Diff for /imach/src/imach.c between versions 1.22 and 1.132

version 1.22, 2002/02/22 17:54:20 version 1.132, 2009/07/06 08:22:05
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.132  2009/07/06 08:22:05  brouard
      Many tings
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.131  2009/06/20 16:22:47  brouard
   first survey ("cross") where individuals from different ages are    Some dimensions resccaled
   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    Revision 1.130  2009/05/26 06:44:34  brouard
   second wave of interviews ("longitudinal") which measure each change    (Module): Max Covariate is now set to 20 instead of 8. A
   (if any) in individual health status.  Health expectancies are    lot of cleaning with variables initialized to 0. Trying to make
   computed from the time spent in each health state according to a    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.129  2007/08/31 13:49:27  lievre
   simplest model is the multinomial logistic model where pij is the    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.128  2006/06/30 13:02:05  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): Clarifications on computing e.j
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.127  2006/04/28 18:11:50  brouard
   where the markup *Covariates have to be included here again* invites    (Module): Yes the sum of survivors was wrong since
   you to do it.  More covariates you add, slower the    imach-114 because nhstepm was no more computed in the age
   convergence.    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
   The advantage of this computer programme, compared to a simple    compute health expectancies (without variances) in a first step
   multinomial logistic model, is clear when the delay between waves is not    and then all the health expectancies with variances or standard
   identical for each individual. Also, if a individual missed an    deviation (needs data from the Hessian matrices) which slows the
   intermediate interview, the information is lost, but taken into    computation.
   account using an interpolation or extrapolation.      In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   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    Revision 1.126  2006/04/28 17:23:28  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    (Module): Yes the sum of survivors was wrong since
   states. This elementary transition (by month or quarter trimester,    imach-114 because nhstepm was no more computed in the age
   semester or year) is model as a multinomial logistic.  The hPx    loop. Now we define nhstepma in the age loop.
   matrix is simply the matrix product of nh*stepm elementary matrices    Version 0.98h
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
   Also this programme outputs the covariance matrix of the parameters but also    Forecasting file added.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.124  2006/03/22 17:13:53  lievre
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Parameters are printed with %lf instead of %f (more numbers after the comma).
            Institut national d'études démographiques, Paris.    The log-likelihood is printed in the log file
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.123  2006/03/20 10:52:43  brouard
   It is copyrighted identically to a GNU software product, ie programme and    * imach.c (Module): <title> changed, corresponds to .htm file
   software can be distributed freely for non commercial use. Latest version    name. <head> headers where missing.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    * imach.c (Module): Weights can have a decimal point as for
      English (a comma might work with a correct LC_NUMERIC environment,
 #include <math.h>    otherwise the weight is truncated).
 #include <stdio.h>    Modification of warning when the covariates values are not 0 or
 #include <stdlib.h>    1.
 #include <unistd.h>    Version 0.98g
   
 #define MAXLINE 256    Revision 1.122  2006/03/20 09:45:41  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    (Module): Weights can have a decimal point as for
 #define FILENAMELENGTH 80    English (a comma might work with a correct LC_NUMERIC environment,
 /*#define DEBUG*/    otherwise the weight is truncated).
 #define windows    Modification of warning when the covariates values are not 0 or
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    1.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Version 0.98g
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.121  2006/03/16 17:45:01  lievre
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    * imach.c (Module): Comments concerning covariates added
   
 #define NINTERVMAX 8    * imach.c (Module): refinements in the computation of lli if
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    status=-2 in order to have more reliable computation if stepm is
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    not 1 month. Version 0.98f
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.120  2006/03/16 15:10:38  lievre
 #define YEARM 12. /* Number of months per year */    (Module): refinements in the computation of lli if
 #define AGESUP 130    status=-2 in order to have more reliable computation if stepm is
 #define AGEBASE 40    not 1 month. Version 0.98f
   
     Revision 1.119  2006/03/15 17:42:26  brouard
 int erreur; /* Error number */    (Module): Bug if status = -2, the loglikelihood was
 int nvar;    computed as likelihood omitting the logarithm. Version O.98e
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.118  2006/03/14 18:20:07  brouard
 int nlstate=2; /* Number of live states */    (Module): varevsij Comments added explaining the second
 int ndeath=1; /* Number of dead states */    table of variances if popbased=1 .
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int popbased=0;    (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 1.117  2006/03/14 17:16:22  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): varevsij Comments added explaining the second
 int mle, weightopt;    table of variances if popbased=1 .
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Function pstamp added
 double jmean; /* Mean space between 2 waves */    (Module): Version 0.98d
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.116  2006/03/06 10:29:27  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    (Module): Variance-covariance wrong links and
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    varian-covariance of ej. is needed (Saito).
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.115  2006/02/27 12:17:45  brouard
  FILE  *ficresvij;    (Module): One freematrix added in mlikeli! 0.98c
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.114  2006/02/26 12:57:58  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Some improvements in processing parameter
     filename with strsep.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.113  2006/02/24 14:20:24  brouard
 #define FTOL 1.0e-10    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 #define NRANSI    allocation too.
 #define ITMAX 200  
     Revision 1.112  2006/01/30 09:55:26  brouard
 #define TOL 2.0e-4    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 #define CGOLD 0.3819660    Revision 1.111  2006/01/25 20:38:18  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);    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.110  2006/01/25 00:51:50  brouard
 #define TINY 1.0e-20    (Module): Lots of cleaning and bugs added (Gompertz)
   
 static double maxarg1,maxarg2;    Revision 1.109  2006/01/24 19:37:15  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): Comments (lines starting with a #) are allowed in data.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.108  2006/01/19 18:05:42  lievre
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Gnuplot problem appeared...
 #define rint(a) floor(a+0.5)    To be fixed
   
 static double sqrarg;    Revision 1.107  2006/01/19 16:20:37  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Test existence of gnuplot in imach path
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.106  2006/01/19 13:24:36  brouard
 int imx;    Some cleaning and links added in html output
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.104  2005/09/30 16:11:43  lievre
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): sump fixed, loop imx fixed, and simplifications.
 double **pmmij, ***probs, ***mobaverage;    (Module): If the status is missing at the last wave but we know
 double dateintmean=0;    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 double *weight;    contributions to the likelihood is 1 - Prob of dying from last
 int **s; /* Status */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double *agedc, **covar, idx;    the healthy state at last known wave). Version is 0.98
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.103  2005/09/30 15:54:49  lievre
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): sump fixed, loop imx fixed, and simplifications.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.102  2004/09/15 17:31:30  brouard
 /**************** split *************************/    Add the possibility to read data file including tab characters.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.101  2004/09/15 10:38:38  brouard
    char *s;                             /* pointer */    Fix on curr_time
    int  l1, l2;                         /* length counters */  
     Revision 1.100  2004/07/12 18:29:06  brouard
    l1 = strlen( path );                 /* length of path */    Add version for Mac OS X. Just define UNIX in Makefile
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.99  2004/06/05 08:57:40  brouard
    s = strrchr( path, '\\' );           /* find last / */    *** empty log message ***
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.98  2004/05/16 15:05:56  brouard
 #endif    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)
 #ifdef windows    suppressed.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.96  2003/07/15 15:38:55  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #endif    rewritten within the same printf. Workaround: many printfs.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.95  2003/07/08 07:54:34  brouard
    strcpy(ext,s);                       /* save extension */    * imach.c (Repository):
    l1= strlen( name);    (Repository): Using imachwizard code to output a more meaningful covariance
    l2= strlen( s)+1;    matrix (cov(a12,c31) instead of numbers.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.94  2003/06/27 13:00:02  brouard
    return( 0 );                         /* we're done */    Just cleaning
 }  
     Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /******************************************/    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 void replace(char *s, char*t)  
 {    Revision 1.92  2003/06/25 16:30:45  brouard
   int i;    (Module): On windows (cygwin) function asctime_r doesn't
   int lg=20;    exist so I changed back to asctime which exists.
   i=0;  
   lg=strlen(t);    Revision 1.91  2003/06/25 15:30:29  brouard
   for(i=0; i<= lg; i++) {    * imach.c (Repository): Duplicated warning errors corrected.
     (s[i] = t[i]);    (Repository): Elapsed time after each iteration is now output. It
     if (t[i]== '\\') s[i]='/';    helps to forecast when convergence will be reached. Elapsed time
   }    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 int nbocc(char *s, char occ)    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int i,j=0;    mle=-1 a template is output in file "or"mypar.txt with the design
   int lg=20;    of the covariance matrix to be input.
   i=0;  
   lg=strlen(s);    Revision 1.89  2003/06/24 12:30:52  brouard
   for(i=0; i<= lg; i++) {    (Module): Some bugs corrected for windows. Also, when
   if  (s[i] == occ ) j++;    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
   return j;  
 }    Revision 1.88  2003/06/23 17:54:56  brouard
     * 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.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.87  2003/06/18 12:26:01  brouard
   int i,lg,j,p=0;    Version 0.96
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.86  2003/06/17 20:04:08  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Change position of html and gnuplot routines and added
   }    routine fileappend.
   
   lg=strlen(t);    Revision 1.85  2003/06/17 13:12:43  brouard
   for(j=0; j<p; j++) {    * imach.c (Repository): Check when date of death was earlier that
     (u[j] = t[j]);    current date of interview. It may happen when the death was just
   }    prior to the death. In this case, dh was negative and likelihood
      u[p]='\0';    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
    for(j=0; j<= lg; j++) {    interview.
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Repository): Because some people have very long ID (first column)
   }    we changed int to long in num[] and we added a new lvector for
 }    memory allocation. But we also truncated to 8 characters (left
     truncation)
 /********************** nrerror ********************/    (Repository): No more line truncation errors.
   
 void nrerror(char error_text[])    Revision 1.84  2003/06/13 21:44:43  brouard
 {    * imach.c (Repository): Replace "freqsummary" at a correct
   fprintf(stderr,"ERREUR ...\n");    place. It differs from routine "prevalence" which may be called
   fprintf(stderr,"%s\n",error_text);    many times. Probs is memory consuming and must be used with
   exit(1);    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.82  2003/06/05 15:57:20  brouard
   if (!v) nrerror("allocation failure in vector");    Add log in  imach.c and  fullversion number is now printed.
   return v-nl+NR_END;  
 }  */
   /*
 /************************ free vector ******************/     Interpolated Markov Chain
 void free_vector(double*v, int nl, int nh)  
 {    Short summary of the programme:
   free((FREE_ARG)(v+nl-NR_END));    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /************************ivector *******************************/    first survey ("cross") where individuals from different ages are
 int *ivector(long nl,long nh)    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
   int *v;    second wave of interviews ("longitudinal") which measure each change
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (if any) in individual health status.  Health expectancies are
   if (!v) nrerror("allocation failure in ivector");    computed from the time spent in each health state according to a
   return v-nl+NR_END;    model. More health states you consider, more time is necessary to reach the
 }    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 /******************free ivector **************************/    probability to be observed in state j at the second wave
 void free_ivector(int *v, long nl, long nh)    conditional to be observed in state i at the first wave. Therefore
 {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   free((FREE_ARG)(v+nl-NR_END));    'age' is age and 'sex' is a covariate. If you want to have a more
 }    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 /******************* imatrix *******************************/    you to do it.  More covariates you add, slower the
 int **imatrix(long nrl, long nrh, long ncl, long nch)    convergence.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    The advantage of this computer programme, compared to a simple
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    multinomial logistic model, is clear when the delay between waves is not
   int **m;    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
   /* allocate pointers to rows */    account using an interpolation or extrapolation.  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    hPijx is the probability to be observed in state i at age x+h
   m += NR_END;    conditional to the observed state i at age x. The delay 'h' can be
   m -= nrl;    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
   /* allocate rows and set pointers to them */    matrix is simply the matrix product of nh*stepm elementary matrices
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    and the contribution of each individual to the likelihood is simply
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    hPijx.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Also this programme outputs the covariance matrix of the parameters but also
      of the life expectancies. It also computes the period (stable) prevalence. 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   /* return pointer to array of pointers to rows */             Institut national d'études démographiques, Paris.
   return m;    This software have been partly granted by Euro-REVES, a concerted action
 }    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 /****************** free_imatrix *************************/    software can be distributed freely for non commercial use. Latest version
 void free_imatrix(m,nrl,nrh,ncl,nch)    can be accessed at http://euroreves.ined.fr/imach .
       int **m;  
       long nch,ncl,nrh,nrl;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
      /* free an int matrix allocated by imatrix() */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 {    
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    **********************************************************************/
   free((FREE_ARG) (m+nrl-NR_END));  /*
 }    main
     read parameterfile
 /******************* matrix *******************************/    read datafile
 double **matrix(long nrl, long nrh, long ncl, long nch)    concatwav
 {    freqsummary
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if (mle >= 1)
   double **m;      mlikeli
     print results files
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if mle==1 
   if (!m) nrerror("allocation failure 1 in matrix()");       computes hessian
   m += NR_END;    read end of parameter file: agemin, agemax, bage, fage, estepm
   m -= nrl;        begin-prev-date,...
     open gnuplot file
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    open html file
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    period (stable) prevalence
   m[nrl] += NR_END;     for age prevalim()
   m[nrl] -= ncl;    h Pij x
     variance of p varprob
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    forecasting if prevfcast==1 prevforecast call prevalence()
   return m;    health expectancies
 }    Variance-covariance of DFLE
     prevalence()
 /*************************free matrix ************************/     movingaverage()
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    total life expectancies
   free((FREE_ARG)(m+nrl-NR_END));    Variance of period (stable) prevalence
 }   end
   */
 /******************* ma3x *******************************/  
 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;  #include <math.h>
   #include <stdio.h>
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <stdlib.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <string.h>
   m += NR_END;  #include <unistd.h>
   m -= nrl;  
   #include <limits.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <sys/types.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <sys/stat.h>
   m[nrl] += NR_END;  #include <errno.h>
   m[nrl] -= ncl;  extern int errno;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* #include <sys/time.h> */
   #include <time.h>
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #include "timeval.h"
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /* #include <libintl.h> */
   m[nrl][ncl] -= nll;  /* #define _(String) gettext (String) */
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  #define MAXLINE 256
    
