) {
     }      (u[j] = t[j]);
     fptt=(*func)(ptt);    }
     if (fptt < fp) {       u[p]='\0';
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {     for(j=0; j<= lg; j++) {
         linmin(p,xit,n,fret,func);      if (j>=(p+1))(v[j-p-1] = t[j]);
         for (j=1;j<=n;j++) {    }
           xi[j][ibig]=xi[j][n];  }
           xi[j][n]=xit[j];  
         }  /********************** nrerror ********************/
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  void nrerror(char error_text[])
         for(j=1;j<=n;j++)  {
           printf(" %.12e",xit[j]);    fprintf(stderr,"ERREUR ...\n");
         printf("\n");    fprintf(stderr,"%s\n",error_text);
 #endif    exit(EXIT_FAILURE);
       }  }
     }  /*********************** vector *******************/
   }  double *vector(int nl, int nh)
 }  {
     double *v;
 /**** Prevalence limit ****************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    return v-nl+NR_END;
 {  }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    free((FREE_ARG)(v+nl-NR_END));
   double **matprod2();  }
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /************************ivector *******************************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  int *ivector(long nl,long nh)
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    int *v;
     for (j=1;j<=nlstate+ndeath;j++){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
   }
    cov[1]=1.;  
    /******************free ivector **************************/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  void free_ivector(int *v, long nl, long nh)
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  {
     newm=savm;    free((FREE_ARG)(v+nl-NR_END));
     /* Covariates have to be included here again */  }
      cov[2]=agefin;  
    /************************lvector *******************************/
       for (k=1; k<=cptcovn;k++) {  long *lvector(long nl,long nh)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    long *v;
       }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       for (k=1; k<=cptcovage;k++)    if (!v) nrerror("allocation failure in ivector");
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return v-nl+NR_END;
       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 **************************/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  void free_lvector(long *v, long nl, long nh)
   {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    free((FREE_ARG)(v+nl-NR_END));
   }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   /******************* imatrix *******************************/
     savm=oldm;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     oldm=newm;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     maxmax=0.;  { 
     for(j=1;j<=nlstate;j++){    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       min=1.;    int **m; 
       max=0.;    
       for(i=1; i<=nlstate; i++) {    /* allocate pointers to rows */ 
         sumnew=0;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    if (!m) nrerror("allocation failure 1 in matrix()"); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    m += NR_END; 
         max=FMAX(max,prlim[i][j]);    m -= nrl; 
         min=FMIN(min,prlim[i][j]);    
       }    
       maxmin=max-min;    /* allocate rows and set pointers to them */ 
       maxmax=FMAX(maxmax,maxmin);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     if(maxmax < ftolpl){    m[nrl] += NR_END; 
       return prlim;    m[nrl] -= ncl; 
     }    
   }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 }    
     /* return pointer to array of pointers to rows */ 
 /*************** transition probabilities **********/    return m; 
   } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /****************** free_imatrix *************************/
   double s1, s2;  void free_imatrix(m,nrl,nrh,ncl,nch)
   /*double t34;*/        int **m;
   int i,j,j1, nc, ii, jj;        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
     for(i=1; i<= nlstate; i++){  { 
     for(j=1; j<i;j++){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free((FREE_ARG) (m+nrl-NR_END)); 
         /*s2 += param[i][j][nc]*cov[nc];*/  } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!m) nrerror("allocation failure 1 in matrix()");
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    m += NR_END;
       }    m -= nrl;
       ps[i][j]=s2;  
     }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(i=1; i<= nlstate; i++){    m[nrl] += NR_END;
      s1=0;    m[nrl] -= ncl;
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=i+1; j<=nlstate+ndeath; j++)    return m;
       s1+=exp(ps[i][j]);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     ps[i][i]=1./(s1+1.);     */
     for(j=1; j<i; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************************free matrix ************************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  {
   } /* end i */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /******************* ma3x *******************************/
       ps[ii][ii]=1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
   }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      printf("%lf ",ps[ii][jj]);    if (!m) nrerror("allocation failure 1 in matrix()");
    }    m += NR_END;
     printf("\n ");    m -= nrl;
     }  
     printf("\n ");printf("%lf ",cov[2]);*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /*    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    m[nrl] += NR_END;
   goto end;*/    m[nrl] -= ncl;
     return ps;  
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
 /**************** Product of 2 matrices ******************/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    m[nrl][ncl] += NR_END;
 {    m[nrl][ncl] -= nll;
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    for (j=ncl+1; j<=nch; j++) 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      m[nrl][j]=m[nrl][j-1]+nlay;
   /* in, b, out are matrice of pointers which should have been initialized    
      before: only the contents of out is modified. The function returns    for (i=nrl+1; i<=nrh; i++) {
      a pointer to pointers identical to out */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   long i, j, k;      for (j=ncl+1; j<=nch; j++) 
   for(i=nrl; i<= nrh; i++)        m[i][j]=m[i][j-1]+nlay;
     for(k=ncolol; k<=ncoloh; k++)    }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    return m; 
         out[i][k] +=in[i][j]*b[j][k];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   return out;    */
 }  }
   
   /*************************free ma3x ************************/
 /************* Higher Matrix Product ***************/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    free((FREE_ARG)(m+nrl-NR_END));
      duration (i.e. until  }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /*************** function subdirf ***********/
      (typically every 2 years instead of every month which is too big).  char *subdirf(char fileres[])
      Model is determined by parameters x and covariates have to be  {
      included manually here.    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
      */    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
   int i, j, d, h, k;    return tmpout;
   double **out, cov[NCOVMAX];  }
   double **newm;  
   /*************** function subdirf2 ***********/
   /* Hstepm could be zero and should return the unit matrix */  char *subdirf2(char fileres[], char *preop)
   for (i=1;i<=nlstate+ndeath;i++)  {
     for (j=1;j<=nlstate+ndeath;j++){    
       oldm[i][j]=(i==j ? 1.0 : 0.0);    /* Caution optionfilefiname is hidden */
       po[i][j][0]=(i==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,preop);
   for(h=1; h <=nhstepm; h++){    strcat(tmpout,fileres);
     for(d=1; d <=hstepm; d++){    return tmpout;
       newm=savm;  }
       /* Covariates have to be included here again */  
       cov[1]=1.;  /*************** function subdirf3 ***********/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
 for (k=1; k<=cptcovage;k++)    
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* Caution optionfilefiname is hidden */
    for (k=1; k<=cptcovprod;k++)    strcpy(tmpout,optionfilefiname);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,preop2);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    strcat(tmpout,fileres);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    return tmpout;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  /***************** f1dim *************************/
       oldm=newm;  extern int ncom; 
     }  extern double *pcom,*xicom;
     for(i=1; i<=nlstate+ndeath; i++)  extern double (*nrfunc)(double []); 
       for(j=1;j<=nlstate+ndeath;j++) {   
         po[i][j][h]=newm[i][j];  double f1dim(double x) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  { 
          */    int j; 
       }    double f;
   } /* end h */    double *xt; 
   return po;   
 }    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 /*************** log-likelihood *************/    free_vector(xt,1,ncom); 
 double func( double *x)    return f; 
 {  } 
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*****************brent *************************/
   double **out;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double sw; /* Sum of weights */  { 
   double lli; /* Individual log likelihood */    int iter; 
   long ipmx;    double a,b,d,etemp;
   /*extern weight */    double fu,fv,fw,fx;
   /* We are differentiating ll according to initial status */    double ftemp;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   /*for(i=1;i<imx;i++)    double e=0.0; 
 printf(" %d\n",s[4][i]);   
   */    a=(ax < cx ? ax : cx); 
   cov[1]=1.;    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    fw=fv=fx=(*f)(x); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (iter=1;iter<=ITMAX;iter++) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      xm=0.5*(a+b); 
        for(mi=1; mi<= wav[i]-1; mi++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       for (ii=1;ii<=nlstate+ndeath;ii++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf(".");fflush(stdout);
             for(d=0; d<dh[mi][i]; d++){      fprintf(ficlog,".");fflush(ficlog);
               newm=savm;  #ifdef DEBUG
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
               for (kk=1; kk<=cptcovage;kk++) {      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                  /*printf("%d %d",kk,Tage[kk]);*/  #endif
               }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/        *xmin=x; 
               /*cov[3]=pow(cov[2],2)/1000.;*/        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); 
     if (*fb > *fa) { 
   hess=matrix(1,npar,1,npar);      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
   printf("\nCalculation of the hessian matrix. Wait...\n");        } 
   for (i=1;i<=npar;i++){    *cx=(*bx)+GOLD*(*bx-*ax); 
     printf("%d",i);fflush(stdout);    *fc=(*func)(*cx); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    while (*fb > *fc) { 
     /*printf(" %f ",p[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); 
       }        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) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        u=ulim; 
          fu=(*func)(u); 
   a=matrix(1,npar,1,npar);      } else { 
   y=matrix(1,npar,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
   x=vector(1,npar);        fu=(*func)(u); 
   indx=ivector(1,npar);      } 
   for (i=1;i<=npar;i++)      SHFT(*ax,*bx,*cx,u) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        SHFT(*fa,*fb,*fc,fu) 
   ludcmp(a,npar,indx,&pd);        } 
   } 
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /*************** linmin ************************/
     x[j]=1;  
     lubksb(a,npar,indx,x);  int ncom; 
     for (i=1;i<=npar;i++){  double *pcom,*xicom;
       matcov[i][j]=x[i];  double (*nrfunc)(double []); 
     }   
   }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
   printf("\n#Hessian matrix#\n");    double brent(double ax, double bx, double cx, 
   for (i=1;i<=npar;i++) {                 double (*f)(double), double tol, double *xmin); 
     for (j=1;j<=npar;j++) {    double f1dim(double x); 
       printf("%.3e ",hess[i][j]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     }                double *fc, double (*func)(double)); 
     printf("\n");    int j; 
   }    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   /* Recompute Inverse */   
   for (i=1;i<=npar;i++)    ncom=n; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    pcom=vector(1,n); 
   ludcmp(a,npar,indx,&pd);    xicom=vector(1,n); 
     nrfunc=func; 
   /*  printf("\n#Hessian matrix recomputed#\n");    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   for (j=1;j<=npar;j++) {      xicom[j]=xi[j]; 
     for (i=1;i<=npar;i++) x[i]=0;    } 
     x[j]=1;    ax=0.0; 
     lubksb(a,npar,indx,x);    xx=1.0; 
     for (i=1;i<=npar;i++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       y[i][j]=x[i];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       printf("%.3e ",y[i][j]);  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }  #endif
   */    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
   free_matrix(a,1,npar,1,npar);      p[j] += xi[j]; 
   free_matrix(y,1,npar,1,npar);    } 
   free_vector(x,1,npar);    free_vector(xicom,1,n); 
   free_ivector(indx,1,npar);    free_vector(pcom,1,n); 
   free_matrix(hess,1,npar,1,npar);  } 
   