   for (i=nrl+1; i<=nrh; i++) {  #define GNUPLOTPROGRAM "gnuplot"
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     for (j=ncl+1; j<=nch; j++)  #define FILENAMELENGTH 132
       m[i][j]=m[i][j-1]+nlay;  
   }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   return m;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 128 /* Maximum number of parameters for the optimization */
 /*************************free ma3x ************************/  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #define NINTERVMAX 8
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   free((FREE_ARG)(m+nrl-NR_END));  #define NCOVMAX 20 /* Maximum number of covariates */
 }  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 /***************** f1dim *************************/  #define AGESUP 130
 extern int ncom;  #define AGEBASE 40
 extern double *pcom,*xicom;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 extern double (*nrfunc)(double []);  #ifdef UNIX
    #define DIRSEPARATOR '/'
 double f1dim(double x)  #define CHARSEPARATOR "/"
 {  #define ODIRSEPARATOR '\\'
   int j;  #else
   double f;  #define DIRSEPARATOR '\\'
   double *xt;  #define CHARSEPARATOR "\\"
    #define ODIRSEPARATOR '/'
   xt=vector(1,ncom);  #endif
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  /* $Id$ */
   free_vector(xt,1,ncom);  /* $State$ */
   return f;  
 }  char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";
   char fullversion[]="$Revision$ $Date$"; 
 /*****************brent *************************/  char strstart[80];
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int iter;  int nvar=0;
   double a,b,d,etemp;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   double fu,fv,fw,fx;  int npar=NPARMAX;
   double ftemp;  int nlstate=2; /* Number of live states */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int ndeath=1; /* Number of dead states */
   double e=0.0;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  int *wav; /* Number of waves for this individuual 0 is possible */
   x=w=v=bx;  int maxwav=0; /* Maxim number of waves */
   fw=fv=fx=(*f)(x);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   for (iter=1;iter<=ITMAX;iter++) {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     xm=0.5*(a+b);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);                     to the likelihood and the sum of weights (done by funcone)*/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int mle=1, weightopt=0;
     printf(".");fflush(stdout);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #ifdef DEBUG  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     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 **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 #endif  double jmean=1; /* Mean space between 2 waves */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double **oldm, **newm, **savm; /* Working pointers to matrices */
       *xmin=x;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       return fx;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     }  FILE *ficlog, *ficrespow;
     ftemp=fu;  int globpr=0; /* Global variable for printing or not */
     if (fabs(e) > tol1) {  double fretone; /* Only one call to likelihood */
       r=(x-w)*(fx-fv);  long ipmx=0; /* Number of contributions */
       q=(x-v)*(fx-fw);  double sw; /* Sum of weights */
       p=(x-v)*q-(x-w)*r;  char filerespow[FILENAMELENGTH];
       q=2.0*(q-r);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       if (q > 0.0) p = -p;  FILE *ficresilk;
       q=fabs(q);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       etemp=e;  FILE *ficresprobmorprev;
       e=d;  FILE *fichtm, *fichtmcov; /* Html File */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  FILE *ficreseij;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  char filerese[FILENAMELENGTH];
       else {  FILE *ficresstdeij;
         d=p/q;  char fileresstde[FILENAMELENGTH];
         u=x+d;  FILE *ficrescveij;
         if (u-a < tol2 || b-u < tol2)  char filerescve[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  FILE  *ficresvij;
       }  char fileresv[FILENAMELENGTH];
     } else {  FILE  *ficresvpl;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char fileresvpl[FILENAMELENGTH];
     }  char title[MAXLINE];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     fu=(*f)(u);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     if (fu <= fx) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       if (u >= x) a=x; else b=x;  char command[FILENAMELENGTH];
       SHFT(v,w,x,u)  int  outcmd=0;
         SHFT(fv,fw,fx,fu)  
         } else {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  char filelog[FILENAMELENGTH]; /* Log file */
             v=w;  char filerest[FILENAMELENGTH];
             w=u;  char fileregp[FILENAMELENGTH];
             fv=fw;  char popfile[FILENAMELENGTH];
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
             v=u;  
             fv=fu;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
           }  struct timezone tzp;
         }  extern int gettimeofday();
   }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   nrerror("Too many iterations in brent");  long time_value;
   *xmin=x;  extern long time();
   return fx;  char strcurr[80], strfor[80];
 }  
   char *endptr;
 /****************** mnbrak ***********************/  long lval;
   double dval;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  #define NR_END 1
 {  #define FREE_ARG char*
   double ulim,u,r,q, dum;  #define FTOL 1.0e-10
   double fu;  
    #define NRANSI 
   *fa=(*func)(*ax);  #define ITMAX 200 
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  #define TOL 2.0e-4 
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  #define CGOLD 0.3819660 
       }  #define ZEPS 1.0e-10 
   *cx=(*bx)+GOLD*(*bx-*ax);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #define GOLD 1.618034 
     r=(*bx-*ax)*(*fb-*fc);  #define GLIMIT 100.0 
     q=(*bx-*cx)*(*fb-*fa);  #define TINY 1.0e-20 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  static double maxarg1,maxarg2;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     if ((*bx-u)*(u-*cx) > 0.0) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       fu=(*func)(u);    
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       fu=(*func)(u);  #define rint(a) floor(a+0.5)
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  static double sqrarg;
           SHFT(*fb,*fc,fu,(*func)(u))  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
           }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int agegomp= AGEGOMP;
       u=ulim;  
       fu=(*func)(u);  int imx; 
     } else {  int stepm=1;
       u=(*cx)+GOLD*(*cx-*bx);  /* Stepm, step in month: minimum step interpolation*/
       fu=(*func)(u);  
     }  int estepm;
     SHFT(*ax,*bx,*cx,u)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       SHFT(*fa,*fb,*fc,fu)  
       }  int m,nb;
 }  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 /*************** linmin ************************/  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 int ncom;  double *ageexmed,*agecens;
 double *pcom,*xicom;  double dateintmean=0;
 double (*nrfunc)(double []);  
    double *weight;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  int **s; /* Status */
 {  double *agedc, **covar, idx;
   double brent(double ax, double bx, double cx,  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
                double (*f)(double), double tol, double *xmin);  double *lsurv, *lpop, *tpop;
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
               double *fc, double (*func)(double));  double ftolhess; /* Tolerance for computing hessian */
   int j;  
   double xx,xmin,bx,ax;  /**************** split *************************/
   double fx,fb,fa;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    {
   ncom=n;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   pcom=vector(1,n);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   xicom=vector(1,n);    */ 
   nrfunc=func;    char  *ss;                            /* pointer */
   for (j=1;j<=n;j++) {    int   l1, l2;                         /* length counters */
     pcom[j]=p[j];  
     xicom[j]=xi[j];    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   ax=0.0;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   xx=1.0;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      strcpy( name, path );               /* we got the fullname name because no directory */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 #ifdef DEBUG        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      /* get current working directory */
 #endif      /*    extern  char* getcwd ( char *buf , int len);*/
   for (j=1;j<=n;j++) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     xi[j] *= xmin;        return( GLOCK_ERROR_GETCWD );
     p[j] += xi[j];      }
   }      /* got dirc from getcwd*/
   free_vector(xicom,1,n);      printf(" DIRC = %s \n",dirc);
   free_vector(pcom,1,n);    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /*************** powell ************************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      strcpy( name, ss );         /* save file name */
             double (*func)(double []))      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   void linmin(double p[], double xi[], int n, double *fret,      printf(" DIRC2 = %s \n",dirc);
               double (*func)(double []));    }
   int i,ibig,j;    /* We add a separator at the end of dirc if not exists */
   double del,t,*pt,*ptt,*xit;    l1 = strlen( dirc );                  /* length of directory */
   double fp,fptt;    if( dirc[l1-1] != DIRSEPARATOR ){
   double *xits;      dirc[l1] =  DIRSEPARATOR;
   pt=vector(1,n);      dirc[l1+1] = 0; 
   ptt=vector(1,n);      printf(" DIRC3 = %s \n",dirc);
   xit=vector(1,n);    }
   xits=vector(1,n);    ss = strrchr( name, '.' );            /* find last / */
   *fret=(*func)(p);    if (ss >0){
   for (j=1;j<=n;j++) pt[j]=p[j];      ss++;
   for (*iter=1;;++(*iter)) {      strcpy(ext,ss);                     /* save extension */
     fp=(*fret);      l1= strlen( name);
     ibig=0;      l2= strlen(ss)+1;
     del=0.0;      strncpy( finame, name, l1-l2);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      finame[l1-l2]= 0;
     for (i=1;i<=n;i++)    }
       printf(" %d %.12f",i, p[i]);  
     printf("\n");    return( 0 );                          /* we're done */
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  
 #ifdef DEBUG  /******************************************/
       printf("fret=%lf \n",*fret);  
 #endif  void replace_back_to_slash(char *s, char*t)
       printf("%d",i);fflush(stdout);  {
       linmin(p,xit,n,fret,func);    int i;
       if (fabs(fptt-(*fret)) > del) {    int lg=0;
         del=fabs(fptt-(*fret));    i=0;
         ibig=i;    lg=strlen(t);
       }    for(i=0; i<= lg; i++) {
 #ifdef DEBUG      (s[i] = t[i]);
       printf("%d %.12e",i,(*fret));      if (t[i]== '\\') s[i]='/';
       for (j=1;j<=n;j++) {    }
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  char *trimbb(char *out, char *in)
       for(j=1;j<=n;j++)  { /* Trim multiple blanks in line */
         printf(" p=%.12e",p[j]);    char *s;
       printf("\n");    s=out;
 #endif    while (*in != '\0'){
     }      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        in++;
 #ifdef DEBUG      }
       int k[2],l;      *out++ = *in++;
       k[0]=1;    }
       k[1]=-1;    *out='\0';
       printf("Max: %.12e",(*func)(p));    return s;
       for (j=1;j<=n;j++)  }
         printf(" %.12e",p[j]);  
       printf("\n");  int nbocc(char *s, char occ)
       for(l=0;l<=1;l++) {  {
         for (j=1;j<=n;j++) {    int i,j=0;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    int lg=20;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    i=0;
         }    lg=strlen(s);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    for(i=0; i<= lg; i++) {
       }    if  (s[i] == occ ) j++;
 #endif    }
     return j;
   }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  void cutv(char *u,char *v, char*t, char occ)
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       return;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     }       gives u="abcedf" and v="ghi2j" */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    int i,lg,j,p=0;
     for (j=1;j<=n;j++) {    i=0;
       ptt[j]=2.0*p[j]-pt[j];    for(j=0; j<=strlen(t)-1; j++) {
       xit[j]=p[j]-pt[j];      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       pt[j]=p[j];    }
     }  
     fptt=(*func)(ptt);    lg=strlen(t);
     if (fptt < fp) {    for(j=0; j<p; j++) {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      (u[j] = t[j]);
       if (t < 0.0) {    }
         linmin(p,xit,n,fret,func);       u[p]='\0';
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];     for(j=0; j<= lg; j++) {
           xi[j][n]=xit[j];      if (j>=(p+1))(v[j-p-1] = t[j]);
         }    }
 #ifdef DEBUG  }
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  /********************** nrerror ********************/
           printf(" %.12e",xit[j]);  
         printf("\n");  void nrerror(char error_text[])
 #endif  {
       }    fprintf(stderr,"ERREUR ...\n");
     }    fprintf(stderr,"%s\n",error_text);
   }    exit(EXIT_FAILURE);
 }  }
   /*********************** vector *******************/
 /**** Prevalence limit ****************/  double *vector(int nl, int nh)
   {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double *v;
 {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (!v) nrerror("allocation failure in vector");
      matrix by transitions matrix until convergence is reached */    return v-nl+NR_END;
   }
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  /************************ free vector ******************/
   double **matprod2();  void free_vector(double*v, int nl, int nh)
   double **out, cov[NCOVMAX], **pmij();  {
   double **newm;    free((FREE_ARG)(v+nl-NR_END));
   double agefin, delaymax=50 ; /* Max number of years to converge */  }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /************************ivector *******************************/
     for (j=1;j<=nlstate+ndeath;j++){  int *ivector(long nl,long nh)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
     }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
    cov[1]=1.;    if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  /******************free ivector **************************/
     /* Covariates have to be included here again */  void free_ivector(int *v, long nl, long nh)
      cov[2]=agefin;  {
      free((FREE_ARG)(v+nl-NR_END));
       for (k=1; k<=cptcovn;k++) {  }
         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]);*/  /************************lvector *******************************/
       }  long *lvector(long nl,long nh)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    long *v;
       for (k=1; k<=cptcovprod;k++)    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   /******************free lvector **************************/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  void free_lvector(long *v, long nl, long nh)
   {
     savm=oldm;    free((FREE_ARG)(v+nl-NR_END));
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /******************* imatrix *******************************/
       min=1.;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       max=0.;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       for(i=1; i<=nlstate; i++) {  { 
         sumnew=0;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    int **m; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    
         max=FMAX(max,prlim[i][j]);    /* allocate pointers to rows */ 
         min=FMIN(min,prlim[i][j]);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       }    if (!m) nrerror("allocation failure 1 in matrix()"); 
       maxmin=max-min;    m += NR_END; 
       maxmax=FMAX(maxmax,maxmin);    m -= nrl; 
     }    
     if(maxmax < ftolpl){    
       return prlim;    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 }    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
 /*************** transition probabilities ***************/    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    
 {    /* return pointer to array of pointers to rows */ 
   double s1, s2;    return m; 
   /*double t34;*/  } 
   int i,j,j1, nc, ii, jj;  
   /****************** free_imatrix *************************/
     for(i=1; i<= nlstate; i++){  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(j=1; j<i;j++){        int **m;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        long nch,ncl,nrh,nrl; 
         /*s2 += param[i][j][nc]*cov[nc];*/       /* free an int matrix allocated by imatrix() */ 
         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);*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       }    free((FREE_ARG) (m+nrl-NR_END)); 
       ps[i][j]=s2;  } 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  /******************* matrix *******************************/
     for(j=i+1; j<=nlstate+ndeath;j++){  double **matrix(long nrl, long nrh, long ncl, long nch)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double **m;
       }  
       ps[i][j]=s2;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
     /*ps[3][2]=1;*/    m -= nrl;
   
   for(i=1; i<= nlstate; i++){    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      s1=0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(j=1; j<i; j++)    m[nrl] += NR_END;
       s1+=exp(ps[i][j]);    m[nrl] -= ncl;
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     ps[i][i]=1./(s1+1.);    return m;
     for(j=1; j<i; j++)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];     */
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /*************************free matrix ************************/
   } /* end i */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(jj=1; jj<= nlstate+ndeath; jj++){    free((FREE_ARG)(m+nrl-NR_END));
       ps[ii][jj]=0;  }
       ps[ii][ii]=1;  
     }  /******************* ma3x *******************************/
   }  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;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double ***m;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
    }    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\n ");    m += NR_END;
     }    m -= nrl;
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   goto end;*/    m[nrl] += NR_END;
     return ps;    m[nrl] -= ncl;
 }  
     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)));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    m[nrl][ncl] -= nll;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    for (j=ncl+1; j<=nch; j++) 
   /* in, b, out are matrice of pointers which should have been initialized      m[nrl][j]=m[nrl][j-1]+nlay;
      before: only the contents of out is modified. The function returns    
      a pointer to pointers identical to out */    for (i=nrl+1; i<=nrh; i++) {
   long i, j, k;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for(i=nrl; i<= nrh; i++)      for (j=ncl+1; j<=nch; j++) 
     for(k=ncolol; k<=ncoloh; k++)        m[i][j]=m[i][j-1]+nlay;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    }
         out[i][k] +=in[i][j]*b[j][k];    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   return out;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 }    */
   }
   
 /************* Higher Matrix Product ***************/  /*************************free ma3x ************************/
   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));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      duration (i.e. until    free((FREE_ARG)(m+nrl-NR_END));
      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  
      (typically every 2 years instead of every month which is too big).  /*************** function subdirf ***********/
      Model is determined by parameters x and covariates have to be  char *subdirf(char fileres[])
      included manually here.  {
     /* Caution optionfilefiname is hidden */
      */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   int i, j, d, h, k;    strcat(tmpout,fileres);
   double **out, cov[NCOVMAX];    return tmpout;
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  /*************** function subdirf2 ***********/
   for (i=1;i<=nlstate+ndeath;i++)  char *subdirf2(char fileres[], char *preop)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[i][j]=(i==j ? 1.0 : 0.0);    
       po[i][j][0]=(i==j ? 1.0 : 0.0);    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,"/");
   for(h=1; h <=nhstepm; h++){    strcat(tmpout,preop);
     for(d=1; d <=hstepm; d++){    strcat(tmpout,fileres);
       newm=savm;    return tmpout;
       /* Covariates have to be included here again */  }
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*************** function subdirf3 ***********/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    
       for (k=1; k<=cptcovprod;k++)    /* Caution optionfilefiname is hidden */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    strcat(tmpout,preop2);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    strcat(tmpout,fileres);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    return tmpout;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  }
       savm=oldm;  
       oldm=newm;  /***************** f1dim *************************/
     }  extern int ncom; 
     for(i=1; i<=nlstate+ndeath; i++)  extern double *pcom,*xicom;
       for(j=1;j<=nlstate+ndeath;j++) {  extern double (*nrfunc)(double []); 
         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]);  double f1dim(double x) 
          */  { 
       }    int j; 
   } /* end h */    double f;
   return po;    double *xt; 
 }   
     xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 /*************** log-likelihood *************/    f=(*nrfunc)(xt); 
 double func( double *x)    free_vector(xt,1,ncom); 
 {    return f; 
   int i, ii, j, k, mi, d, kk;  } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  /*****************brent *************************/
   double sw; /* Sum of weights */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double lli; /* Individual log likelihood */  { 
   long ipmx;    int iter; 
   /*extern weight */    double a,b,d,etemp;
   /* We are differentiating ll according to initial status */    double fu,fv,fw,fx;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double ftemp;
   /*for(i=1;i<imx;i++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     printf(" %d\n",s[4][i]);    double e=0.0; 
   */   
   cov[1]=1.;    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    x=w=v=bx; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    fw=fv=fx=(*f)(x); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for (iter=1;iter<=ITMAX;iter++) { 
     for(mi=1; mi<= wav[i]-1; mi++){      xm=0.5*(a+b); 
       for (ii=1;ii<=nlstate+ndeath;ii++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for(d=0; d<dh[mi][i]; d++){      printf(".");fflush(stdout);
         newm=savm;      fprintf(ficlog,".");fflush(ficlog);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  #ifdef DEBUG
         for (kk=1; kk<=cptcovage;kk++) {      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);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      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);
         }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
          #endif
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        *xmin=x; 
         savm=oldm;        return fx; 
         oldm=newm;      } 
              ftemp=fu;
              if (fabs(e) > tol1) { 
       } /* end mult */        r=(x-w)*(fx-fv); 
              q=(x-v)*(fx-fw); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        p=(x-v)*q-(x-w)*r; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        q=2.0*(q-r); 
       ipmx +=1;        if (q > 0.0) p = -p; 
       sw += weight[i];        q=fabs(q); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        etemp=e; 
     } /* end of wave */        e=d; 
   } /* end of individual */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        else { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          d=p/q; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          u=x+d; 
   return -l;          if (u-a < tol2 || b-u < tol2) 
 }            d=SIGN(tol1,xm-x); 
         } 
       } else { 
 /*********** Maximum Likelihood Estimation ***************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 {      fu=(*f)(u); 
   int i,j, iter;      if (fu <= fx) { 
   double **xi,*delti;        if (u >= x) a=x; else b=x; 
   double fret;        SHFT(v,w,x,u) 
   xi=matrix(1,npar,1,npar);          SHFT(fv,fw,fx,fu) 
   for (i=1;i<=npar;i++)          } else { 
     for (j=1;j<=npar;j++)            if (u < x) a=u; else b=u; 
       xi[i][j]=(i==j ? 1.0 : 0.0);            if (fu <= fw || w == x) { 
   printf("Powell\n");              v=w; 
   powell(p,xi,npar,ftol,&iter,&fret,func);              w=u; 
               fv=fw; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));              fw=fu; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 }              fv=fu; 
             } 
 /**** Computes Hessian and covariance matrix ***/          } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    } 
 {    nrerror("Too many iterations in brent"); 
   double  **a,**y,*x,pd;    *xmin=x; 
   double **hess;    return fx; 
   int i, j,jk;  } 
   int *indx;  
   /****************** mnbrak ***********************/
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   void lubksb(double **a, int npar, int *indx, double b[]) ;              double (*func)(double)) 
   void ludcmp(double **a, int npar, int *indx, double *d) ;  { 
     double ulim,u,r,q, dum;
   hess=matrix(1,npar,1,npar);    double fu; 
    
   printf("\nCalculation of the hessian matrix. Wait...\n");    *fa=(*func)(*ax); 
   for (i=1;i<=npar;i++){    *fb=(*func)(*bx); 
     printf("%d",i);fflush(stdout);    if (*fb > *fa) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);      SHFT(dum,*ax,*bx,dum) 
     /*printf(" %f ",p[i]);*/        SHFT(dum,*fb,*fa,dum) 
     /*printf(" %lf ",hess[i][i]);*/        } 
   }    *cx=(*bx)+GOLD*(*bx-*ax); 
      *fc=(*func)(*cx); 
   for (i=1;i<=npar;i++) {    while (*fb > *fc) { 
     for (j=1;j<=npar;j++)  {      r=(*bx-*ax)*(*fb-*fc); 
       if (j>i) {      q=(*bx-*cx)*(*fb-*fa); 
         printf(".%d%d",i,j);fflush(stdout);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         hess[i][j]=hessij(p,delti,i,j);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         hess[j][i]=hess[i][j];          ulim=(*bx)+GLIMIT*(*cx-*bx); 
         /*printf(" %lf ",hess[i][j]);*/      if ((*bx-u)*(u-*cx) > 0.0) { 
       }        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   }        fu=(*func)(u); 
   printf("\n");        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   a=matrix(1,npar,1,npar);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   y=matrix(1,npar,1,npar);        u=ulim; 
   x=vector(1,npar);        fu=(*func)(u); 
   indx=ivector(1,npar);      } else { 
   for (i=1;i<=npar;i++)        u=(*cx)+GOLD*(*cx-*bx); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fu=(*func)(u); 
   ludcmp(a,npar,indx,&pd);      } 
       SHFT(*ax,*bx,*cx,u) 
   for (j=1;j<=npar;j++) {        SHFT(*fa,*fb,*fc,fu) 
     for (i=1;i<=npar;i++) x[i]=0;        } 
     x[j]=1;  } 
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /*************** linmin ************************/
       matcov[i][j]=x[i];  
     }  int ncom; 
   }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   printf("\n#Hessian matrix#\n");   
   for (i=1;i<=npar;i++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for (j=1;j<=npar;j++) {  { 
       printf("%.3e ",hess[i][j]);    double brent(double ax, double bx, double cx, 
     }                 double (*f)(double), double tol, double *xmin); 
     printf("\n");    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   /* Recompute Inverse */    int j; 
   for (i=1;i<=npar;i++)    double xx,xmin,bx,ax; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double fx,fb,fa;
   ludcmp(a,npar,indx,&pd);   
     ncom=n; 
   /*  printf("\n#Hessian matrix recomputed#\n");    pcom=vector(1,n); 
     xicom=vector(1,n); 
   for (j=1;j<=npar;j++) {    nrfunc=func; 
     for (i=1;i<=npar;i++) x[i]=0;    for (j=1;j<=n;j++) { 
     x[j]=1;      pcom[j]=p[j]; 
     lubksb(a,npar,indx,x);      xicom[j]=xi[j]; 
     for (i=1;i<=npar;i++){    } 
       y[i][j]=x[i];    ax=0.0; 
       printf("%.3e ",y[i][j]);    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     printf("\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   }  #ifdef DEBUG
   */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_matrix(a,1,npar,1,npar);  #endif
   free_matrix(y,1,npar,1,npar);    for (j=1;j<=n;j++) { 
   free_vector(x,1,npar);      xi[j] *= xmin; 
   free_ivector(indx,1,npar);      p[j] += xi[j]; 
   free_matrix(hess,1,npar,1,npar);    } 
     free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 }  } 
   
 /*************** hessian matrix ****************/  char *asc_diff_time(long time_sec, char ascdiff[])
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    long sec_left, days, hours, minutes;
   int i;    days = (time_sec) / (60*60*24);
   int l=1, lmax=20;    sec_left = (time_sec) % (60*60*24);
   double k1,k2;    hours = (sec_left) / (60*60) ;
   double p2[NPARMAX+1];    sec_left = (sec_left) %(60*60);
   double res;    minutes = (sec_left) /60;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    sec_left = (sec_left) % (60);
   double fx;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   int k=0,kmax=10;    return ascdiff;
   double l1;  }
   