   char *asc_diff_time(long time_sec, char ascdiff[])
 }  {
     long sec_left, days, hours, minutes;
 /*************** hessian matrix ****************/    days = (time_sec) / (60*60*24);
 double hessii( double x[], double delta, int theta, double delti[])    sec_left = (time_sec) % (60*60*24);
 {    hours = (sec_left) / (60*60) ;
   int i;    sec_left = (sec_left) %(60*60);
   int l=1, lmax=20;    minutes = (sec_left) /60;
   double k1,k2;    sec_left = (sec_left) % (60);
   double p2[NPARMAX+1];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double res;    return ascdiff;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  }
   double fx;  
   int k=0,kmax=10;  /*************** powell ************************/
   double l1;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   fx=func(x);  { 
   for (i=1;i<=npar;i++) p2[i]=x[i];    void linmin(double p[], double xi[], int n, double *fret, 
   for(l=0 ; l <=lmax; l++){                double (*func)(double [])); 
     l1=pow(10,l);    int i,ibig,j; 
     delts=delt;    double del,t,*pt,*ptt,*xit;
     for(k=1 ; k <kmax; k=k+1){    double fp,fptt;
       delt = delta*(l1*k);    double *xits;
       p2[theta]=x[theta] +delt;    int niterf, itmp;
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;    pt=vector(1,n); 
       k2=func(p2)-fx;    ptt=vector(1,n); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    xit=vector(1,n); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    xits=vector(1,n); 
          *fret=(*func)(p); 
 #ifdef DEBUG    for (j=1;j<=n;j++) pt[j]=p[j]; 
       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);    for (*iter=1;;++(*iter)) { 
 #endif      fp=(*fret); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      ibig=0; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      del=0.0; 
         k=kmax;      last_time=curr_time;
       }      (void) gettimeofday(&curr_time,&tzp);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      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);
         k=kmax; l=lmax*10.;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
       }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){     for (i=1;i<=n;i++) {
         delts=delt;        printf(" %d %.12f",i, p[i]);
       }        fprintf(ficlog," %d %.12lf",i, p[i]);
     }        fprintf(ficrespow," %.12lf", p[i]);
   }      }
   delti[theta]=delts;      printf("\n");
   return res;      fprintf(ficlog,"\n");
        fprintf(ficrespow,"\n");fflush(ficrespow);
 }      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
 double hessij( double x[], double delti[], int thetai,int thetaj)        strcpy(strcurr,asctime(&tm));
 {  /*       asctime_r(&tm,strcurr); */
   int i;        forecast_time=curr_time; 
   int l=1, l1, lmax=20;        itmp = strlen(strcurr);
   double k1,k2,k3,k4,res,fx;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double p2[NPARMAX+1];          strcurr[itmp-1]='\0';
   int k;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   fx=func(x);        for(niterf=10;niterf<=30;niterf+=10){
   for (k=1; k<=2; k++) {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     for (i=1;i<=npar;i++) p2[i]=x[i];          tmf = *localtime(&forecast_time.tv_sec);
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*      asctime_r(&tmf,strfor); */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          strcpy(strfor,asctime(&tmf));
     k1=func(p2)-fx;          itmp = strlen(strfor);
            if(strfor[itmp-1]=='\n')
     p2[thetai]=x[thetai]+delti[thetai]/k;          strfor[itmp-1]='\0';
     p2[thetaj]=x[thetaj]-delti[thetaj]/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);
     k2=func(p2)-fx;          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);
          }
     p2[thetai]=x[thetai]-delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      for (i=1;i<=n;i++) { 
     k3=func(p2)-fx;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
          fptt=(*fret); 
     p2[thetai]=x[thetai]-delti[thetai]/k;  #ifdef DEBUG
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        printf("fret=%lf \n",*fret);
     k4=func(p2)-fx;        fprintf(ficlog,"fret=%lf \n",*fret);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #endif
 #ifdef DEBUG        printf("%d",i);fflush(stdout);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif        linmin(p,xit,n,fret,func); 
   }        if (fabs(fptt-(*fret)) > del) { 
   return res;          del=fabs(fptt-(*fret)); 
 }          ibig=i; 
         } 
 /************** Inverse of matrix **************/  #ifdef DEBUG
 void ludcmp(double **a, int n, int *indx, double *d)        printf("%d %.12e",i,(*fret));
 {        fprintf(ficlog,"%d %.12e",i,(*fret));
   int i,imax,j,k;        for (j=1;j<=n;j++) {
   double big,dum,sum,temp;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double *vv;          printf(" x(%d)=%.12e",j,xit[j]);
            fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   vv=vector(1,n);        }
   *d=1.0;        for(j=1;j<=n;j++) {
   for (i=1;i<=n;i++) {          printf(" p=%.12e",p[j]);
     big=0.0;          fprintf(ficlog," p=%.12e",p[j]);
     for (j=1;j<=n;j++)        }
       if ((temp=fabs(a[i][j])) > big) big=temp;        printf("\n");
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        fprintf(ficlog,"\n");
     vv[i]=1.0/big;  #endif
   }      } 
   for (j=1;j<=n;j++) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for (i=1;i<j;i++) {  #ifdef DEBUG
       sum=a[i][j];        int k[2],l;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        k[0]=1;
       a[i][j]=sum;        k[1]=-1;
     }        printf("Max: %.12e",(*func)(p));
     big=0.0;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for (i=j;i<=n;i++) {        for (j=1;j<=n;j++) {
       sum=a[i][j];          printf(" %.12e",p[j]);
       for (k=1;k<j;k++)          fprintf(ficlog," %.12e",p[j]);
         sum -= a[i][k]*a[k][j];        }
       a[i][j]=sum;        printf("\n");
       if ( (dum=vv[i]*fabs(sum)) >= big) {        fprintf(ficlog,"\n");
         big=dum;        for(l=0;l<=1;l++) {
         imax=i;          for (j=1;j<=n;j++) {
       }            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]);
     if (j != imax) {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (k=1;k<=n;k++) {          }
         dum=a[imax][k];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         a[imax][k]=a[j][k];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         a[j][k]=dum;        }
       }  #endif
       *d = -(*d);  
       vv[imax]=vv[j];  
     }        free_vector(xit,1,n); 
     indx[j]=imax;        free_vector(xits,1,n); 
     if (a[j][j] == 0.0) a[j][j]=TINY;        free_vector(ptt,1,n); 
     if (j != n) {        free_vector(pt,1,n); 
       dum=1.0/(a[j][j]);        return; 
       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++) { 
   free_vector(vv,1,n);  /* Doesn't work */        ptt[j]=2.0*p[j]-pt[j]; 
 ;        xit[j]=p[j]-pt[j]; 
 }        pt[j]=p[j]; 
       } 
 void lubksb(double **a, int n, int *indx, double b[])      fptt=(*func)(ptt); 
 {      if (fptt < fp) { 
   int i,ii=0,ip,j;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double sum;        if (t < 0.0) { 
            linmin(p,xit,n,fret,func); 
   for (i=1;i<=n;i++) {          for (j=1;j<=n;j++) { 
     ip=indx[i];            xi[j][ibig]=xi[j][n]; 
     sum=b[ip];            xi[j][n]=xit[j]; 
     b[ip]=b[i];          }
     if (ii)  #ifdef DEBUG
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     else if (sum) ii=i;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     b[i]=sum;          for(j=1;j<=n;j++){
   }            printf(" %.12e",xit[j]);
   for (i=n;i>=1;i--) {            fprintf(ficlog," %.12e",xit[j]);
     sum=b[i];          }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          printf("\n");
     b[i]=sum/a[i][i];          fprintf(ficlog,"\n");
   }  #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 ***freq; /* Frequencies */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double *pp;  {
   double pos;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   FILE *ficresp;       matrix by transitions matrix until convergence is reached */
   char fileresp[FILENAMELENGTH];  
     int i, ii,j,k;
   pp=vector(1,nlstate);    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   strcpy(fileresp,"p");    double **out, cov[NCOVMAX], **pmij();
   strcat(fileresp,fileres);    double **newm;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double agefin, delaymax=50 ; /* Max number of years to converge */
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j1=0;      }
   