   fx=func(x);  /*************** powell ************************/
   for (i=1;i<=npar;i++) p2[i]=x[i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for(l=0 ; l <=lmax; l++){              double (*func)(double [])) 
     l1=pow(10,l);  { 
     delts=delt;    void linmin(double p[], double xi[], int n, double *fret, 
     for(k=1 ; k <kmax; k=k+1){                double (*func)(double [])); 
       delt = delta*(l1*k);    int i,ibig,j; 
       p2[theta]=x[theta] +delt;    double del,t,*pt,*ptt,*xit;
       k1=func(p2)-fx;    double fp,fptt;
       p2[theta]=x[theta]-delt;    double *xits;
       k2=func(p2)-fx;    int niterf, itmp;
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    pt=vector(1,n); 
          ptt=vector(1,n); 
 #ifdef DEBUG    xit=vector(1,n); 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    xits=vector(1,n); 
 #endif    *fret=(*func)(p); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (*iter=1;;++(*iter)) { 
         k=kmax;      fp=(*fret); 
       }      ibig=0; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      del=0.0; 
         k=kmax; l=lmax*10.;      last_time=curr_time;
       }      (void) gettimeofday(&curr_time,&tzp);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
         delts=delt;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
       }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     }     for (i=1;i<=n;i++) {
   }        printf(" %d %.12f",i, p[i]);
   delti[theta]=delts;        fprintf(ficlog," %d %.12lf",i, p[i]);
   return res;        fprintf(ficrespow," %.12lf", p[i]);
        }
 }      printf("\n");
       fprintf(ficlog,"\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)      fprintf(ficrespow,"\n");fflush(ficrespow);
 {      if(*iter <=3){
   int i;        tm = *localtime(&curr_time.tv_sec);
   int l=1, l1, lmax=20;        strcpy(strcurr,asctime(&tm));
   double k1,k2,k3,k4,res,fx;  /*       asctime_r(&tm,strcurr); */
   double p2[NPARMAX+1];        forecast_time=curr_time; 
   int k;        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   fx=func(x);          strcurr[itmp-1]='\0';
   for (k=1; k<=2; k++) {        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (i=1;i<=npar;i++) p2[i]=x[i];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(niterf=10;niterf<=30;niterf+=10){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     k1=func(p2)-fx;          tmf = *localtime(&forecast_time.tv_sec);
    /*      asctime_r(&tmf,strfor); */
     p2[thetai]=x[thetai]+delti[thetai]/k;          strcpy(strfor,asctime(&tmf));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          itmp = strlen(strfor);
     k2=func(p2)-fx;          if(strfor[itmp-1]=='\n')
            strfor[itmp-1]='\0';
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     k3=func(p2)-fx;        }
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (i=1;i<=n;i++) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     k4=func(p2)-fx;        fptt=(*fret); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #ifdef DEBUG
 #ifdef DEBUG        printf("fret=%lf \n",*fret);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        fprintf(ficlog,"fret=%lf \n",*fret);
 #endif  #endif
   }        printf("%d",i);fflush(stdout);
   return res;        fprintf(ficlog,"%d",i);fflush(ficlog);
 }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 /************** Inverse of matrix **************/          del=fabs(fptt-(*fret)); 
 void ludcmp(double **a, int n, int *indx, double *d)          ibig=i; 
 {        } 
   int i,imax,j,k;  #ifdef DEBUG
   double big,dum,sum,temp;        printf("%d %.12e",i,(*fret));
   double *vv;        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
   vv=vector(1,n);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   *d=1.0;          printf(" x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=n;i++) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     big=0.0;        }
     for (j=1;j<=n;j++)        for(j=1;j<=n;j++) {
       if ((temp=fabs(a[i][j])) > big) big=temp;          printf(" p=%.12e",p[j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          fprintf(ficlog," p=%.12e",p[j]);
     vv[i]=1.0/big;        }
   }        printf("\n");
   for (j=1;j<=n;j++) {        fprintf(ficlog,"\n");
     for (i=1;i<j;i++) {  #endif
       sum=a[i][j];      } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       a[i][j]=sum;  #ifdef DEBUG
     }        int k[2],l;
     big=0.0;        k[0]=1;
     for (i=j;i<=n;i++) {        k[1]=-1;
       sum=a[i][j];        printf("Max: %.12e",(*func)(p));
       for (k=1;k<j;k++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         sum -= a[i][k]*a[k][j];        for (j=1;j<=n;j++) {
       a[i][j]=sum;          printf(" %.12e",p[j]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          fprintf(ficlog," %.12e",p[j]);
         big=dum;        }
         imax=i;        printf("\n");
       }        fprintf(ficlog,"\n");
     }        for(l=0;l<=1;l++) {
     if (j != imax) {          for (j=1;j<=n;j++) {
       for (k=1;k<=n;k++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         dum=a[imax][k];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[imax][k]=a[j][k];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         a[j][k]=dum;          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       *d = -(*d);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       vv[imax]=vv[j];        }
     }  #endif
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {        free_vector(xit,1,n); 
       dum=1.0/(a[j][j]);        free_vector(xits,1,n); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
   }        return; 
   free_vector(vv,1,n);  /* Doesn't work */      } 
 ;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 void lubksb(double **a, int n, int *indx, double b[])        xit[j]=p[j]-pt[j]; 
 {        pt[j]=p[j]; 
   int i,ii=0,ip,j;      } 
   double sum;      fptt=(*func)(ptt); 
        if (fptt < fp) { 
   for (i=1;i<=n;i++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     ip=indx[i];        if (t < 0.0) { 
     sum=b[ip];          linmin(p,xit,n,fret,func); 
     b[ip]=b[i];          for (j=1;j<=n;j++) { 
     if (ii)            xi[j][ibig]=xi[j][n]; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            xi[j][n]=xit[j]; 
     else if (sum) ii=i;          }
     b[i]=sum;  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=n;i>=1;i--) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     sum=b[i];          for(j=1;j<=n;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            printf(" %.12e",xit[j]);
     b[i]=sum/a[i][i];            fprintf(ficlog," %.12e",xit[j]);
   }          }
 }          printf("\n");
           fprintf(ficlog,"\n");
 /************ Frequencies ********************/  #endif
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)        }
 {  /* Some frequencies */      } 
      } 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  } 
   double ***freq; /* Frequencies */  
   double *pp;  /**** Prevalence limit (stable or period prevalence)  ****************/
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   char fileresp[FILENAMELENGTH];  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   pp=vector(1,nlstate);       matrix by transitions matrix until convergence is reached */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");    int i, ii,j,k;
   strcat(fileresp,fileres);    double min, max, maxmin, maxmax,sumnew=0.;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double **matprod2();
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double **out, cov[NCOVMAX+1], **pmij();
     exit(0);    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   j=cptcoveff;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
   
   for(k1=1; k1<=j;k1++){     cov[1]=1.;
    for(i1=1; i1<=ncodemax[k1];i1++){   
        j1++;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
          scanf("%d", i);*/      newm=savm;
         for (i=-1; i<=nlstate+ndeath; i++)        /* Covariates have to be included here again */
          for (jk=-1; jk<=nlstate+ndeath; jk++)         cov[2]=agefin;
            for(m=agemin; m <= agemax+3; m++)    
              freq[i][jk][m]=0;        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         dateintsum=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]]);*/
         k2cpt=0;        }
        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]])        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                bool=0;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
          }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
          if (bool==1) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
            for(m=firstpass; m<=lastpass; m++){  
              k2=anint[m][i]+(mint[m][i]/12.);      savm=oldm;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      oldm=newm;
                if(agev[m][i]==0) agev[m][i]=agemax+1;      maxmax=0.;
                if(agev[m][i]==1) agev[m][i]=agemax+2;      for(j=1;j<=nlstate;j++){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        min=1.;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        max=0.;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        for(i=1; i<=nlstate; i++) {
                  dateintsum=dateintsum+k2;          sumnew=0;
                  k2cpt++;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
                }          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
              }          min=FMIN(min,prlim[i][j]);
            }        }
          }        maxmin=max-min;
        }        maxmax=FMAX(maxmax,maxmin);
         if  (cptcovn>0) {      }
          fprintf(ficresp, "\n#********** Variable ");      if(maxmax < ftolpl){
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        return prlim;
        fprintf(ficresp, "**********\n#");      }
         }    }
        for(i=1; i<=nlstate;i++)  }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");  /*************** transition probabilities ***************/ 
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     if(i==(int)agemax+3)  {
       printf("Total");    double s1, s2;
     else    /*double t34;*/
       printf("Age %d", i);    int i,j,j1, nc, ii, jj;
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for(i=1; i<= nlstate; i++){
         pp[jk] += freq[jk][m][i];        for(j=1; j<i;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(jk=1; jk <=nlstate ; jk++){            /*s2 += param[i][j][nc]*cov[nc];*/
       for(m=-1, pos=0; m <=0 ; m++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         pos += freq[jk][m][i];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       if(pp[jk]>=1.e-10)          }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          ps[i][j]=s2;
       else  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      for(jk=1; jk <=nlstate ; jk++){            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         pp[jk] += freq[jk][m][i];          }
      }          ps[i][j]=s2;
         }
     for(jk=1,pos=0; jk <=nlstate ; jk++)      }
       pos += pp[jk];      /*ps[3][2]=1;*/
     for(jk=1; jk <=nlstate ; jk++){      
       if(pos>=1.e-5)      for(i=1; i<= nlstate; i++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        s1=0;
       else        for(j=1; j<i; j++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          s1+=exp(ps[i][j]);
       if( i <= (int) agemax){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         if(pos>=1.e-5){        }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for(j=i+1; j<=nlstate+ndeath; j++){
           probs[i][jk][j1]= pp[jk]/pos;          s1+=exp(ps[i][j]);
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }        }
       else        ps[i][i]=1./(s1+1.);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        for(j=1; j<i; j++)
       }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        for(j=i+1; j<=nlstate+ndeath; j++)
     for(jk=-1; jk <=nlstate+ndeath; jk++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(m=-1; m <=nlstate+ndeath; m++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      } /* end i */
     if(i <= (int) agemax)      
       fprintf(ficresp,"\n");      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     printf("\n");        for(jj=1; jj<= nlstate+ndeath; jj++){
     }          ps[ii][jj]=0;
     }          ps[ii][ii]=1;
  }        }
   dateintmean=dateintsum/k2cpt;      }
        
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   free_vector(pp,1,nlstate);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
   /* End of Freq */  /*       } */
 }  /*       printf("\n "); */
   /*        } */
 /************ Prevalence ********************/  /*        printf("\n ");printf("%lf ",cov[2]); */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)         /*
 {  /* Some frequencies */        for(i=1; i<= npar; i++) printf("%f ",x[i]);
          goto end;*/
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      return ps;
   double ***freq; /* Frequencies */  }
   double *pp;  
   double pos, k2;  /**************** Product of 2 matrices ******************/
   
   pp=vector(1,nlstate);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
      /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   j1=0;    /* in, b, out are matrice of pointers which should have been initialized 
         before: only the contents of out is modified. The function returns
   j=cptcoveff;       a pointer to pointers identical to out */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    long i, j, k;
      for(i=nrl; i<= nrh; i++)
  for(k1=1; k1<=j;k1++){      for(k=ncolol; k<=ncoloh; k++)
     for(i1=1; i1<=ncodemax[k1];i1++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       j1++;          out[i][k] +=in[i][j]*b[j][k];
    
       for (i=-1; i<=nlstate+ndeath; i++)      return out;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    }
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  
        /************* Higher Matrix Product ***************/
       for (i=1; i<=imx; i++) {  
         bool=1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         if  (cptcovn>0) {  {
           for (z1=1; z1<=cptcoveff; z1++)    /* Computes the transition matrix starting at age 'age' over 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       'nhstepm*hstepm*stepm' months (i.e. until
               bool=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         }       nhstepm*hstepm matrices. 
         if (bool==1) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           for(m=firstpass; m<=lastpass; m++){       (typically every 2 years instead of every month which is too big 
             k2=anint[m][i]+(mint[m][i]/12.);       for the memory).
             if ((k2>=dateprev1) && (k2<=dateprev2)) {       Model is determined by parameters x and covariates have to be 
               if(agev[m][i]==0) agev[m][i]=agemax+1;       included manually here. 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];       */
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];    
             }    int i, j, d, h, k;
           }    double **out, cov[NCOVMAX+1];
         }    double **newm;
       }  
          /* Hstepm could be zero and should return the unit matrix */
         for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=nlstate+ndeath;i++)
           for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=nlstate+ndeath;j++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
               pp[jk] += freq[jk][m][i];        po[i][j][0]=(i==j ? 1.0 : 0.0);
           }      }
           for(jk=1; jk <=nlstate ; jk++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             for(m=-1, pos=0; m <=0 ; m++)    for(h=1; h <=nhstepm; h++){
             pos += freq[jk][m][i];      for(d=1; d <=hstepm; d++){
         }        newm=savm;
                /* Covariates have to be included here again */
          for(jk=1; jk <=nlstate ; jk++){        cov[1]=1.;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
              pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) 
          }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                  for (k=1; k<=cptcovage;k++)
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
          for(jk=1; jk <=nlstate ; jk++){                    cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            if( i <= (int) agemax){  
              if(pos>=1.e-5){  
                probs[i][jk][j1]= pp[jk]/pos;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
              }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
            }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
          }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
         }        oldm=newm;
     }      }
   }      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   free_vector(pp,1,nlstate);        }
        /*printf("h=%d ",h);*/
 }  /* End of Freq */    } /* end h */
   /*     printf("\n H=%d \n",h); */
 /************* Waves Concatenation ***************/    return po;
   }
 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.  /*************** log-likelihood *************/
      Death is a valid wave (if date is known).  double func( double *x)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    int i, ii, j, k, mi, d, kk;
      and mw[mi+1][i]. dh depends on stepm.    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      */    double **out;
     double sw; /* Sum of weights */
   int i, mi, m;    double lli; /* Individual log likelihood */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    int s1, s2;
      double sum=0., jmean=0.;*/    double bbh, survp;
     long ipmx;
   int j, k=0,jk, ju, jl;    /*extern weight */
   double sum=0.;    /* We are differentiating ll according to initial status */
   jmin=1e+5;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   jmax=-1;    /*for(i=1;i<imx;i++) 
   jmean=0.;      printf(" %d\n",s[4][i]);
   for(i=1; i<=imx; i++){    */
     mi=0;    cov[1]=1.;
     m=firstpass;  
     while(s[m][i] <= nlstate){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    if(mle==1){
       if(m >=lastpass)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         break;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else        for(mi=1; mi<= wav[i]-1; mi++){
         m++;          for (ii=1;ii<=nlstate+ndeath;ii++)
     }/* end while */            for (j=1;j<=nlstate+ndeath;j++){
     if (s[m][i] > nlstate){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       mi++;     /* Death is another wave */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */            }
          /* Only death is a correct wave */          for(d=0; d<dh[mi][i]; d++){
       mw[mi][i]=m;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     wav[i]=mi;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if(mi==0)            }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for(i=1; i<=imx; i++){            oldm=newm;
     for(mi=1; mi<wav[i];mi++){          } /* end mult */
       if (stepm <=0)        
         dh[mi][i]=1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       else{          /* But now since version 0.9 we anticipate for bias at large stepm.
         if (s[mw[mi+1][i]][i] > nlstate) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           if (agedc[i] < 2*AGESUP) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);           * the nearest (and in case of equal distance, to the lowest) interval but now
           if(j==0) j=1;  /* Survives at least one month after exam */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           k=k+1;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           if (j >= jmax) jmax=j;           * probability in order to take into account the bias as a fraction of the way
           if (j <= jmin) jmin=j;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           sum=sum+j;           * -stepm/2 to stepm/2 .
           /* if (j<10) printf("j=%d num=%d ",j,i); */           * For stepm=1 the results are the same as for previous versions of Imach.
           }           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
         else{          s1=s[mw[mi][i]][i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          s2=s[mw[mi+1][i]][i];
           k=k+1;          bbh=(double)bh[mi][i]/(double)stepm; 
           if (j >= jmax) jmax=j;          /* bias bh is positive if real duration
           else if (j <= jmin)jmin=j;           * is higher than the multiple of stepm and negative otherwise.
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */           */
           sum=sum+j;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         }          if( s2 > nlstate){ 
         jk= j/stepm;            /* i.e. if s2 is a death state and if the date of death is known 
         jl= j -jk*stepm;               then the contribution to the likelihood is the probability to 
         ju= j -(jk+1)*stepm;               die between last step unit time and current  step unit time, 
         if(jl <= -ju)               which is also equal to probability to die before dh 
           dh[mi][i]=jk;               minus probability to die before dh-stepm . 
         else               In version up to 0.92 likelihood was computed
           dh[mi][i]=jk+1;          as if date of death was unknown. Death was treated as any other
         if(dh[mi][i]==0)          health state: the date of the interview describes the actual state
           dh[mi][i]=1; /* At least one step */          and not the date of a change in health state. The former idea was
       }          to consider that at each interview the state was recorded
     }          (healthy, disable or death) and IMaCh was corrected; but when we
   }          introduced the exact date of death then we should have modified
   jmean=sum/k;          the contribution of an exact death to the likelihood. This new
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          contribution is smaller and very dependent of the step unit
  }          stepm. It is no more the probability to die between last interview
 /*********** Tricode ****************************/          and month of death but the probability to survive from last
 void tricode(int *Tvar, int **nbcode, int imx)          interview up to one month before death multiplied by the
 {          probability to die within a month. Thanks to Chris
   int Ndum[20],ij=1, k, j, i;          Jackson for correcting this bug.  Former versions increased
   int cptcode=0;          mortality artificially. The bad side is that we add another loop
   cptcoveff=0;          which slows down the processing. The difference can be up to 10%
            lower mortality.
   for (k=0; k<19; k++) Ndum[k]=0;            */
   for (k=1; k<=7; k++) ncodemax[k]=0;            lli=log(out[s1][s2] - savm[s1][s2]);
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {          } else if  (s2==-2) {
       ij=(int)(covar[Tvar[j]][i]);            for (j=1,survp=0. ; j<=nlstate; j++) 
       Ndum[ij]++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            /*survp += out[s1][j]; */
       if (ij > cptcode) cptcode=ij;            lli= log(survp);
     }          }
           
     for (i=0; i<=cptcode; i++) {          else if  (s2==-4) { 
       if(Ndum[i]!=0) ncodemax[j]++;            for (j=3,survp=0. ; j<=nlstate; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     ij=1;            lli= log(survp); 
           } 
   
     for (i=1; i<=ncodemax[j]; i++) {          else if  (s2==-5) { 
       for (k=0; k<=19; k++) {            for (j=1,survp=0. ; j<=2; j++)  
         if (Ndum[k] != 0) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           nbcode[Tvar[j]][ij]=k;            lli= log(survp); 
           ij++;          } 
         }          
         if (ij > ncodemax[j]) break;          else{
       }              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   }            } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
  for (k=0; k<19; k++) Ndum[k]=0;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
  for (i=1; i<=ncovmodel-2; i++) {          ipmx +=1;
       ij=Tvar[i];          sw += weight[i];
       Ndum[ij]++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
       } /* end of individual */
  ij=1;    }  else if(mle==2){
  for (i=1; i<=10; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    if((Ndum[i]!=0) && (i<=ncov)){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Tvaraff[ij]=i;        for(mi=1; mi<= wav[i]-1; mi++){
      ij++;          for (ii=1;ii<=nlstate+ndeath;ii++)
    }            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);
     cptcoveff=ij-1;            }
 }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
 /*********** Health Expectancies ****************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   /* Health expectancies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, j, nhstepm, hstepm, h;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double age, agelim,hf;            savm=oldm;
   double ***p3mat;            oldm=newm;
            } /* end mult */
   fprintf(ficreseij,"# Health expectancies\n");        
   fprintf(ficreseij,"# Age");          s1=s[mw[mi][i]][i];
   for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
     for(j=1; j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
       fprintf(ficreseij," %1d-%1d",i,j);          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 */
   fprintf(ficreseij,"\n");          ipmx +=1;
           sw += weight[i];
   hstepm=1*YEARM; /*  Every j years of age (in month) */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } /* end of wave */
       } /* end of individual */
   agelim=AGESUP;    }  else if(mle==3){  /* exponential inter-extrapolation */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* nhstepm age range expressed in number of stepm */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for(mi=1; mi<= wav[i]-1; mi++){
     /* Typically if 20 years = 20*12/6=40 stepm */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (stepm >= YEARM) hstepm=1;            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(d=0; d<dh[mi][i]; d++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           eij[i][j][(int)age] +=p3mat[i][j][h];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
                oldm=newm;
     hf=1;          } /* end mult */
     if (stepm >= YEARM) hf=stepm/YEARM;        
     fprintf(ficreseij,"%.0f",age );          s1=s[mw[mi][i]][i];
     for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       for(j=1; j<=nlstate;j++){          bbh=(double)bh[mi][i]/(double)stepm; 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          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 */
       }          ipmx +=1;
     fprintf(ficreseij,"\n");          sw += weight[i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
 }      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
 /************ Variance ******************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 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)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   /* Variance of health expectancies */          for (ii=1;ii<=nlstate+ndeath;ii++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (j=1;j<=nlstate+ndeath;j++){
   double **newm;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **dnewm,**doldm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h;            }
   int k, cptcode;          for(d=0; d<dh[mi][i]; d++){
   double *xp;            newm=savm;
   double **gp, **gm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***gradg, ***trgradg;            for (kk=1; kk<=cptcovage;kk++) {
   double ***p3mat;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double age,agelim;            }
   int theta;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    fprintf(ficresvij,"# Covariances of life expectancies\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficresvij,"# Age");            savm=oldm;
   for(i=1; i<=nlstate;i++)            oldm=newm;
     for(j=1; j<=nlstate;j++)          } /* end mult */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        
   fprintf(ficresvij,"\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   xp=vector(1,npar);          if( s2 > nlstate){ 
   dnewm=matrix(1,nlstate,1,npar);            lli=log(out[s1][s2] - savm[s1][s2]);
   doldm=matrix(1,nlstate,1,nlstate);          }else{
              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   hstepm=1*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          ipmx +=1;
   agelim = AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     if (stepm >= YEARM) hstepm=1;        } /* end of wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } /* end of individual */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gp=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gm=matrix(0,nhstepm,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){ /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (popbased==1) {            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<= nlstate; j++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(h=0; h<=nhstepm; h++){            savm=oldm;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            oldm=newm;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          } /* end mult */
         }        
       }          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ipmx +=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            sw += weight[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       if (popbased==1) {        } /* end of wave */
         for(i=1; i<=nlstate;i++)      } /* end of individual */
           prlim[i][i]=probs[(int)age][i][ij];    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<= nlstate; j++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(h=0; h<=nhstepm; h++){    return -l;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  /*************** log-likelihood *************/
       }  double funcone( double *x)
   {
       for(j=1; j<= nlstate; j++)    /* Same as likeli but slower because of a lot of printf and if */
         for(h=0; h<=nhstepm; h++){    int i, ii, j, k, mi, d, kk;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         }    double **out;
     } /* End theta */    double lli; /* Individual log likelihood */
     double llt;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int s1, s2;
     double bbh, survp;
     for(h=0; h<=nhstepm; h++)    /*extern weight */
       for(j=1; j<=nlstate;j++)    /* We are differentiating ll according to initial status */
         for(theta=1; theta <=npar; theta++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           trgradg[h][j][theta]=gradg[h][theta][j];    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     for(i=1;i<=nlstate;i++)    */
       for(j=1;j<=nlstate;j++)    cov[1]=1.;
         vareij[i][j][(int)age] =0.;  
     for(h=0;h<=nhstepm;h++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=1;i<=nlstate;i++)      for(mi=1; mi<= wav[i]-1; mi++){
           for(j=1;j<=nlstate;j++)        for (ii=1;ii<=nlstate+ndeath;ii++)
             vareij[i][j][(int)age] += doldm[i][j];          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);
     h=1;          }
     if (stepm >= YEARM) h=stepm/YEARM;        for(d=0; d<dh[mi][i]; d++){
     fprintf(ficresvij,"%.0f ",age );          newm=savm;
     for(i=1; i<=nlstate;i++)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1; j<=nlstate;j++){          for (kk=1; kk<=cptcovage;kk++) {
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }          }
     fprintf(ficresvij,"\n");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_matrix(gp,0,nhstepm,1,nlstate);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_matrix(gm,0,nhstepm,1,nlstate);          savm=oldm;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          oldm=newm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        } /* end mult */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
   } /* End age */        s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
   free_vector(xp,1,npar);        bbh=(double)bh[mi][i]/(double)stepm; 
   free_matrix(doldm,1,nlstate,1,npar);        /* bias is positive if real duration
   free_matrix(dnewm,1,nlstate,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
          */
 }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
 /************ Variance of prevlim ******************/        } else if  (s2==-2) {
 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)          for (j=1,survp=0. ; j<=nlstate; j++) 
 {            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* Variance of prevalence limit */          lli= log(survp);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }else if (mle==1){
   double **newm;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **dnewm,**doldm;        } else if(mle==2){
   int i, j, nhstepm, hstepm;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   int k, cptcode;        } else if(mle==3){  /* exponential inter-extrapolation */
   double *xp;          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 *gp, *gm;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **gradg, **trgradg;          lli=log(out[s1][s2]); /* Original formula */
   double age,agelim;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   int theta;          lli=log(out[s1][s2]); /* Original formula */
            } /* End of if */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        ipmx +=1;
   fprintf(ficresvpl,"# Age");        sw += weight[i];
   for(i=1; i<=nlstate;i++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresvpl," %1d-%1d",i,i);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   fprintf(ficresvpl,"\n");        if(globpr){
           fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   xp=vector(1,npar);   %11.6f %11.6f %11.6f ", \
   dnewm=matrix(1,nlstate,1,npar);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   doldm=matrix(1,nlstate,1,nlstate);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   hstepm=1*YEARM; /* Every year of age */            llt +=ll[k]*gipmx/gsw;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   agelim = AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          fprintf(ficresilk," %10.6f\n", -llt);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;      } /* end of wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    } /* end of individual */
     gradg=matrix(1,npar,1,nlstate);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     gp=vector(1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     gm=vector(1,nlstate);    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 */
     for(theta=1; theta <=npar; theta++){      gipmx=ipmx;
       for(i=1; i<=npar; i++){ /* Computes gradient */      gsw=sw;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    return -l;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];  
      /*************** function likelione ***********/
       for(i=1; i<=npar; i++) /* Computes gradient */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* This routine should help understanding what is done with 
       for(i=1;i<=nlstate;i++)       the selection of individuals/waves and
         gm[i] = prlim[i][i];       to check the exact contribution to the likelihood.
        Plotting could be done.
       for(i=1;i<=nlstate;i++)     */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int k;
     } /* End theta */  
     if(*globpri !=0){ /* Just counts and sums, no printings */
     trgradg =matrix(1,nlstate,1,npar);      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
     for(j=1; j<=nlstate;j++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(theta=1; theta <=npar; theta++)        printf("Problem with resultfile: %s\n", fileresilk);
         trgradg[j][theta]=gradg[theta][j];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
     for(i=1;i<=nlstate;i++)      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");
       varpl[i][(int)age] =0.;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for(k=1; k<=nlstate; k++) 
     for(i=1;i<=nlstate;i++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    *fretone=(*funcone)(p);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    if(*globpri !=0){
     fprintf(ficresvpl,"\n");      fclose(ficresilk);
     free_vector(gp,1,nlstate);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     free_vector(gm,1,nlstate);      fflush(fichtm); 
     free_matrix(gradg,1,npar,1,nlstate);    } 
     free_matrix(trgradg,1,nlstate,1,npar);    return;
   } /* End age */  }
   