   j=cptcoveff;     cov[1]=1.;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(k1=1; k1<=j;k1++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
    for(i1=1; i1<=ncodemax[k1];i1++){      newm=savm;
        j1++;      /* Covariates have to be included here again */
        cov[2]=agefin;
         for (i=-1; i<=nlstate+ndeath; i++)      
          for (jk=-1; jk<=nlstate+ndeath; jk++)          for (k=1; k<=cptcovn;k++) {
            for(m=agemin; m <= agemax+3; m++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
              freq[i][jk][m]=0;          /*      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 (i=1; i<=imx; i++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          bool=1;        for (k=1; k<=cptcovprod;k++)
          if  (cptcovn>0) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;        /*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]);*/
           if (bool==1) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
            for(m=firstpass; m<=lastpass-1; m++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
              if(agev[m][i]==0) agev[m][i]=agemax+1;  
              if(agev[m][i]==1) agev[m][i]=agemax+2;      savm=oldm;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      oldm=newm;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      maxmax=0.;
            }      for(j=1;j<=nlstate;j++){
          }        min=1.;
        }        max=0.;
         if  (cptcovn>0) {        for(i=1; i<=nlstate; i++) {
          fprintf(ficresp, "\n#********** Variable ");          sumnew=0;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
        }          prlim[i][j]= newm[i][j]/(1-sumnew);
        fprintf(ficresp, "**********\n#");          max=FMAX(max,prlim[i][j]);
        for(i=1; i<=nlstate;i++)          min=FMIN(min,prlim[i][j]);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        }
        fprintf(ficresp, "\n");        maxmin=max-min;
                maxmax=FMAX(maxmax,maxmin);
   for(i=(int)agemin; i <= (int)agemax+3; i++){      }
     if(i==(int)agemax+3)      if(maxmax < ftolpl){
       printf("Total");        return prlim;
     else      }
       printf("Age %d", i);    }
     for(jk=1; jk <=nlstate ; jk++){  }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
         pp[jk] += freq[jk][m][i];  /*************** transition probabilities ***************/ 
     }  
     for(jk=1; jk <=nlstate ; jk++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(m=-1, pos=0; m <=0 ; m++)  {
         pos += freq[jk][m][i];    double s1, s2;
       if(pp[jk]>=1.e-10)    /*double t34;*/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    int i,j,j1, nc, ii, jj;
       else  
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      for(i=1; i<= nlstate; i++){
     }        for(j=1; j<i;j++){
     for(jk=1; jk <=nlstate ; jk++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)            /*s2 += param[i][j][nc]*cov[nc];*/
         pp[jk] += freq[jk][m][i];            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); */
     for(jk=1,pos=0; jk <=nlstate ; jk++)          }
       pos += pp[jk];          ps[i][j]=s2;
     for(jk=1; jk <=nlstate ; jk++){  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       if(pos>=1.e-5)        }
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for(j=i+1; j<=nlstate+ndeath;j++){
       else          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       if( i <= (int) agemax){  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         if(pos>=1.e-5)          }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          ps[i][j]=s2;
       else        }
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      }
       }      /*ps[3][2]=1;*/
     }      
     for(jk=-1; jk <=nlstate+ndeath; jk++)      for(i=1; i<= nlstate; i++){
       for(m=-1; m <=nlstate+ndeath; m++)        s1=0;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        for(j=1; j<i; j++)
     if(i <= (int) agemax)          s1+=exp(ps[i][j]);
       fprintf(ficresp,"\n");        for(j=i+1; j<=nlstate+ndeath; j++)
     printf("\n");          s1+=exp(ps[i][j]);
     }        ps[i][i]=1./(s1+1.);
     }        for(j=1; j<i; j++)
  }          ps[i][j]= exp(ps[i][j])*ps[i][i];
          for(j=i+1; j<=nlstate+ndeath; j++)
   fclose(ficresp);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   free_vector(pp,1,nlstate);      } /* end i */
       
 }  /* End of Freq */      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jj=1; jj<= nlstate+ndeath; jj++){
 /************* Waves Concatenation ***************/          ps[ii][jj]=0;
           ps[ii][ii]=1;
 void  concatwav(int wav[], int **dh, 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).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
      and mw[mi+1][i]. dh depends on stepm.  /*         printf("ddd %lf ",ps[ii][jj]); */
      */  /*       } */
   /*       printf("\n "); */
   int i, mi, m;  /*        } */
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  /*        printf("\n ");printf("%lf ",cov[2]); */
 float sum=0.;         /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for(i=1; i<=imx; i++){        goto end;*/
     mi=0;      return ps;
     m=firstpass;  }
     while(s[m][i] <= nlstate){  
       if(s[m][i]>=1)  /**************** Product of 2 matrices ******************/
         mw[++mi][i]=m;  
       if(m >=lastpass)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         break;  {
       else    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         m++;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     }/* end while */    /* in, b, out are matrice of pointers which should have been initialized 
     if (s[m][i] > nlstate){       before: only the contents of out is modified. The function returns
       mi++;     /* Death is another wave */       a pointer to pointers identical to out */
       /* if(mi==0)  never been interviewed correctly before death */    long i, j, k;
          /* Only death is a correct wave */    for(i=nrl; i<= nrh; i++)
       mw[mi][i]=m;      for(k=ncolol; k<=ncoloh; k++)
     }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
     wav[i]=mi;  
     if(mi==0)    return out;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  }
   }  
   