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  /*********** Maximum Likelihood Estimation ***************/
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 }  {
     int i,j, iter;
 /************ Variance of one-step probabilities  ******************/    double **xi;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double fret;
 {    double fretone; /* Only one call to likelihood */
   int i, j;    /*  char filerespow[FILENAMELENGTH];*/
   int k=0, cptcode;    xi=matrix(1,npar,1,npar);
   double **dnewm,**doldm;    for (i=1;i<=npar;i++)
   double *xp;      for (j=1;j<=npar;j++)
   double *gp, *gm;        xi[i][j]=(i==j ? 1.0 : 0.0);
   double **gradg, **trgradg;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double age,agelim, cov[NCOVMAX];    strcpy(filerespow,"pow"); 
   int theta;    strcat(filerespow,fileres);
   char fileresprob[FILENAMELENGTH];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   strcpy(fileresprob,"prob");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   strcat(fileresprob,fileres);    }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     printf("Problem with resultfile: %s\n", fileresprob);    for (i=1;i<=nlstate;i++)
   }      for(j=1;j<=nlstate+ndeath;j++)
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   
   xp=vector(1,npar);    powell(p,xi,npar,ftol,&iter,&fret,func);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   cov[1]=1;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (age=bage; age<=fage; age ++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     cov[2]=age;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  /**** Computes Hessian and covariance matrix ***/
      void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++)    double  **a,**y,*x,pd;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **hess;
          int i, j,jk;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    int *indx;
      
       k=0;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(i=1; i<= (nlstate+ndeath); i++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         for(j=1; j<=(nlstate+ndeath);j++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
            k=k+1;    void ludcmp(double **a, int npar, int *indx, double *d) ;
           gp[k]=pmmij[i][j];    double gompertz(double p[]);
         }    hess=matrix(1,npar,1,npar);
       }  
     printf("\nCalculation of the hessian matrix. Wait...\n");
       for(i=1; i<=npar; i++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++){
          printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);     
       k=0;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(i=1; i<=(nlstate+ndeath); i++){      
         for(j=1; j<=(nlstate+ndeath);j++){      /*  printf(" %f ",p[i]);
           k=k+1;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
           gm[k]=pmmij[i][j];    }
         }    
       }    for (i=1;i<=npar;i++) {
            for (j=1;j<=npar;j++)  {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        if (j>i) { 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          
       for(theta=1; theta <=npar; theta++)          hess[j][i]=hess[i][j];    
       trgradg[j][theta]=gradg[theta][j];          /*printf(" %lf ",hess[i][j]);*/
          }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    }
     printf("\n");
      pmij(pmmij,cov,ncovmodel,x,nlstate);    fprintf(ficlog,"\n");
   
      k=0;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        for(j=1; j<=(nlstate+ndeath);j++){    
          k=k+1;    a=matrix(1,npar,1,npar);
          gm[k]=pmmij[i][j];    y=matrix(1,npar,1,npar);
         }    x=vector(1,npar);
      }    indx=ivector(1,npar);
          for (i=1;i<=npar;i++)
      /*printf("\n%d ",(int)age);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    ludcmp(a,npar,indx,&pd);
          
     for (j=1;j<=npar;j++) {
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      for (i=1;i<=npar;i++) x[i]=0;
      }*/      x[j]=1;
       lubksb(a,npar,indx,x);
   fprintf(ficresprob,"\n%d ",(int)age);      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      }
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=1;i<=npar;i++) { 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=npar;j++) { 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        printf("%.3e ",hess[i][j]);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        fprintf(ficlog,"%.3e ",hess[i][j]);
 }      }
  free_vector(xp,1,npar);      printf("\n");
 fclose(ficresprob);      fprintf(ficlog,"\n");
  exit(0);    }
 }  
     /* Recompute Inverse */
 /***********************************************/    for (i=1;i<=npar;i++)
 /**************** Main Program *****************/      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 /***********************************************/    ludcmp(a,npar,indx,&pd);
   
 int main(int argc, char *argv[])    /*  printf("\n#Hessian matrix recomputed#\n");
 {  
     for (j=1;j<=npar;j++) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      for (i=1;i<=npar;i++) x[i]=0;
   double agedeb, agefin,hf;      x[j]=1;
   double agemin=1.e20, agemax=-1.e20;      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   double fret;        y[i][j]=x[i];
   double **xi,tmp,delta;        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
   double dum; /* Dummy variable */      }
   double ***p3mat;      printf("\n");
   int *indx;      fprintf(ficlog,"\n");
   char line[MAXLINE], linepar[MAXLINE];    }
   char title[MAXLINE];    */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    free_matrix(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   char filerest[FILENAMELENGTH];    free_matrix(hess,1,npar,1,npar);
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  }
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */  /*************** hessian matrix ****************/
   int c,  h , cpt,l;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   int ju,jl, mi;  {
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int i;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int l=1, lmax=20;
   int mobilav=0,popforecast=0;    double k1,k2;
   int hstepm, nhstepm;    double p2[MAXPARM+1]; /* identical to x */
   int *popage;/*boolprev=0 if date and zero if wave*/    double res;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
   double bage, fage, age, agelim, agebase;    int k=0,kmax=10;
   double ftolpl=FTOL;    double l1;
   double **prlim;  
   double *severity;    fx=func(x);
   double ***param; /* Matrix of parameters */    for (i=1;i<=npar;i++) p2[i]=x[i];
   double  *p;    for(l=0 ; l <=lmax; l++){
   double **matcov; /* Matrix of covariance */      l1=pow(10,l);
   double ***delti3; /* Scale */      delts=delt;
   double *delti; /* Scale */      for(k=1 ; k <kmax; k=k+1){
   double ***eij, ***vareij;        delt = delta*(l1*k);
   double **varpl; /* Variances of prevalence limits by age */        p2[theta]=x[theta] +delt;
   double *epj, vepp;        k1=func(p2)-fx;
   double kk1, kk2;        p2[theta]=x[theta]-delt;
   double *popeffectif,*popcount;        k2=func(p2)-fx;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double yp,yp1,yp2;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";  #ifdef DEBUGHESS
   char *alph[]={"a","a","b","c","d","e"}, str[4];        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
   char z[1]="c", occ;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 #include <sys/time.h>        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 #include <time.h>          k=kmax;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   /* long total_usecs;          k=kmax; l=lmax*10.;
   struct timeval start_time, end_time;        }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          delts=delt;
         }
       }
   printf("\n%s",version);    }
   if(argc <=1){    delti[theta]=delts;
     printf("\nEnter the parameter file name: ");    return res; 
     scanf("%s",pathtot);    
   }  }
   else{  
     strcpy(pathtot,argv[1]);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   }  {
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    int i;
   /*cygwin_split_path(pathtot,path,optionfile);    int l=1, l1, lmax=20;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double k1,k2,k3,k4,res,fx;
   /* cutv(path,optionfile,pathtot,'\\');*/    double p2[MAXPARM+1];
     int k;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    fx=func(x);
   chdir(path);    for (k=1; k<=2; k++) {
   replace(pathc,path);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
 /*-------- arguments in the command line --------*/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
   strcpy(fileres,"r");    
   strcat(fileres, optionfilefiname);      p2[thetai]=x[thetai]+delti[thetai]/k;
   strcat(fileres,".txt");    /* Other files have txt extension */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
   /*---------arguments file --------*/    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     printf("Problem with optionfile %s\n",optionfile);      k3=func(p2)-fx;
     goto end;    
   }      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   strcpy(filereso,"o");      k4=func(p2)-fx;
   strcat(filereso,fileres);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   if((ficparo=fopen(filereso,"w"))==NULL) {  #ifdef DEBUG
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      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 %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    return res;
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************** Inverse of matrix **************/
     fputs(line,ficparo);  void ludcmp(double **a, int n, int *indx, double *d) 
   }  { 
   ungetc(c,ficpar);    int i,imax,j,k; 
     double big,dum,sum,temp; 
   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);    double *vv; 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);   
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    vv=vector(1,n); 
 while((c=getc(ficpar))=='#' && c!= EOF){    *d=1.0; 
     ungetc(c,ficpar);    for (i=1;i<=n;i++) { 
     fgets(line, MAXLINE, ficpar);      big=0.0; 
     puts(line);      for (j=1;j<=n;j++) 
     fputs(line,ficparo);        if ((temp=fabs(a[i][j])) > big) big=temp; 
   }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   ungetc(c,ficpar);      vv[i]=1.0/big; 
      } 
        for (j=1;j<=n;j++) { 
   covar=matrix(0,NCOVMAX,1,n);      for (i=1;i<j;i++) { 
   cptcovn=0;        sum=a[i][j]; 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   ncovmodel=2+cptcovn;      } 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      big=0.0; 
        for (i=j;i<=n;i++) { 
   /* Read guess parameters */        sum=a[i][j]; 
   /* Reads comments: lines beginning with '#' */        for (k=1;k<j;k++) 
   while((c=getc(ficpar))=='#' && c!= EOF){          sum -= a[i][k]*a[k][j]; 
     ungetc(c,ficpar);        a[i][j]=sum; 
     fgets(line, MAXLINE, ficpar);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     puts(line);          big=dum; 
     fputs(line,ficparo);          imax=i; 
   }        } 
   ungetc(c,ficpar);      } 
        if (j != imax) { 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for (k=1;k<=n;k++) { 
     for(i=1; i <=nlstate; i++)          dum=a[imax][k]; 
     for(j=1; j <=nlstate+ndeath-1; j++){          a[imax][k]=a[j][k]; 
       fscanf(ficpar,"%1d%1d",&i1,&j1);          a[j][k]=dum; 
       fprintf(ficparo,"%1d%1d",i1,j1);        } 
       printf("%1d%1d",i,j);        *d = -(*d); 
       for(k=1; k<=ncovmodel;k++){        vv[imax]=vv[j]; 
         fscanf(ficpar," %lf",&param[i][j][k]);      } 
         printf(" %lf",param[i][j][k]);      indx[j]=imax; 
         fprintf(ficparo," %lf",param[i][j][k]);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       }      if (j != n) { 
       fscanf(ficpar,"\n");        dum=1.0/(a[j][j]); 
       printf("\n");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       fprintf(ficparo,"\n");      } 
     }    } 
      free_vector(vv,1,n);  /* Doesn't work */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  ;
   } 
   p=param[1][1];  
    void lubksb(double **a, int n, int *indx, double b[]) 
   /* Reads comments: lines beginning with '#' */  { 
   while((c=getc(ficpar))=='#' && c!= EOF){    int i,ii=0,ip,j; 
     ungetc(c,ficpar);    double sum; 
     fgets(line, MAXLINE, ficpar);   
     puts(line);    for (i=1;i<=n;i++) { 
     fputs(line,ficparo);      ip=indx[i]; 
   }      sum=b[ip]; 
   ungetc(c,ficpar);      b[ip]=b[i]; 
       if (ii) 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      else if (sum) ii=i; 
   for(i=1; i <=nlstate; i++){      b[i]=sum; 
     for(j=1; j <=nlstate+ndeath-1; j++){    } 
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (i=n;i>=1;i--) { 
       printf("%1d%1d",i,j);      sum=b[i]; 
       fprintf(ficparo,"%1d%1d",i1,j1);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       for(k=1; k<=ncovmodel;k++){      b[i]=sum/a[i][i]; 
         fscanf(ficpar,"%le",&delti3[i][j][k]);    } 
         printf(" %le",delti3[i][j][k]);  } 
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }  void pstamp(FILE *fichier)
       fscanf(ficpar,"\n");  {
       printf("\n");    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       fprintf(ficparo,"\n");  }
     }  
   }  /************ Frequencies ********************/
   delti=delti3[1][1];  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
    {  /* Some frequencies */
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    int i, m, jk, k1,i1, j1, bool, z1,j;
     ungetc(c,ficpar);    int first;
     fgets(line, MAXLINE, ficpar);    double ***freq; /* Frequencies */
     puts(line);    double *pp, **prop;
     fputs(line,ficparo);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   }    char fileresp[FILENAMELENGTH];
   ungetc(c,ficpar);    
      pp=vector(1,nlstate);
   matcov=matrix(1,npar,1,npar);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   for(i=1; i <=npar; i++){    strcpy(fileresp,"p");
     fscanf(ficpar,"%s",&str);    strcat(fileresp,fileres);
     printf("%s",str);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     fprintf(ficparo,"%s",str);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     for(j=1; j <=i; j++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fscanf(ficpar," %le",&matcov[i][j]);      exit(0);
       printf(" %.5le",matcov[i][j]);    }
       fprintf(ficparo," %.5le",matcov[i][j]);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     }    j1=0;
     fscanf(ficpar,"\n");    
     printf("\n");    j=cptcoveff;
     fprintf(ficparo,"\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }  
   for(i=1; i <=npar; i++)    first=1;
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    for(k1=1; k1<=j;k1++){
          for(i1=1; i1<=ncodemax[k1];i1++){
   printf("\n");        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
     /*-------- data file ----------*/        for (i=-5; i<=nlstate+ndeath; i++)  
     if((ficres =fopen(fileres,"w"))==NULL) {          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       printf("Problem with resultfile: %s\n", fileres);goto end;            for(m=iagemin; m <= iagemax+3; m++)
     }              freq[i][jk][m]=0;
     fprintf(ficres,"#%s\n",version);  
          for (i=1; i<=nlstate; i++)  
     if((fic=fopen(datafile,"r"))==NULL)    {        for(m=iagemin; m <= iagemax+3; m++)
       printf("Problem with datafile: %s\n", datafile);goto end;          prop[i][m]=0;
     }        
         dateintsum=0;
     n= lastobs;        k2cpt=0;
     severity = vector(1,maxwav);        for (i=1; i<=imx; i++) {
     outcome=imatrix(1,maxwav+1,1,n);          bool=1;
     num=ivector(1,n);          if  (cptcovn>0) {
     moisnais=vector(1,n);            for (z1=1; z1<=cptcoveff; z1++) 
     annais=vector(1,n);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     moisdc=vector(1,n);                bool=0;
     andc=vector(1,n);          }
     agedc=vector(1,n);          if (bool==1){
     cod=ivector(1,n);            for(m=firstpass; m<=lastpass; m++){
     weight=vector(1,n);              k2=anint[m][i]+(mint[m][i]/12.);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     mint=matrix(1,maxwav,1,n);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     anint=matrix(1,maxwav,1,n);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     s=imatrix(1,maxwav+1,1,n);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     adl=imatrix(1,maxwav+1,1,n);                    if (m<lastpass) {
     tab=ivector(1,NCOVMAX);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     ncodemax=ivector(1,8);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
     i=1;                
     while (fgets(line, MAXLINE, fic) != NULL)    {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       if ((i >= firstobs) && (i <=lastobs)) {                  dateintsum=dateintsum+k2;
                          k2cpt++;
         for (j=maxwav;j>=1;j--){                }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                /*}*/
           strcpy(line,stra);            }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
         }         
                /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        pstamp(ficresp);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresp, "**********\n#");
         }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=1; i<=nlstate;i++) 
         for (j=ncov;j>=1;j--){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresp, "\n");
         }        
         num[i]=atol(stra);        for(i=iagemin; i <= iagemax+3; i++){
                  if(i==iagemax+3){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            fprintf(ficlog,"Total");
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          }else{
             if(first==1){
         i=i+1;              first=0;
       }              printf("See log file for details...\n");
     }            }
     /* printf("ii=%d", ij);            fprintf(ficlog,"Age %d", i);
        scanf("%d",i);*/          }
   imx=i-1; /* Number of individuals */          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   /* for (i=1; i<=imx; i++){              pp[jk] += freq[jk][m][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;          for(jk=1; jk <=nlstate ; jk++){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     for (i=1; i<=imx; i++)              if(first==1){
     if (covar[1][i]==0) 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]));*/                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
   /* Calculation of the number of parameter from char model*/              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   Tvar=ivector(1,15);            }else{
   Tprod=ivector(1,15);              if(first==1)
   Tvaraff=ivector(1,15);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   Tvard=imatrix(1,15,1,2);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   Tage=ivector(1,15);                  }
              }
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;          for(jk=1; jk <=nlstate ; jk++){
     j=nbocc(model,'+');            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     j1=nbocc(model,'*');              pp[jk] += freq[jk][m][i];
     cptcovn=j+1;          }       
     cptcovprod=j1;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                pos += pp[jk];
                posprop += prop[jk][i];
     strcpy(modelsav,model);          }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for(jk=1; jk <=nlstate ; jk++){
       printf("Error. Non available option model=%s ",model);            if(pos>=1.e-5){
       goto end;              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(i=(j+1); i>=1;i--){            }else{
       cutv(stra,strb,modelsav,'+');              if(first==1)
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       /*scanf("%d",i);*/            }
       if (strchr(strb,'*')) {            if( i <= iagemax){
         cutv(strd,strc,strb,'*');              if(pos>=1.e-5){
         if (strcmp(strc,"age")==0) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           cptcovprod--;                /*probs[i][jk][j1]= pp[jk]/pos;*/
           cutv(strb,stre,strd,'V');                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           Tvar[i]=atoi(stre);              }
           cptcovage++;              else
             Tage[cptcovage]=i;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             /*printf("stre=%s ", stre);*/            }
         }          }
         else if (strcmp(strd,"age")==0) {          
           cptcovprod--;          for(jk=-1; jk <=nlstate+ndeath; jk++)
           cutv(strb,stre,strc,'V');            for(m=-1; m <=nlstate+ndeath; m++)
           Tvar[i]=atoi(stre);              if(freq[jk][m][i] !=0 ) {
           cptcovage++;              if(first==1)
           Tage[cptcovage]=i;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         else {              }
           cutv(strb,stre,strc,'V');          if(i <= iagemax)
           Tvar[i]=ncov+k1;            fprintf(ficresp,"\n");
           cutv(strb,strc,strd,'V');          if(first==1)
           Tprod[k1]=i;            printf("Others in log...\n");
           Tvard[k1][1]=atoi(strc);          fprintf(ficlog,"\n");
           Tvard[k1][2]=atoi(stre);        }
           Tvar[cptcovn+k2]=Tvard[k1][1];      }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    }
           for (k=1; k<=lastobs;k++)    dateintmean=dateintsum/k2cpt; 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   
           k1++;    fclose(ficresp);
           k2=k2+2;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         }    free_vector(pp,1,nlstate);
       }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       else {    /* End of Freq */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  }
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');  /************ Prevalence ********************/
       Tvar[i]=atoi(strc);  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)
       }  {  
       strcpy(modelsav,stra);      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       in each health status at the date of interview (if between dateprev1 and dateprev2).
         scanf("%d",i);*/       We still use firstpass and lastpass as another selection.
     }    */
 }   
      int i, m, jk, k1, i1, j1, bool, z1,j;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double ***freq; /* Frequencies */
   printf("cptcovprod=%d ", cptcovprod);    double *pp, **prop;
   scanf("%d ",i);*/    double pos,posprop; 
     fclose(fic);    double  y2; /* in fractional years */
     int iagemin, iagemax;
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    iagemin= (int) agemin;
       for(i=1;i<=n;i++) weight[i]=1.0;    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
     /*-calculation of age at interview from date of interview and age at death -*/    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     agev=matrix(1,maxwav,1,imx);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
    for (i=1; i<=imx; i++)    
      for(m=2; (m<= maxwav); m++)    j=cptcoveff;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
          anint[m][i]=9999;    
          s[m][i]=-1;    for(k1=1; k1<=j;k1++){
        }      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
     for (i=1; i<=imx; i++)  {        
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for (i=1; i<=nlstate; i++)  
       for(m=1; (m<= maxwav); m++){          for(m=iagemin; m <= iagemax+3; m++)
         if(s[m][i] >0){            prop[i][m]=0.0;
           if (s[m][i] == nlstate+1) {       
             if(agedc[i]>0)        for (i=1; i<=imx; i++) { /* Each individual */
               if(moisdc[i]!=99 && andc[i]!=9999)          bool=1;
               agev[m][i]=agedc[i];          if  (cptcovn>0) {
             else {            for (z1=1; z1<=cptcoveff; z1++) 
               if (andc[i]!=9999){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                bool=0;
               agev[m][i]=-1;          } 
               }          if (bool==1) { 
             }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           else if(s[m][i] !=9){ /* Should no more exist */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             if(mint[m][i]==99 || anint[m][i]==9999)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               agev[m][i]=1;                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); 
             else if(agev[m][i] <agemin){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
               agemin=agev[m][i];                  /*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]]);*/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
             }                  prop[s[m][i]][iagemax+3] += weight[i]; 
             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);*/            } /* end selection of waves */
             }          }
             /*agev[m][i]=anint[m][i]-annais[i];*/        }
             /*   agev[m][i] = age[i]+2*m;*/        for(i=iagemin; i <= iagemax+3; i++){  
           }          
           else { /* =9 */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             agev[m][i]=1;            posprop += prop[jk][i]; 
             s[m][i]=-1;          } 
           }  
         }          for(jk=1; jk <=nlstate ; jk++){     
         else /*= 0 Unknown */            if( i <=  iagemax){ 
           agev[m][i]=1;              if(posprop>=1.e-5){ 
       }                probs[i][jk][j1]= prop[jk][i]/posprop;
                  } else
     }                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
     for (i=1; i<=imx; i++)  {            } 
       for(m=1; (m<= maxwav); m++){          }/* end jk */ 
         if (s[m][i] > (nlstate+ndeath)) {        }/* end i */ 
           printf("Error: Wrong value in nlstate or ndeath\n");        } /* end i1 */
           goto end;    } /* end k1 */
         }    
       }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     }    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  }  /* End of prevalence */
   
     free_vector(severity,1,maxwav);  /************* Waves Concatenation ***************/
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);  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)
     free_vector(annais,1,n);  {
     /* free_matrix(mint,1,maxwav,1,n);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        free_matrix(anint,1,maxwav,1,n);*/       Death is a valid wave (if date is known).
     free_vector(moisdc,1,n);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     free_vector(andc,1,n);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
           */
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    int i, mi, m;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           double sum=0., jmean=0.;*/
     /* Concatenates waves */    int first;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    int j, k=0,jk, ju, jl;
     double sum=0.;
     first=0;
       Tcode=ivector(1,100);    jmin=1e+5;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    jmax=-1;
       ncodemax[1]=1;    jmean=0.;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    for(i=1; i<=imx; i++){
            mi=0;
    codtab=imatrix(1,100,1,10);      m=firstpass;
    h=0;      while(s[m][i] <= nlstate){
    m=pow(2,cptcoveff);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
            mw[++mi][i]=m;
    for(k=1;k<=cptcoveff; k++){        if(m >=lastpass)
      for(i=1; i <=(m/pow(2,k));i++){          break;
        for(j=1; j <= ncodemax[k]; j++){        else
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          m++;
            h++;      }/* end while */
            if (h>m) h=1;codtab[h][k]=j;      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(i=1; i <=m ;i++){      wav[i]=mi;
      for(k=1; k <=cptcovn; k++){      if(mi==0){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        nbwarn++;
      }        if(first==0){
      printf("\n");          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
    }          first=1;
    scanf("%d",i);*/        }
            if(first==1){
    /* Calculates basic frequencies. Computes observed prevalence at single age          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
        and prints on file fileres'p'. */        }
       } /* end mi==0 */
        } /* End individuals */
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(i=1; i<=imx; i++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(mi=1; mi<wav[i];mi++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (stepm <=0)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          dh[mi][i]=1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        else{
                if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     /* For Powell, parameters are in a vector p[] starting at p[1]            if (agedc[i] < 2*AGESUP) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
     if(mle==1){                nberr++;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                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]);
     }                j=1; /* Temporary Dangerous patch */
                    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);
     /*--------- results files --------------*/                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(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);                fprintf(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);
                }
               k=k+1;
    jk=1;              if (j >= jmax){
    fprintf(ficres,"# Parameters\n");                jmax=j;
    printf("# Parameters\n");                ijmax=i;
    for(i=1,jk=1; i <=nlstate; i++){              }
      for(k=1; k <=(nlstate+ndeath); k++){              if (j <= jmin){
        if (k != i)                jmin=j;
          {                ijmin=i;
            printf("%d%d ",i,k);              }
            fprintf(ficres,"%1d%1d ",i,k);              sum=sum+j;
            for(j=1; j <=ncovmodel; j++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
              printf("%f ",p[jk]);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              fprintf(ficres,"%f ",p[jk]);            }
              jk++;          }
            }          else{
            printf("\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
            fprintf(ficres,"\n");  /*        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]); */
          }  
      }            k=k+1;
    }            if (j >= jmax) {
  if(mle==1){              jmax=j;
     /* Computing hessian and covariance matrix */              ijmax=i;
     ftolhess=ftol; /* Usually correct */            }
     hesscov(matcov, p, npar, delti, ftolhess, func);            else if (j <= jmin){
  }              jmin=j;
     fprintf(ficres,"# Scales\n");              ijmin=i;
     printf("# Scales\n");            }
      for(i=1,jk=1; i <=nlstate; i++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(j=1; j <=nlstate+ndeath; j++){            /*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!=i) {            if(j<0){
           fprintf(ficres,"%1d%1d",i,j);              nberr++;
           printf("%1d%1d",i,j);              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]);
           for(k=1; k<=ncovmodel;k++){              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]);
             printf(" %.5e",delti[jk]);            }
             fprintf(ficres," %.5e",delti[jk]);            sum=sum+j;
             jk++;          }
           }          jk= j/stepm;
           printf("\n");          jl= j -jk*stepm;
           fprintf(ficres,"\n");          ju= j -(jk+1)*stepm;
         }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       }            if(jl==0){
      }              dh[mi][i]=jk;
                  bh[mi][i]=0;
     k=1;            }else{ /* We want a negative bias in order to only have interpolation ie
     fprintf(ficres,"# Covariance\n");                    * at the price of an extra matrix product in likelihood */
     printf("# Covariance\n");              dh[mi][i]=jk+1;
     for(i=1;i<=npar;i++){              bh[mi][i]=ju;
       /*  if (k>nlstate) k=1;            }
       i1=(i-1)/(ncovmodel*nlstate)+1;          }else{
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            if(jl <= -ju){
       printf("%s%d%d",alph[k],i1,tab[i]);*/              dh[mi][i]=jk;
       fprintf(ficres,"%3d",i);              bh[mi][i]=jl;       /* bias is positive if real duration
       printf("%3d",i);                                   * is higher than the multiple of stepm and negative otherwise.
       for(j=1; j<=i;j++){                                   */
         fprintf(ficres," %.5e",matcov[i][j]);            }
         printf(" %.5e",matcov[i][j]);            else{
       }              dh[mi][i]=jk+1;
       fprintf(ficres,"\n");              bh[mi][i]=ju;
       printf("\n");            }
       k++;            if(dh[mi][i]==0){
     }              dh[mi][i]=1; /* At least one step */
                  bh[mi][i]=ju; /* At least one step */
     while((c=getc(ficpar))=='#' && c!= EOF){              /*  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);*/
       ungetc(c,ficpar);            }
       fgets(line, MAXLINE, ficpar);          } /* end if mle */
       puts(line);        }
       fputs(line,ficparo);      } /* end wave */
     }    }
     ungetc(c,ficpar);    jmean=sum/k;
      printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    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 (fage <= 2) {  
       bage = agemin;  /*********** Tricode ****************************/
       fage = agemax;  void tricode(int *Tvar, int **nbcode, int imx)
     }  {
        