   for(i=1; i<=imx; i++){  /************* Higher Matrix Product ***************/
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         dh[mi][i]=1;  {
       else{    /* Computes the transition matrix starting at age 'age' over 
         if (s[mw[mi+1][i]][i] > nlstate) {       'nhstepm*hstepm*stepm' months (i.e. until
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           if(j=0) j=1;  /* Survives at least one month after exam */       nhstepm*hstepm matrices. 
         }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         else{       (typically every 2 years instead of every month which is too big 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));       for the memory).
           k=k+1;       Model is determined by parameters x and covariates have to be 
           if (j >= jmax) jmax=j;       included manually here. 
           else if (j <= jmin)jmin=j;  
           sum=sum+j;       */
         }  
         jk= j/stepm;    int i, j, d, h, k;
         jl= j -jk*stepm;    double **out, cov[NCOVMAX];
         ju= j -(jk+1)*stepm;    double **newm;
         if(jl <= -ju)  
           dh[mi][i]=jk;    /* Hstepm could be zero and should return the unit matrix */
         else    for (i=1;i<=nlstate+ndeath;i++)
           dh[mi][i]=jk+1;      for (j=1;j<=nlstate+ndeath;j++){
         if(dh[mi][i]==0)        oldm[i][j]=(i==j ? 1.0 : 0.0);
           dh[mi][i]=1; /* At least one step */        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }      }
     }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(h=1; h <=nhstepm; h++){
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);      for(d=1; d <=hstepm; d++){
 }        newm=savm;
 /*********** Tricode ****************************/        /* Covariates have to be included here again */
 void tricode(int *Tvar, int **nbcode, int imx)        cov[1]=1.;
 {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int Ndum[20],ij=1, k, j, i;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int cptcode=0;        for (k=1; k<=cptcovage;k++)
   cptcoveff=0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
   for (k=0; k<19; k++) Ndum[k]=0;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for (k=1; k<=7; k++) ncodemax[k]=0;  
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (i=1; i<=imx; i++) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       ij=(int)(covar[Tvar[j]][i]);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       Ndum[ij]++;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       if (ij > cptcode) cptcode=ij;        savm=oldm;
     }        oldm=newm;
       }
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/      for(i=1; i<=nlstate+ndeath; i++)
     for (i=0; i<=cptcode; i++) {        for(j=1;j<=nlstate+ndeath;j++) {
       if(Ndum[i]!=0) ncodemax[j]++;          po[i][j][h]=newm[i][j];
     }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     ij=1;           */
         }
     for (i=1; i<=ncodemax[j]; i++) {    } /* end h */
       for (k=0; k<=19; k++) {    return po;
         if (Ndum[k] != 0) {  }
           nbcode[Tvar[j]][ij]=k;  
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/  
           ij++;  /*************** log-likelihood *************/
         }  double func( double *x)
         if (ij > ncodemax[j]) break;  {
       }      int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   }      double **out;
  for (i=1; i<=10; i++) {    double sw; /* Sum of weights */
       ij=Tvar[i];    double lli; /* Individual log likelihood */
       Ndum[ij]++;    int s1, s2;
     }    double bbh, survp;
  ij=1;    long ipmx;
  for (i=1; i<=cptcovn; i++) {    /*extern weight */
    if((Ndum[i]!=0) && (i<=ncov)){    /* We are differentiating ll according to initial status */
      Tvaraff[i]=ij;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
    ij++;    /*for(i=1;i<imx;i++) 
    }      printf(" %d\n",s[4][i]);
  }    */
      cov[1]=1.;
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];    for(k=1; k<=nlstate; k++) ll[k]=0.;
    /*printf("j=%d %d\n",j,Tvar[j]);*/  
  }    if(mle==1){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     scanf("%d",i);*/        for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 /*********** Health Expectancies ****************/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            }
 {          for(d=0; d<dh[mi][i]; d++){
   /* Health expectancies */            newm=savm;
   int i, j, nhstepm, hstepm, h;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double age, agelim,hf;            for (kk=1; kk<=cptcovage;kk++) {
   double ***p3mat;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   fprintf(ficreseij,"# Health expectancies\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficreseij,"# Age");                         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;
       fprintf(ficreseij," %1d-%1d",i,j);          } /* end mult */
   fprintf(ficreseij,"\n");        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   hstepm=1*YEARM; /*  Every j years of age (in month) */          /* But now since version 0.9 we anticipate for bias at large stepm.
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */           * 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 
   agelim=AGESUP;           * the nearest (and in case of equal distance, to the lowest) interval but now
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     /* nhstepm age range expressed in number of stepm */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);           * probability in order to take into account the bias as a fraction of the way
     /* Typically if 20 years = 20*12/6=40 stepm */           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     if (stepm >= YEARM) hstepm=1;           * -stepm/2 to stepm/2 .
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */           * For stepm=1 the results are the same as for previous versions of Imach.
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * For stepm > 1 the results are less biased than in previous versions. 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored           */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          s1=s[mw[mi][i]][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
     for(i=1; i<=nlstate;i++)           * is higher than the multiple of stepm and negative otherwise.
       for(j=1; j<=nlstate;j++)           */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           eij[i][j][(int)age] +=p3mat[i][j][h];          if( s2 > nlstate){ 
         }            /* i.e. if s2 is a death state and if the date of death is known 
                   then the contribution to the likelihood is the probability to 
     hf=1;               die between last step unit time and current  step unit time, 
     if (stepm >= YEARM) hf=stepm/YEARM;               which is also equal to probability to die before dh 
     fprintf(ficreseij,"%.0f",age );               minus probability to die before dh-stepm . 
     for(i=1; i<=nlstate;i++)               In version up to 0.92 likelihood was computed
       for(j=1; j<=nlstate;j++){          as if date of death was unknown. Death was treated as any other
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          health state: the date of the interview describes the actual state
       }          and not the date of a change in health state. The former idea was
     fprintf(ficreseij,"\n");          to consider that at each interview the state was recorded
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          (healthy, disable or death) and IMaCh was corrected; but when we
   }          introduced the exact date of death then we should have modified
 }          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
 /************ Variance ******************/          stepm. It is no more the probability to die between last interview
 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)          and month of death but the probability to survive from last
 {          interview up to one month before death multiplied by the
   /* Variance of health expectancies */          probability to die within a month. Thanks to Chris
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          Jackson for correcting this bug.  Former versions increased
   double **newm;          mortality artificially. The bad side is that we add another loop
   double **dnewm,**doldm;          which slows down the processing. The difference can be up to 10%
   int i, j, nhstepm, hstepm, h;          lower mortality.
   int k, cptcode;            */
    double *xp;            lli=log(out[s1][s2] - savm[s1][s2]);
   double **gp, **gm;  
   double ***gradg, ***trgradg;  
   double ***p3mat;          } else if  (s2==-2) {
   double age,agelim;            for (j=1,survp=0. ; j<=nlstate; j++) 
   int theta;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
    fprintf(ficresvij,"# Covariances of life expectancies\n");            lli= log(survp);
   fprintf(ficresvij,"# Age");          }
   for(i=1; i<=nlstate;i++)          
     for(j=1; j<=nlstate;j++)          else if  (s2==-4) { 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for (j=3,survp=0. ; j<=nlstate; j++)  
   fprintf(ficresvij,"\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   xp=vector(1,npar);          } 
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);          else if  (s2==-5) { 
              for (j=1,survp=0. ; j<=2; j++)  
   hstepm=1*YEARM; /* Every year of age */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            lli= log(survp); 
   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 */          else{
     if (stepm >= YEARM) hstepm=1;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            /*  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 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     gp=matrix(0,nhstepm,1,nlstate);          /*if(lli ==000.0)*/
     gm=matrix(0,nhstepm,1,nlstate);          /*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); */
           ipmx +=1;
     for(theta=1; theta <=npar; theta++){          sw += weight[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } /* end of wave */
       }      } /* end of individual */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      }  else if(mle==2){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<= nlstate; j++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(h=0; h<=nhstepm; h++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
       for(i=1; i<=npar; i++) /* Computes gradient */          for(d=0; d<=dh[mi][i]; d++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            newm=savm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<= nlstate; j++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       }            oldm=newm;
       for(j=1; j<= nlstate; j++)          } /* end mult */
         for(h=0; h<=nhstepm; h++){        
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
     } /* End theta */          bbh=(double)bh[mi][i]/(double)stepm; 
           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 */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          ipmx +=1;
           sw += weight[i];
     for(h=0; h<=nhstepm; h++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<=nlstate;j++)        } /* end of wave */
         for(theta=1; theta <=npar; theta++)      } /* end of individual */
           trgradg[h][j][theta]=gradg[h][theta][j];    }  else if(mle==3){  /* exponential inter-extrapolation */
       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++){
         vareij[i][j][(int)age] =0.;          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(h=0;h<=nhstepm;h++){            for (j=1;j<=nlstate+ndeath;j++){
       for(k=0;k<=nhstepm;k++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            }
         for(i=1;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
           for(j=1;j<=nlstate;j++)            newm=savm;
             vareij[i][j][(int)age] += doldm[i][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     h=1;            }
     if (stepm >= YEARM) h=stepm/YEARM;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficresvij,"%.0f ",age );                         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;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          } /* end mult */
       }        
     fprintf(ficresvij,"\n");          s1=s[mw[mi][i]][i];
     free_matrix(gp,0,nhstepm,1,nlstate);          s2=s[mw[mi+1][i]][i];
     free_matrix(gm,0,nhstepm,1,nlstate);          bbh=(double)bh[mi][i]/(double)stepm; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          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 */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          ipmx +=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sw += weight[i];
   } /* End age */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   free_vector(xp,1,npar);      } /* end of individual */
   free_matrix(doldm,1,nlstate,1,npar);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************ Variance of prevlim ******************/            for (j=1;j<=nlstate+ndeath;j++){
 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)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Variance of prevalence limit */            }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(d=0; d<dh[mi][i]; d++){
   double **newm;            newm=savm;
   double **dnewm,**doldm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, j, nhstepm, hstepm;            for (kk=1; kk<=cptcovage;kk++) {
   int k, cptcode;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *xp;            }
   double *gp, *gm;          
   double **gradg, **trgradg;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double age,agelim;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int theta;            savm=oldm;
                oldm=newm;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          } /* end mult */
   fprintf(ficresvpl,"# Age");        
   for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
       fprintf(ficresvpl," %1d-%1d",i,i);          s2=s[mw[mi+1][i]][i];
   fprintf(ficresvpl,"\n");          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
   xp=vector(1,npar);          }else{
   dnewm=matrix(1,nlstate,1,npar);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   doldm=matrix(1,nlstate,1,nlstate);          }
            ipmx +=1;
   hstepm=1*YEARM; /* Every year of age */          sw += weight[i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   agelim = AGESUP;  /*      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 (age=bage; age<=fage; age ++){ /* If stepm=6 months */        } /* end of wave */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* end of individual */
     if (stepm >= YEARM) hstepm=1;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gradg=matrix(1,npar,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gp=vector(1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
     gm=vector(1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     for(theta=1; theta <=npar; theta++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++){ /* Computes gradient */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            }
       }          for(d=0; d<dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
       for(i=1;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         gp[i] = prlim[i][i];            for (kk=1; kk<=cptcovage;kk++) {
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       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);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         gm[i] = prlim[i][i];            savm=oldm;
             oldm=newm;
       for(i=1;i<=nlstate;i++)          } /* end mult */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        
     } /* End theta */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     trgradg =matrix(1,nlstate,1,npar);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
     for(j=1; j<=nlstate;j++)          sw += weight[i];
       for(theta=1; theta <=npar; theta++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         trgradg[j][theta]=gradg[theta][j];          /*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]);*/
         } /* end of wave */
     for(i=1;i<=nlstate;i++)      } /* end of individual */
       varpl[i][(int)age] =0.;    } /* End of if */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for(i=1;i<=nlstate;i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    return -l;
   }
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /*************** log-likelihood *************/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  double funcone( double *x)
     fprintf(ficresvpl,"\n");  {
     free_vector(gp,1,nlstate);    /* Same as likeli but slower because of a lot of printf and if */
     free_vector(gm,1,nlstate);    int i, ii, j, k, mi, d, kk;
     free_matrix(gradg,1,npar,1,nlstate);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     free_matrix(trgradg,1,nlstate,1,npar);    double **out;
   } /* End age */    double lli; /* Individual log likelihood */
     double llt;
   free_vector(xp,1,npar);    int s1, s2;
   free_matrix(doldm,1,nlstate,1,npar);    double bbh, survp;
   free_matrix(dnewm,1,nlstate,1,nlstate);    /*extern weight */
     /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     */
 /***********************************************/    cov[1]=1.;
 /**************** Main Program *****************/  
 /***********************************************/    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 /*int main(int argc, char *argv[])*/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 int main()      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;          for (j=1;j<=nlstate+ndeath;j++){
   double agedeb, agefin,hf;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double agemin=1.e20, agemax=-1.e20;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   double fret;        for(d=0; d<dh[mi][i]; d++){
   double **xi,tmp,delta;          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double dum; /* Dummy variable */          for (kk=1; kk<=cptcovage;kk++) {
   double ***p3mat;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int *indx;          }
   char line[MAXLINE], linepar[MAXLINE];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   char title[MAXLINE];                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          savm=oldm;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];          oldm=newm;
   char filerest[FILENAMELENGTH];        } /* end mult */
   char fileregp[FILENAMELENGTH];        
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        s1=s[mw[mi][i]][i];
   int firstobs=1, lastobs=10;        s2=s[mw[mi+1][i]][i];
   int sdeb, sfin; /* Status at beginning and end */        bbh=(double)bh[mi][i]/(double)stepm; 
   int c,  h , cpt,l;        /* bias is positive if real duration
   int ju,jl, mi;         * is higher than the multiple of stepm and negative otherwise.
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;         */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
            lli=log(out[s1][s2] - savm[s1][s2]);
   int hstepm, nhstepm;        } else if  (s2==-2) {
   double bage, fage, age, agelim, agebase;          for (j=1,survp=0. ; j<=nlstate; j++) 
   double ftolpl=FTOL;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double **prlim;          lli= log(survp);
   double *severity;        }else if (mle==1){
   double ***param; /* Matrix of parameters */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double  *p;        } else if(mle==2){
   double **matcov; /* Matrix of covariance */          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 */
   double ***delti3; /* Scale */        } else if(mle==3){  /* exponential inter-extrapolation */
   double *delti; /* Scale */          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double ***eij, ***vareij;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **varpl; /* Variances of prevalence limits by age */          lli=log(out[s1][s2]); /* Original formula */
   double *epj, vepp;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";          lli=log(out[s1][s2]); /* Original formula */
   char *alph[]={"a","a","b","c","d","e"}, str[4];        } /* End of if */
         ipmx +=1;
   char z[1]="c", occ;        sw += weight[i];
 #include <sys/time.h>        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 #include <time.h>  /*       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]); */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        if(globpr){
   /* long total_usecs;          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   struct timeval start_time, end_time;   %11.6f %11.6f %11.6f ", \
                    num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
   printf("\nIMACH, Version 0.64a");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   printf("\nEnter the parameter file name: ");          }
           fprintf(ficresilk," %10.6f\n", -llt);
 #ifdef windows        }
   scanf("%s",pathtot);      } /* end of wave */
   getcwd(pathcd, size);    } /* end of individual */
   /*cygwin_split_path(pathtot,path,optionfile);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /* cutv(path,optionfile,pathtot,'\\');*/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
 split(pathtot, path,optionfile);      gipmx=ipmx;
   chdir(path);      gsw=sw;
   replace(pathc,path);    }
 #endif    return -l;
 #ifdef unix  }
   scanf("%s",optionfile);  
 #endif  
   /*************** function likelione ***********/
 /*-------- arguments in the command line --------*/  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
   strcpy(fileres,"r");    /* This routine should help understanding what is done with 
   strcat(fileres, optionfile);       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
   /*---------arguments file --------*/       Plotting could be done.
      */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    int k;
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    if(*globpri !=0){ /* Just counts and sums, no printings */
   }      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
   strcpy(filereso,"o");      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   strcat(filereso,fileres);        printf("Problem with resultfile: %s\n", fileresilk);
   if((ficparo=fopen(filereso,"w"))==NULL) {        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      }
   }      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");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   /* Reads comments: lines beginning with '#' */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   while((c=getc(ficpar))=='#' && c!= EOF){      for(k=1; k<=nlstate; k++) 
     ungetc(c,ficpar);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     fgets(line, MAXLINE, ficpar);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     puts(line);    }
     fputs(line,ficparo);  
   }    *fretone=(*funcone)(p);
   ungetc(c,ficpar);    if(*globpri !=0){
       fclose(ficresilk);
   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);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   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);      fflush(fichtm); 
   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);    } 
     return;
   covar=matrix(0,NCOVMAX,1,n);      }
   if (strlen(model)<=1) cptcovn=0;  
   else {  
     j=0;  /*********** Maximum Likelihood Estimation ***************/
     j=nbocc(model,'+');  
     cptcovn=j+1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
     int i,j, iter;
   ncovmodel=2+cptcovn;    double **xi;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double fret;
      double fretone; /* Only one call to likelihood */
   /* Read guess parameters */    /*  char filerespow[FILENAMELENGTH];*/
   /* Reads comments: lines beginning with '#' */    xi=matrix(1,npar,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=npar;i++)
     ungetc(c,ficpar);      for (j=1;j<=npar;j++)
     fgets(line, MAXLINE, ficpar);        xi[i][j]=(i==j ? 1.0 : 0.0);
     puts(line);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     fputs(line,ficparo);    strcpy(filerespow,"pow"); 
   }    strcat(filerespow,fileres);
   ungetc(c,ficpar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", filerespow);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(i=1; i <=nlstate; i++)    }
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (i=1;i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);      for(j=1;j<=nlstate+ndeath;j++)
       printf("%1d%1d",i,j);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       for(k=1; k<=ncovmodel;k++){    fprintf(ficrespow,"\n");
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);    powell(p,xi,npar,ftol,&iter,&fret,func);
         fprintf(ficparo," %lf",param[i][j][k]);  
       }    free_matrix(xi,1,npar,1,npar);
       fscanf(ficpar,"\n");    fclose(ficrespow);
       printf("\n");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       fprintf(ficparo,"\n");    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  }
   p=param[1][1];  
    /**** Computes Hessian and covariance matrix ***/
   /* Reads comments: lines beginning with '#' */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    double  **a,**y,*x,pd;
     fgets(line, MAXLINE, ficpar);    double **hess;
     puts(line);    int i, j,jk;
     fputs(line,ficparo);    int *indx;
   }  
   ungetc(c,ficpar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    void lubksb(double **a, int npar, int *indx, double b[]) ;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    void ludcmp(double **a, int npar, int *indx, double *d) ;
   for(i=1; i <=nlstate; i++){    double gompertz(double p[]);
     for(j=1; j <=nlstate+ndeath-1; j++){    hess=matrix(1,npar,1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    printf("\nCalculation of the hessian matrix. Wait...\n");
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       for(k=1; k<=ncovmodel;k++){    for (i=1;i<=npar;i++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);      printf("%d",i);fflush(stdout);
         printf(" %le",delti3[i][j][k]);      fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficparo," %le",delti3[i][j][k]);     
       }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       fscanf(ficpar,"\n");      
       printf("\n");      /*  printf(" %f ",p[i]);
       fprintf(ficparo,"\n");          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }    }
   }    
   delti=delti3[1][1];    for (i=1;i<=npar;i++) {
        for (j=1;j<=npar;j++)  {
   /* Reads comments: lines beginning with '#' */        if (j>i) { 
   while((c=getc(ficpar))=='#' && c!= EOF){          printf(".%d%d",i,j);fflush(stdout);
     ungetc(c,ficpar);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     fgets(line, MAXLINE, ficpar);          hess[i][j]=hessij(p,delti,i,j,func,npar);
     puts(line);          
     fputs(line,ficparo);          hess[j][i]=hess[i][j];    
   }          /*printf(" %lf ",hess[i][j]);*/
   ungetc(c,ficpar);        }
        }
   matcov=matrix(1,npar,1,npar);    }
   for(i=1; i <=npar; i++){    printf("\n");
     fscanf(ficpar,"%s",&str);    fprintf(ficlog,"\n");
     printf("%s",str);  
     fprintf(ficparo,"%s",str);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(j=1; j <=i; j++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       fscanf(ficpar," %le",&matcov[i][j]);    
       printf(" %.5le",matcov[i][j]);    a=matrix(1,npar,1,npar);
       fprintf(ficparo," %.5le",matcov[i][j]);    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
     fscanf(ficpar,"\n");    indx=ivector(1,npar);
     printf("\n");    for (i=1;i<=npar;i++)
     fprintf(ficparo,"\n");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   }    ludcmp(a,npar,indx,&pd);
   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];      for (i=1;i<=npar;i++) x[i]=0;
          x[j]=1;
   printf("\n");      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
     /*-------- data file ----------*/      }
     if((ficres =fopen(fileres,"w"))==NULL) {    }
       printf("Problem with resultfile: %s\n", fileres);goto end;  
     }    printf("\n#Hessian matrix#\n");
     fprintf(ficres,"#%s\n",version);    fprintf(ficlog,"\n#Hessian matrix#\n");
        for (i=1;i<=npar;i++) { 
     if((fic=fopen(datafile,"r"))==NULL)    {      for (j=1;j<=npar;j++) { 
       printf("Problem with datafile: %s\n", datafile);goto end;        printf("%.3e ",hess[i][j]);
     }        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
     n= lastobs;      printf("\n");
     severity = vector(1,maxwav);      fprintf(ficlog,"\n");
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);  
     moisnais=vector(1,n);    /* Recompute Inverse */
     annais=vector(1,n);    for (i=1;i<=npar;i++)
     moisdc=vector(1,n);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     andc=vector(1,n);    ludcmp(a,npar,indx,&pd);
     agedc=vector(1,n);  
     cod=ivector(1,n);    /*  printf("\n#Hessian matrix recomputed#\n");
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    for (j=1;j<=npar;j++) {
     mint=matrix(1,maxwav,1,n);      for (i=1;i<=npar;i++) x[i]=0;
     anint=matrix(1,maxwav,1,n);      x[j]=1;
     s=imatrix(1,maxwav+1,1,n);      lubksb(a,npar,indx,x);
     adl=imatrix(1,maxwav+1,1,n);          for (i=1;i<=npar;i++){ 
     tab=ivector(1,NCOVMAX);        y[i][j]=x[i];
     ncodemax=ivector(1,8);        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
     i=1;      }
     while (fgets(line, MAXLINE, fic) != NULL)    {      printf("\n");
       if ((i >= firstobs) && (i <=lastobs)) {      fprintf(ficlog,"\n");
            }
         for (j=maxwav;j>=1;j--){    */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);    free_matrix(a,1,npar,1,npar);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(y,1,npar,1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(x,1,npar);
         }    free_ivector(indx,1,npar);
            free_matrix(hess,1,npar,1,npar);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
   }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  {
         for (j=ncov;j>=1;j--){    int i;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int l=1, lmax=20;
         }    double k1,k2;
         num[i]=atol(stra);    double p2[NPARMAX+1];
     double res;
         /*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]));*/    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
         i=i+1;    int k=0,kmax=10;
       }    double l1;
     }  
     fx=func(x);
     /*scanf("%d",i);*/    for (i=1;i<=npar;i++) p2[i]=x[i];
   imx=i-1; /* Number of individuals */    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
   /* Calculation of the number of parameter from char model*/      delts=delt;
   Tvar=ivector(1,15);      for(k=1 ; k <kmax; k=k+1){
   Tprod=ivector(1,15);        delt = delta*(l1*k);
   Tvaraff=ivector(1,15);        p2[theta]=x[theta] +delt;
   Tvard=imatrix(1,15,1,2);        k1=func(p2)-fx;
   Tage=ivector(1,15);              p2[theta]=x[theta]-delt;
            k2=func(p2)-fx;
   if (strlen(model) >1){        /*res= (k1-2.0*fx+k2)/delt/delt; */
     j=0, j1=0, k1=1, k2=1;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     j=nbocc(model,'+');        
     j1=nbocc(model,'*');  #ifdef DEBUG
     cptcovn=j+1;        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);
     cptcovprod=j1;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
      #endif
     strcpy(modelsav,model);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
    if (j==0) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       if (j1==0){          k=kmax;
         cutv(stra,strb,modelsav,'V');        }
         Tvar[1]=atoi(strb);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       }          k=kmax; l=lmax*10.;
       else if (j1==1) {        }
         cutv(stra,strb,modelsav,'*');        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         Tage[1]=1; cptcovage++;          delts=delt;
         if (strcmp(stra,"age")==0) {        }
           cptcovprod--;      }
           cutv(strd,strc,strb,'V');    }
           Tvar[1]=atoi(strc);    delti[theta]=delts;
         }    return res; 
         else if (strcmp(strb,"age")==0) {    
           cptcovprod--;  }
           cutv(strd,strc,stra,'V');  
           Tvar[1]=atoi(strc);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         }  {
         else {    int i;
           cutv(strd,strc,strb,'V');    int l=1, l1, lmax=20;
           cutv(stre,strd,stra,'V');    double k1,k2,k3,k4,res,fx;
           Tvar[1]=ncov+1;    double p2[NPARMAX+1];
           for (k=1; k<=lastobs;k++)    int k;
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];  
         }    fx=func(x);
         /*printf("%s %s %s\n", stra,strb,modelsav);    for (k=1; k<=2; k++) {
 printf("%d ",Tvar[1]);      for (i=1;i<=npar;i++) p2[i]=x[i];
 scanf("%d",i);*/      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }      k1=func(p2)-fx;
    else {    
       for(i=j; i>=1;i--){      p2[thetai]=x[thetai]+delti[thetai]/k;
         cutv(stra,strb,modelsav,'+');      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         /*printf("%s %s %s\n", stra,strb,modelsav);      k2=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) {      k3=func(p2)-fx;
             cptcovprod--;    
             cutv(strb,stre,strd,'V');      p2[thetai]=x[thetai]-delti[thetai]/k;
             Tvar[i+1]=atoi(stre);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             cptcovage++;      k4=func(p2)-fx;
             Tage[cptcovage]=i+1;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
             printf("stre=%s ", stre);  #ifdef DEBUG
           }      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);
           else if (strcmp(strd,"age")==0) {      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);
             cptcovprod--;  #endif
             cutv(strb,stre,strc,'V');    }
             Tvar[i+1]=atoi(stre);    return res;
             cptcovage++;  }
             Tage[cptcovage]=i+1;  
           }  /************** Inverse of matrix **************/
           else {  void ludcmp(double **a, int n, int *indx, double *d) 
             cutv(strb,stre,strc,'V');  { 
             Tvar[i+1]=ncov+k1;    int i,imax,j,k; 
             cutv(strb,strc,strd,'V');    double big,dum,sum,temp; 
             Tprod[k1]=i+1;    double *vv; 
             Tvard[k1][1]=atoi(strc);   
             Tvard[k1][2]=atoi(stre);    vv=vector(1,n); 
             Tvar[cptcovn+k2]=Tvard[k1][1];    *d=1.0; 
             Tvar[cptcovn+k2+1]=Tvard[k1][2];    for (i=1;i<=n;i++) { 
             for (k=1; k<=lastobs;k++)      big=0.0; 
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for (j=1;j<=n;j++) 
             k1++;        if ((temp=fabs(a[i][j])) > big) big=temp; 
             k2=k2+2;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           }      vv[i]=1.0/big; 
         }    } 
         else {    for (j=1;j<=n;j++) { 
           cutv(strd,strc,strb,'V');      for (i=1;i<j;i++) { 
           /* printf("%s %s %s", strd,strc,strb);*/        sum=a[i][j]; 
           Tvar[i+1]=atoi(strc);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
         strcpy(modelsav,stra);        } 
       }      big=0.0; 
       cutv(strd,strc,stra,'V');      for (i=j;i<=n;i++) { 
       Tvar[1]=atoi(strc);        sum=a[i][j]; 
     }        for (k=1;k<j;k++) 
   }          sum -= a[i][k]*a[k][j]; 
   /* for (i=1; i<=5; i++)        a[i][j]=sum; 
      printf("i=%d %d ",i,Tvar[i]);*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/          big=dum; 
  /*printf("cptcovprod=%d ", cptcovprod);*/          imax=i; 
   /*  scanf("%d ",i);*/        } 
     fclose(fic);      } 
       if (j != imax) { 
     /*  if(mle==1){*/        for (k=1;k<=n;k++) { 
     if (weightopt != 1) { /* Maximisation without weights*/          dum=a[imax][k]; 
       for(i=1;i<=n;i++) weight[i]=1.0;          a[imax][k]=a[j][k]; 
     }          a[j][k]=dum; 
     /*-calculation of age at interview from date of interview and age at death -*/        } 
     agev=matrix(1,maxwav,1,imx);        *d = -(*d); 
            vv[imax]=vv[j]; 
     for (i=1; i<=imx; i++)  {      } 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      indx[j]=imax; 
       for(m=1; (m<= maxwav); m++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
         if(s[m][i] >0){      if (j != n) { 
           if (s[m][i] == nlstate+1) {        dum=1.0/(a[j][j]); 
             if(agedc[i]>0)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
               if(moisdc[i]!=99 && andc[i]!=9999)      } 
               agev[m][i]=agedc[i];    } 
             else{    free_vector(vv,1,n);  /* Doesn't work */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  ;
               agev[m][i]=-1;  } 
             }  
           }  void lubksb(double **a, int n, int *indx, double b[]) 
           else if(s[m][i] !=9){ /* Should no more exist */  { 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    int i,ii=0,ip,j; 
             if(mint[m][i]==99 || anint[m][i]==9999)    double sum; 
               agev[m][i]=1;   
             else if(agev[m][i] <agemin){    for (i=1;i<=n;i++) { 
               agemin=agev[m][i];      ip=indx[i]; 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      sum=b[ip]; 
             }      b[ip]=b[i]; 
             else if(agev[m][i] >agemax){      if (ii) 
               agemax=agev[m][i];        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      else if (sum) ii=i; 
             }      b[i]=sum; 
             /*agev[m][i]=anint[m][i]-annais[i];*/    } 
             /*   agev[m][i] = age[i]+2*m;*/    for (i=n;i>=1;i--) { 
           }      sum=b[i]; 
           else { /* =9 */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
             agev[m][i]=1;      b[i]=sum/a[i][i]; 
             s[m][i]=-1;    } 
           }  } 
         }  
         else /*= 0 Unknown */  void pstamp(FILE *fichier)
           agev[m][i]=1;  {
       }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
      }
     }  
     for (i=1; i<=imx; i++)  {  /************ Frequencies ********************/
       for(m=1; (m<= maxwav); m++){  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[])
         if (s[m][i] > (nlstate+ndeath)) {  {  /* Some frequencies */
           printf("Error: Wrong value in nlstate or ndeath\n");      
           goto end;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         }    int first;
       }    double ***freq; /* Frequencies */
     }    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    char fileresp[FILENAMELENGTH];
     
     free_vector(severity,1,maxwav);    pp=vector(1,nlstate);
     free_imatrix(outcome,1,maxwav+1,1,n);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     free_vector(moisnais,1,n);    strcpy(fileresp,"p");
     free_vector(annais,1,n);    strcat(fileresp,fileres);
     free_matrix(mint,1,maxwav,1,n);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     free_matrix(anint,1,maxwav,1,n);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     free_vector(moisdc,1,n);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     free_vector(andc,1,n);      exit(0);
     }
        freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     wav=ivector(1,imx);    j1=0;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    j=cptcoveff;
        if (cptcovn<1) {j=1;ncodemax[1]=1;}
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    first=1;
   
     for(k1=1; k1<=j;k1++){
       Tcode=ivector(1,100);      for(i1=1; i1<=ncodemax[k1];i1++){
       nbcode=imatrix(1,nvar,1,8);        j1++;
       ncodemax[1]=1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          scanf("%d", i);*/
              for (i=-5; i<=nlstate+ndeath; i++)  
    codtab=imatrix(1,100,1,10);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
    h=0;            for(m=iagemin; m <= iagemax+3; m++)
    m=pow(2,cptcoveff);              freq[i][jk][m]=0;
    
    for(k=1;k<=cptcoveff; k++){      for (i=1; i<=nlstate; i++)  
      for(i=1; i <=(m/pow(2,k));i++){        for(m=iagemin; m <= iagemax+3; m++)
        for(j=1; j <= ncodemax[k]; j++){          prop[i][m]=0;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        
            h++;        dateintsum=0;
            if (h>m) h=1;codtab[h][k]=j;        k2cpt=0;
          }        for (i=1; i<=imx; i++) {
        }          bool=1;
      }          if  (cptcovn>0) {
    }            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
    /*for(i=1; i <=m ;i++){          }
      for(k=1; k <=cptcovn; k++){          if (bool==1){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);            for(m=firstpass; m<=lastpass; m++){
      }              k2=anint[m][i]+(mint[m][i]/12.);
      printf("\n");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
    }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
    scanf("%d",i);*/                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];
    /* Calculates basic frequencies. Computes observed prevalence at single age                if (m<lastpass) {
        and prints on file fileres'p'. */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  dateintsum=dateintsum+k2;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  k2cpt++;
     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) */        }
          
     if(mle==1){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        pstamp(ficresp);
     }        if  (cptcovn>0) {
              fprintf(ficresp, "\n#********** Variable "); 
     /*--------- results files --------------*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     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=1; i<=nlstate;i++) 
    fprintf(ficres,"# Parameters\n");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
    printf("# Parameters\n");        fprintf(ficresp, "\n");
    for(i=1,jk=1; i <=nlstate; i++){        
      for(k=1; k <=(nlstate+ndeath); k++){        for(i=iagemin; i <= iagemax+3; i++){
        if (k != i)          if(i==iagemax+3){
          {            fprintf(ficlog,"Total");
            printf("%d%d ",i,k);          }else{
            fprintf(ficres,"%1d%1d ",i,k);            if(first==1){
            for(j=1; j <=ncovmodel; j++){              first=0;
              printf("%f ",p[jk]);              printf("See log file for details...\n");
              fprintf(ficres,"%f ",p[jk]);            }
              jk++;            fprintf(ficlog,"Age %d", i);
            }          }
            printf("\n");          for(jk=1; jk <=nlstate ; jk++){
            fprintf(ficres,"\n");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
          }              pp[jk] += freq[jk][m][i]; 
      }          }
    }          for(jk=1; jk <=nlstate ; jk++){
  if(mle==1){            for(m=-1, pos=0; m <=0 ; m++)
     /* Computing hessian and covariance matrix */              pos += freq[jk][m][i];
     ftolhess=ftol; /* Usually correct */            if(pp[jk]>=1.e-10){
     hesscov(matcov, p, npar, delti, ftolhess, func);              if(first==1){
  }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fprintf(ficres,"# Scales\n");              }
     printf("# Scales\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      for(i=1,jk=1; i <=nlstate; i++){            }else{
       for(j=1; j <=nlstate+ndeath; j++){              if(first==1)
         if (j!=i) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           fprintf(ficres,"%1d%1d",i,j);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           printf("%1d%1d",i,j);            }
           for(k=1; k<=ncovmodel;k++){          }
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);          for(jk=1; jk <=nlstate ; jk++){
             jk++;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           }              pp[jk] += freq[jk][m][i];
           printf("\n");          }       
           fprintf(ficres,"\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         }            pos += pp[jk];
       }            posprop += prop[jk][i];
       }          }
              for(jk=1; jk <=nlstate ; jk++){
     k=1;            if(pos>=1.e-5){
     fprintf(ficres,"# Covariance\n");              if(first==1)
     printf("# Covariance\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(i=1;i<=npar;i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       /*  if (k>nlstate) k=1;            }else{
       i1=(i-1)/(ncovmodel*nlstate)+1;              if(first==1)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       printf("%s%d%d",alph[k],i1,tab[i]);*/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficres,"%3d",i);            }
       printf("%3d",i);            if( i <= iagemax){
       for(j=1; j<=i;j++){              if(pos>=1.e-5){
         fprintf(ficres," %.5e",matcov[i][j]);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         printf(" %.5e",matcov[i][j]);                /*probs[i][jk][j1]= pp[jk]/pos;*/
       }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       fprintf(ficres,"\n");              }
       printf("\n");              else
       k++;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     }            }
              }
     while((c=getc(ficpar))=='#' && c!= EOF){          
       ungetc(c,ficpar);          for(jk=-1; jk <=nlstate+ndeath; jk++)
       fgets(line, MAXLINE, ficpar);            for(m=-1; m <=nlstate+ndeath; m++)
       puts(line);              if(freq[jk][m][i] !=0 ) {
       fputs(line,ficparo);              if(first==1)
     }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     ungetc(c,ficpar);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          if(i <= iagemax)
                fprintf(ficresp,"\n");
     if (fage <= 2) {          if(first==1)
       bage = agemin;            printf("Others in log...\n");
       fage = agemax;          fprintf(ficlog,"\n");
     }        }
       }
     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\n",agemin,agemax,bage,fage);    dateintmean=dateintsum/k2cpt; 
    
        fclose(ficresp);
 /*------------ gnuplot -------------*/    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 chdir(pathcd);    free_vector(pp,1,nlstate);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     printf("Problem with file graph.gp");goto end;    /* End of Freq */
   }  }
 #ifdef windows  
   fprintf(ficgp,"cd \"%s\" \n",pathc);  /************ Prevalence ********************/
 #endif  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)
 m=pow(2,cptcoveff);  {  
      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  /* 1eme*/       in each health status at the date of interview (if between dateprev1 and dateprev2).
   for (cpt=1; cpt<= nlstate ; cpt ++) {       We still use firstpass and lastpass as another selection.
    for (k1=1; k1<= m ; k1 ++) {    */
    
 #ifdef windows    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     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);    double ***freq; /* Frequencies */
 #endif    double *pp, **prop;
 #ifdef unix    double pos,posprop; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    double  y2; /* in fractional years */
 #endif    int iagemin, iagemax;
   
 for (i=1; i<= nlstate ; i ++) {    iagemin= (int) agemin;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    iagemax= (int) agemax;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*pp=vector(1,nlstate);*/
 }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     for (i=1; i<= nlstate ; i ++) {    j1=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    j=cptcoveff;
 }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    
      for (i=1; i<= nlstate ; i ++) {    for(k1=1; k1<=j;k1++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(i1=1; i1<=ncodemax[k1];i1++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        j1++;
 }          
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        for (i=1; i<=nlstate; i++)  
 #ifdef unix          for(m=iagemin; m <= iagemax+3; m++)
 fprintf(ficgp,"\nset ter gif small size 400,300");            prop[i][m]=0.0;
 #endif       
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for (i=1; i<=imx; i++) { /* Each individual */
    }          bool=1;
   }          if  (cptcovn>0) {
   /*2 eme*/            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   for (k1=1; k1<= m ; k1 ++) {                bool=0;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          } 
              if (bool==1) { 
     for (i=1; i<= nlstate+1 ; i ++) {            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       k=2*i;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for (j=1; j<= nlstate+1 ; j ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
 }                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                  /*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]]);*/
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for (j=1; j<= nlstate+1 ; j ++) {                } 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              }
         else fprintf(ficgp," \%%*lf (\%%*lf)");            } /* end selection of waves */
 }            }
       fprintf(ficgp,"\" t\"\" w l 0,");        }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(i=iagemin; i <= iagemax+3; i++){  
       for (j=1; j<= nlstate+1 ; j ++) {          
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            posprop += prop[jk][i]; 
 }            } 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");          for(jk=1; jk <=nlstate ; jk++){     
     }            if( i <=  iagemax){ 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);              if(posprop>=1.e-5){ 
   }                probs[i][jk][j1]= prop[jk][i]/posprop;
                } 
   /*3eme*/            } 
           }/* end jk */ 
   for (k1=1; k1<= m ; k1 ++) {        }/* end i */ 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      } /* end i1 */
       k=2+nlstate*(cpt-1);    } /* end k1 */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    
       for (i=1; i< nlstate ; i ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         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);    /*free_vector(pp,1,nlstate);*/
       }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  }  /* End of prevalence */
     }  
   }  /************* Waves Concatenation ***************/
    
   /* CV preval stat */  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)
   for (k1=1; k1<= m ; k1 ++) {  {
     for (cpt=1; cpt<nlstate ; cpt ++) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       k=3;       Death is a valid wave (if date is known).
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for (i=1; i< nlstate ; i ++)       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         fprintf(ficgp,"+$%d",k+i+1);       and mw[mi+1][i]. dh depends on stepm.
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);       */
        
       l=3+(nlstate+ndeath)*cpt;    int i, mi, m;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       for (i=1; i< nlstate ; i ++) {       double sum=0., jmean=0.;*/
         l=3+(nlstate+ndeath)*cpt;    int first;
         fprintf(ficgp,"+$%d",l+i+1);    int j, k=0,jk, ju, jl;
       }    double sum=0.;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      first=0;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    jmin=1e+5;
     }    jmax=-1;
   }    jmean=0.;
     for(i=1; i<=imx; i++){
   /* proba elementaires */      mi=0;
    for(i=1,jk=1; i <=nlstate; i++){      m=firstpass;
     for(k=1; k <=(nlstate+ndeath); k++){      while(s[m][i] <= nlstate){
       if (k != i) {        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         for(j=1; j <=ncovmodel; j++){          mw[++mi][i]=m;
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        if(m >=lastpass)
           /*fprintf(ficgp,"%s",alph[1]);*/          break;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        else
           jk++;          m++;
           fprintf(ficgp,"\n");      }/* end while */
         }      if (s[m][i] > nlstate){
       }        mi++;     /* Death is another wave */
     }        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
         mw[mi][i]=m;
   for(jk=1; jk <=m; jk++) {      }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  
    i=1;      wav[i]=mi;
    for(k2=1; k2<=nlstate; k2++) {      if(mi==0){
      k3=i;        nbwarn++;
      for(k=1; k<=(nlstate+ndeath); k++) {        if(first==0){
        if (k != k2){          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          first=1;
 ij=1;        }
         for(j=3; j <=ncovmodel; j++) {        if(first==1){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        }
             ij++;      } /* end mi==0 */
           }    } /* End individuals */
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for(i=1; i<=imx; i++){
         }      for(mi=1; mi<wav[i];mi++){
           fprintf(ficgp,")/(1");        if (stepm <=0)
                  dh[mi][i]=1;
         for(k1=1; k1 <=nlstate; k1++){          else{
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 ij=1;            if (agedc[i] < 2*AGESUP) {
           for(j=3; j <=ncovmodel; j++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if(j==0) j=1;  /* Survives at least one month after exam */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              else if(j<0){
             ij++;                nberr++;
           }                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]);
           else                j=1; /* Temporary Dangerous patch */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][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);
           }                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(ficgp,")");                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);
         }              }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              k=k+1;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              if (j >= jmax){
         i=i+ncovmodel;                jmax=j;
        }                ijmax=i;
      }              }
    }              if (j <= jmin){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                jmin=j;
   }                ijmin=i;
                  }
   fclose(ficgp);              sum=sum+j;
                  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 chdir(path);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     free_matrix(agev,1,maxwav,1,imx);            }
     free_ivector(wav,1,imx);          }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          else{
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
      /*        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_imatrix(s,1,maxwav+1,1,n);  
                k=k+1;
                if (j >= jmax) {
     free_ivector(num,1,n);              jmax=j;
     free_vector(agedc,1,n);              ijmax=i;
     free_vector(weight,1,n);            }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            else if (j <= jmin){
     fclose(ficparo);              jmin=j;
     fclose(ficres);              ijmin=i;
     /*  }*/            }
                /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
    /*________fin mle=1_________*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                if(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]);
     /* No more information from the sample is required now */              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]);
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){            sum=sum+j;
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          jk= j/stepm;
     puts(line);          jl= j -jk*stepm;
     fputs(line,ficparo);          ju= j -(jk+1)*stepm;
   }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   ungetc(c,ficpar);            if(jl==0){
                dh[mi][i]=jk;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              bh[mi][i]=0;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);            }else{ /* We want a negative bias in order to only have interpolation ie
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                    * at the price of an extra matrix product in likelihood */
 /*--------- index.htm --------*/              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   if((fichtm=fopen("index.htm","w"))==NULL)    {            }
     printf("Problem with index.htm \n");goto end;          }else{
   }            if(jl <= -ju){
               dh[mi][i]=jk;
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n              bh[mi][i]=jl;       /* bias is positive if real duration
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                                   * is higher than the multiple of stepm and negative otherwise.
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                                   */
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            else{
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              dh[mi][i]=jk+1;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>              bh[mi][i]=ju;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            }
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            if(dh[mi][i]==0){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
  fprintf(fichtm," <li>Graphs</li>\n<p>");              /*  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);*/
             }
  m=cptcoveff;          } /* end if mle */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        }
       } /* end wave */
  j1=0;    }
  for(k1=1; k1<=m;k1++){    jmean=sum/k;
    for(i1=1; i1<=ncodemax[k1];i1++){    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);
        j1++;    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);
        if (cptcovn > 0) {   }
          fprintf(fichtm,"<hr>************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)  /*********** Tricode ****************************/
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  void tricode(int *Tvar, int **nbcode, int imx)
          fprintf(fichtm," ************\n<hr>");  {
        }    
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    int Ndum[20],ij=1, k, j, i, maxncov=19;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        int cptcode=0;
        for(cpt=1; cpt<nlstate;cpt++){    cptcoveff=0; 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>   
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    for (k=0; k<maxncov; k++) Ndum[k]=0;
        }    for (k=1; k<=7; k++) ncodemax[k]=0;
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 interval) in state (%d): v%s%d%d.gif <br>      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                                   modality*/ 
      }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
      for(cpt=1; cpt<=nlstate;cpt++) {        Ndum[ij]++; /*store the modality */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
      }                                         Tvar[j]. If V=sex and male is 0 and 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                                         female is 1, then  cptcode=1.*/
 health expectancies in states (1) and (2): e%s%d.gif<br>      }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  
 fprintf(fichtm,"\n</body>");      for (i=0; i<=cptcode; i++) {
    }        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 */
  }      }
 fclose(fichtm);  
       ij=1; 
   /*--------------- Prevalence limit --------------*/      for (i=1; i<=ncodemax[j]; i++) {
          for (k=0; k<= maxncov; k++) {
   strcpy(filerespl,"pl");          if (Ndum[k] != 0) {
   strcat(filerespl,fileres);            nbcode[Tvar[j]][ij]=k; 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            /* 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; */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            
   }            ij++;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          }
   fprintf(ficrespl,"#Prevalence limit\n");          if (ij > ncodemax[j]) break; 
   fprintf(ficrespl,"#Age ");        }  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      } 
   fprintf(ficrespl,"\n");    }  
    
   prlim=matrix(1,nlstate,1,nlstate);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   for (i=1; i<=ncovmodel-2; i++) { 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     ij=Tvar[i];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     Ndum[ij]++;
   k=0;   }
   agebase=agemin;  
   agelim=agemax;   ij=1;
   ftolpl=1.e-10;   for (i=1; i<= maxncov; i++) {
   i1=cptcoveff;     if((Ndum[i]!=0) && (i<=ncovcol)){
   if (cptcovn < 1){i1=1;}       Tvaraff[ij]=i; /*For printing */
        ij++;
   for(cptcov=1;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]);*/   cptcoveff=ij-1; /*Number of simple covariates*/
         fprintf(ficrespl,"\n#******");  }
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*********** Health Expectancies ****************/
         fprintf(ficrespl,"******\n");  
          void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  {
           fprintf(ficrespl,"%.0f",age );    /* Health expectancies, no variances */
           for(i=1; i<=nlstate;i++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
           fprintf(ficrespl," %.5f", prlim[i][i]);    int nhstepma, nstepma; /* Decreasing with age */
           fprintf(ficrespl,"\n");    double age, agelim, hf;
         }    double ***p3mat;
       }    double eip;
     }  
   fclose(ficrespl);    pstamp(ficreseij);
   /*------------- h Pij x at various ages ------------*/    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
      fprintf(ficreseij,"# Age");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for(i=1; i<=nlstate;i++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      for(j=1; j<=nlstate;j++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficreseij," e%1d%1d ",i,j);
   }      }
   printf("Computing pij: result on file '%s' \n", filerespij);      fprintf(ficreseij," e%1d. ",i);
      }
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficreseij,"\n");
   if (stepm<=24) stepsize=2;  
     
   agelim=AGESUP;    if(estepm < stepm){
   hstepm=stepsize*YEARM; /* Every year of age */      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
      else  hstepm=estepm;   
   k=0;    /* We compute the life expectancy from trapezoids spaced every estepm months
   for(cptcov=1;cptcov<=i1;cptcov++){     * This is mainly to measure the difference between two models: for example
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * if stepm=24 months pijx are given only every 2 years and by summing them
       k=k+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
         fprintf(ficrespij,"\n#****** ");     * progression in between and thus overestimating or underestimating according
         for(j=1;j<=cptcoveff;j++)     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficrespij,"******\n");     * to compare the new estimate of Life expectancy with the same linear 
             * hypothesis. A more precise result, taking into account a more precise
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     * curvature will be obtained if estepm is as small as stepm. */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /* For example we decided to compute the life expectancy with the smallest unit */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           oldm=oldms;savm=savms;       nhstepm is the number of hstepm from age to agelim 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         nstepm is the number of stepm from age to agelin. 
           fprintf(ficrespij,"# Age");       Look at hpijx to understand the reason of that which relies in memory size
           for(i=1; i<=nlstate;i++)       and note for a fixed period like estepm months */
             for(j=1; j<=nlstate+ndeath;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               fprintf(ficrespij," %1d-%1d",i,j);       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficrespij,"\n");       means that if the survival funtion is printed only each two years of age and if
           for (h=0; h<=nhstepm; h++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       results. So we changed our mind and took the option of the best precision.
             for(i=1; i<=nlstate;i++)    */
               for(j=1; j<=nlstate+ndeath;j++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    agelim=AGESUP;
           }    /* If stepm=6 months */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           fprintf(ficrespij,"\n");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         }      
     }  /* nhstepm age range expressed in number of stepm */
   }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(ficrespij);    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /*---------- Health expectancies and variances ------------*/    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
   strcpy(filerest,"t");    for (age=bage; age<=fage; age ++){ 
   strcat(filerest,fileres);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   if((ficrest=fopen(filerest,"w"))==NULL) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      /* if (stepm >= YEARM) hstepm=1;*/
   }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
   strcpy(filerese,"e");         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   strcat(filerese,fileres);      
   if((ficreseij=fopen(filerese,"w"))==NULL) {      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      
       printf("%d|",(int)age);fflush(stdout);
  strcpy(fileresv,"v");      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   strcat(fileresv,fileres);      
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      /* Computing expectancies */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   k=0;            
   for(cptcov=1;cptcov<=i1;cptcov++){            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;          }
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      fprintf(ficreseij,"%3.0f",age );
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1; i<=nlstate;i++){
       fprintf(ficrest,"******\n");        eip=0;
         for(j=1; j<=nlstate;j++){
       fprintf(ficreseij,"\n#****** ");          eip +=eij[i][j][(int)age];
       for(j=1;j<=cptcoveff;j++)          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficresvij,"\n#****** ");      fprintf(ficreseij,"\n");
       for(j=1;j<=cptcoveff;j++)      
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }
       fprintf(ficresvij,"******\n");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficlog,"\n");
       oldm=oldms;savm=savms;    
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  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[] )
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
        {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    /* Covariances of health expectancies eij and of total life expectancies according
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);     to initial status i, ei. .
       fprintf(ficrest,"\n");    */
            int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       hf=1;    int nhstepma, nstepma; /* Decreasing with age */
       if (stepm >= YEARM) hf=stepm/YEARM;    double age, agelim, hf;
       epj=vector(1,nlstate+1);    double ***p3matp, ***p3matm, ***varhe;
       for(age=bage; age <=fage ;age++){    double **dnewm,**doldm;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double *xp, *xm;
         fprintf(ficrest," %.0f",age);    double **gp, **gm;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double ***gradg, ***trgradg;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    int theta;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }    double eip, vip;
           epj[nlstate+1] +=epj[j];  
         }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         for(i=1, vepp=0.;i <=nlstate;i++)    xp=vector(1,npar);
           for(j=1;j <=nlstate;j++)    xm=vector(1,npar);
             vepp += vareij[i][j][(int)age];    dnewm=matrix(1,nlstate*nlstate,1,npar);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         for(j=1;j <=nlstate;j++){    
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    pstamp(ficresstdeij);
         }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         fprintf(ficrest,"\n");    fprintf(ficresstdeij,"# Age");
       }    for(i=1; i<=nlstate;i++){
     }      for(j=1; j<=nlstate;j++)
   }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
              fprintf(ficresstdeij," e%1d. ",i);
  fclose(ficreseij);    }
  fclose(ficresvij);    fprintf(ficresstdeij,"\n");
   fclose(ficrest);  
   fclose(ficpar);    pstamp(ficrescveij);
   free_vector(epj,1,nlstate+1);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   /*  scanf("%d ",i); */    fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
   /*------- Variance limit prevalence------*/        for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
 strcpy(fileresvpl,"vpl");        for(i2=1; i2<=nlstate;i2++)
   strcat(fileresvpl,fileres);          for(j2=1; j2<=nlstate;j2++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            cptj2= (j2-1)*nlstate+i2;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            if(cptj2 <= cptj)
     exit(0);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   }          }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      }
     fprintf(ficrescveij,"\n");
  k=0;    
  for(cptcov=1;cptcov<=i1;cptcov++){    if(estepm < stepm){
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
      k=k+1;    }
      fprintf(ficresvpl,"\n#****** ");    else  hstepm=estepm;   
      for(j=1;j<=cptcoveff;j++)    /* We compute the life expectancy from trapezoids spaced every estepm months
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * This is mainly to measure the difference between two models: for example
      fprintf(ficresvpl,"******\n");     * 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 
      varpl=matrix(1,nlstate,(int) bage, (int) fage);     * progression in between and thus overestimating or underestimating according
      oldm=oldms;savm=savms;     * to the curvature of the survival function. If, for the same date, we 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
    }     * to compare the new estimate of Life expectancy with the same linear 
  }     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   fclose(ficresvpl);  
     /* For example we decided to compute the life expectancy with the smallest unit */
   /*---------- End : free ----------------*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);       Look at hpijx to understand the reason of that which relies in memory size
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       means that if the survival funtion is printed only each two years of age and if
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       results. So we changed our mind and took the option of the best precision.
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    /* If stepm=6 months */
      /* nhstepm age range expressed in number of stepm */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   printf("End of Imach\n");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /* if (stepm >= YEARM) hstepm=1;*/
      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /* 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);*/    
   /*printf("Total time was %d uSec.\n", total_usecs);*/    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*------ End -----------*/    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
  end:    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 #ifdef windows    gp=matrix(0,nhstepm,1,nlstate*nlstate);
  chdir(pathcd);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
 #endif  
  system("wgnuplot graph.plt");    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 #ifdef windows      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   while (z[0] != 'q') {      /* if (stepm >= YEARM) hstepm=1;*/
     chdir(pathcd);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);      /* If stepm=6 months */
     if (z[0] == 'c') system("./imach");      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     else if (z[0] == 'e') {         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       chdir(path);      
       system("index.htm");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }  
     else if (z[0] == 'q') exit(0);      /* Computing  Variances of health expectancies */
   }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
 #endif         decrease memory allocation */
 }      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.7  
changed lines
  Added in v.1.127


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