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
      int cptcode=0;
     while((c=getc(ficpar))=='#' && c!= EOF){    cptcoveff=0; 
     ungetc(c,ficpar);   
     fgets(line, MAXLINE, ficpar);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     puts(line);    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
     fputs(line,ficparo);  
   }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
   ungetc(c,ficpar);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                   modality*/ 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        Ndum[ij]++; /*counts the occurence of this modality */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
              if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
   while((c=getc(ficpar))=='#' && c!= EOF){                                         Tvar[j]. If V=sex and male is 0 and 
     ungetc(c,ficpar);                                         female is 1, then  cptcode=1.*/
     fgets(line, MAXLINE, ficpar);      }
     puts(line);  
     fputs(line,ficparo);      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
   }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
   ungetc(c,ficpar);                                         th covariate. In fact
                                           ncodemax[j]=2
                                          (dichotom. variables only) but
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                                         it can be more */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      } /* Ndum[-1] number of undefined modalities */
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);      ij=1; 
    fprintf(ficparo,"pop_based=%d\n",popbased);        for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
    fprintf(ficres,"pop_based=%d\n",popbased);          for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   while((c=getc(ficpar))=='#' && c!= EOF){            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     ungetc(c,ficpar);                                       k is a modality. If we have model=V1+V1*sex 
     fgets(line, MAXLINE, ficpar);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     puts(line);            ij++;
     fputs(line,ficparo);          }
   }          if (ij > ncodemax[j]) break; 
   ungetc(c,ficpar);        }  
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);      } 
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    }  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);  
    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
         /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     /*------------ gnuplot -------------*/     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     /*chdir(pathcd);*/     Ndum[ij]++;
     strcpy(optionfilegnuplot,optionfilefiname);   }
     strcat(optionfilegnuplot,".plt");  
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {   ij=1;
       printf("Problem with file %s",optionfilegnuplot);goto end;   for (i=1; i<= maxncov; i++) {
     }     if((Ndum[i]!=0) && (i<=ncovcol)){
 #ifdef windows       Tvaraff[ij]=i; /*For printing */
     fprintf(ficgp,"cd \"%s\" \n",pathc);       ij++;
 #endif     }
 m=pow(2,cptcoveff);   }
     ij--;
  /* 1eme*/   cptcoveff=ij; /*Number of simple covariates*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {  }
    for (k1=1; k1<= m ; k1 ++) {  
   /*********** Health Expectancies ****************/
 #ifdef windows  
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
 #endif  
 #ifdef unix  {
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    /* Health expectancies, no variances */
 #endif    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
 for (i=1; i<= nlstate ; i ++) {    double age, agelim, hf;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double ***p3mat;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double eip;
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    pstamp(ficreseij);
     for (i=1; i<= nlstate ; i ++) {    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficreseij,"# Age");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(i=1; i<=nlstate;i++){
 }      for(j=1; j<=nlstate;j++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficreseij," e%1d%1d ",i,j);
      for (i=1; i<= nlstate ; i ++) {      }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficreseij," e%1d. ",i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      fprintf(ficreseij,"\n");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    
 fprintf(ficgp,"\nset ter gif small size 400,300");    if(estepm < stepm){
 #endif      printf ("Problem %d lower than %d\n",estepm, stepm);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
    }    else  hstepm=estepm;   
   }    /* We compute the life expectancy from trapezoids spaced every estepm months
   /*2 eme*/     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
   for (k1=1; k1<= m ; k1 ++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);     * progression in between and thus overestimating or underestimating according
         * to the curvature of the survival function. If, for the same date, we 
     for (i=1; i<= nlstate+1 ; i ++) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       k=2*i;     * to compare the new estimate of Life expectancy with the same linear 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);     * hypothesis. A more precise result, taking into account a more precise
       for (j=1; j<= nlstate+1 ; j ++) {     * curvature will be obtained if estepm is as small as stepm. */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* 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. 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       nhstepm is the number of hstepm from age to agelim 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);       nstepm is the number of stepm from age to agelin. 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);       Look at hpijx to understand the reason of that which relies in memory size
       for (j=1; j<= nlstate+1 ; j ++) {       and note for a fixed period like estepm months */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         else fprintf(ficgp," \%%*lf (\%%*lf)");       survival function given by stepm (the optimization length). Unfortunately it
 }         means that if the survival funtion is printed only each two years of age and if
       fprintf(ficgp,"\" t\"\" w l 0,");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);       results. So we changed our mind and took the option of the best precision.
       for (j=1; j<= nlstate+1 ; j ++) {    */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      agelim=AGESUP;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    /* If stepm=6 months */
       else fprintf(ficgp,"\" t\"\" w l 0,");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      
   }  /* nhstepm age range expressed in number of stepm */
      nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   /*3eme*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
   for (k1=1; k1<= m ; k1 ++) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for (cpt=1; cpt<= nlstate ; cpt ++) {    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=2+nlstate*(cpt-1);  
       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 (age=bage; age<=fage; age ++){ 
       for (i=1; i< nlstate ; i ++) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         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);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }      /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     }  
   }      /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepma matrices, stored
   /* CV preval stat */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   for (k1=1; k1<= m ; k1 ++) {      
     for (cpt=1; cpt<nlstate ; cpt ++) {      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       k=3;      
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for (i=1; i< nlstate ; i ++)      
         fprintf(ficgp,"+$%d",k+i+1);      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
            
       l=3+(nlstate+ndeath)*cpt;      /* Computing expectancies */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {        for(j=1; j<=nlstate;j++)
         l=3+(nlstate+ndeath)*cpt;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         fprintf(ficgp,"+$%d",l+i+1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       }            
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              /* 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(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }          }
   }    
       fprintf(ficreseij,"%3.0f",age );
   /* proba elementaires */      for(i=1; i<=nlstate;i++){
    for(i=1,jk=1; i <=nlstate; i++){        eip=0;
     for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<=nlstate;j++){
       if (k != i) {          eip +=eij[i][j][(int)age];
         for(j=1; j <=ncovmodel; j++){          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        }
           /*fprintf(ficgp,"%s",alph[1]);*/        fprintf(ficreseij,"%9.4f", eip );
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      }
           jk++;      fprintf(ficreseij,"\n");
           fprintf(ficgp,"\n");      
         }    }
       }    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    printf("\n");
     }    fprintf(ficlog,"\n");
     
   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;  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;  {
      for(k=1; k<=(nlstate+ndeath); k++) {    /* Covariances of health expectancies eij and of total life expectancies according
        if (k != k2){     to initial status i, ei. .
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    */
 ij=1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
         for(j=3; j <=ncovmodel; j++) {    int nhstepma, nstepma; /* Decreasing with age */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double age, agelim, hf;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double ***p3matp, ***p3matm, ***varhe;
             ij++;    double **dnewm,**doldm;
           }    double *xp, *xm;
           else    double **gp, **gm;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double ***gradg, ***trgradg;
         }    int theta;
           fprintf(ficgp,")/(1");  
            double eip, vip;
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 ij=1;    xp=vector(1,npar);
           for(j=3; j <=ncovmodel; j++){    xm=vector(1,npar);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    dnewm=matrix(1,nlstate*nlstate,1,npar);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
             ij++;    
           }    pstamp(ficresstdeij);
           else    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficresstdeij,"# Age");
           }    for(i=1; i<=nlstate;i++){
           fprintf(ficgp,")");      for(j=1; j<=nlstate;j++)
         }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      fprintf(ficresstdeij," e%1d. ",i);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }
         i=i+ncovmodel;    fprintf(ficresstdeij,"\n");
        }  
      }    pstamp(ficrescveij);
    }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    fprintf(ficrescveij,"# Age");
   }    for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   fclose(ficgp);        cptj= (j-1)*nlstate+i;
   /* end gnuplot */        for(i2=1; i2<=nlstate;i2++)
              for(j2=1; j2<=nlstate;j2++){
 chdir(path);            cptj2= (j2-1)*nlstate+i2;
                if(cptj2 <= cptj)
     free_ivector(wav,1,imx);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        }
     free_ivector(num,1,n);    fprintf(ficrescveij,"\n");
     free_vector(agedc,1,n);    
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    if(estepm < stepm){
     fclose(ficparo);      printf ("Problem %d lower than %d\n",estepm, stepm);
     fclose(ficres);    }
     /*  }*/    else  hstepm=estepm;   
        /* We compute the life expectancy from trapezoids spaced every estepm months
    /*________fin mle=1_________*/     * This is mainly to measure the difference between two models: for example
         * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression in between and thus overestimating or underestimating according
     /* No more information from the sample is required now */     * to the curvature of the survival function. If, for the same date, we 
   /* Reads comments: lines beginning with '#' */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   while((c=getc(ficpar))=='#' && c!= EOF){     * to compare the new estimate of Life expectancy with the same linear 
     ungetc(c,ficpar);     * hypothesis. A more precise result, taking into account a more precise
     fgets(line, MAXLINE, ficpar);     * curvature will be obtained if estepm is as small as stepm. */
     puts(line);  
     fputs(line,ficparo);    /* 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. 
   ungetc(c,ficpar);       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       Look at hpijx to understand the reason of that which relies in memory size
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);       and note for a fixed period like estepm months */
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 /*--------- index.htm --------*/       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   strcpy(optionfilehtm,optionfile);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   strcat(optionfilehtm,".htm");       results. So we changed our mind and took the option of the best precision.
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    */
     printf("Problem with %s \n",optionfilehtm);goto end;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
     /* If stepm=6 months */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    /* nhstepm age range expressed in number of stepm */
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    agelim=AGESUP;
 Total number of observations=%d <br>    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 <hr  size=\"2\" color=\"#EC5E5E\">    /* if (stepm >= YEARM) hstepm=1;*/
 <li>Outputs files<br><br>\n    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    gp=matrix(0,nhstepm,1,nlstate*nlstate);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    for (age=bage; age<=fage; age ++){ 
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
  fprintf(fichtm," <li>Graphs</li><p>");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
  m=cptcoveff;      /* If stepm=6 months */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
  j1=0;      
  for(k1=1; k1<=m;k1++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;      /* Computing  Variances of health expectancies */
        if (cptcovn > 0) {      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         decrease memory allocation */
          for (cpt=1; cpt<=cptcoveff;cpt++)      for(theta=1; theta <=npar; theta++){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        for(i=1; i<=npar; i++){ 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
        for(cpt=1; cpt<nlstate;cpt++){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
          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(j=1; j<= nlstate; j++){
        }          for(i=1; i<=nlstate; i++){
     for(cpt=1; cpt<=nlstate;cpt++) {            for(h=0; h<=nhstepm-1; h++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
 interval) in state (%d): v%s%d%d.gif <br>              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              }
      }          }
      for(cpt=1; cpt<=nlstate;cpt++) {        }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>       
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(ij=1; ij<= nlstate*nlstate; ij++)
      }          for(h=0; h<=nhstepm-1; h++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 health expectancies in states (1) and (2): e%s%d.gif<br>          }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      }/* End theta */
 fprintf(fichtm,"\n</body>");      
    }      
  }      for(h=0; h<=nhstepm-1; h++)
 fclose(fichtm);        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   /*--------------- Prevalence limit --------------*/            trgradg[h][j][theta]=gradg[h][theta][j];
        
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);       for(ij=1;ij<=nlstate*nlstate;ij++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        for(ji=1;ji<=nlstate*nlstate;ji++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          varhe[ij][ji][(int)age] =0.;
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       printf("%d|",(int)age);fflush(stdout);
   fprintf(ficrespl,"#Prevalence limit\n");       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   fprintf(ficrespl,"#Age ");       for(h=0;h<=nhstepm-1;h++){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(k=0;k<=nhstepm-1;k++){
   fprintf(ficrespl,"\n");          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]);
   prlim=matrix(1,nlstate,1,nlstate);          for(ij=1;ij<=nlstate*nlstate;ij++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(ji=1;ji<=nlstate*nlstate;ji++)
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   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 */  
   k=0;      /* Computing expectancies */
   agebase=agemin;      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   agelim=agemax;      for(i=1; i<=nlstate;i++)
   ftolpl=1.e-10;        for(j=1; j<=nlstate;j++)
   i1=cptcoveff;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   if (cptcovn < 1){i1=1;}            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
   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;          }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");      fprintf(ficresstdeij,"%3.0f",age );
         for(j=1;j<=cptcoveff;j++)      for(i=1; i<=nlstate;i++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        eip=0.;
         fprintf(ficrespl,"******\n");        vip=0.;
                for(j=1; j<=nlstate;j++){
         for (age=agebase; age<=agelim; age++){          eip += eij[i][j][(int)age];
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
           fprintf(ficrespl,"%.0f",age );            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           for(i=1; i<=nlstate;i++)          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
           fprintf(ficrespl," %.5f", prlim[i][i]);        }
           fprintf(ficrespl,"\n");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         }      }
       }      fprintf(ficresstdeij,"\n");
     }  
   fclose(ficrespl);      fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
   /*------------- h Pij x at various ages ------------*/        for(j=1; j<=nlstate;j++){
            cptj= (j-1)*nlstate+i;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          for(i2=1; i2<=nlstate;i2++)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            for(j2=1; j2<=nlstate;j2++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;              cptj2= (j2-1)*nlstate+i2;
   }              if(cptj2 <= cptj)
   printf("Computing pij: result on file '%s' \n", filerespij);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
              }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   /*if (stepm<=24) stepsize=2;*/      fprintf(ficrescveij,"\n");
      
   agelim=AGESUP;    }
   hstepm=stepsize*YEARM; /* Every year of age */    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   k=0;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=k+1;    printf("\n");
         fprintf(ficrespij,"\n#****** ");    fprintf(ficlog,"\n");
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(xm,1,npar);
         fprintf(ficrespij,"******\n");    free_vector(xp,1,npar);
            free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /************ Variance ******************/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    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[])
           fprintf(ficrespij,"# Age");  {
           for(i=1; i<=nlstate;i++)    /* Variance of health expectancies */
             for(j=1; j<=nlstate+ndeath;j++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
               fprintf(ficrespij," %1d-%1d",i,j);    /* double **newm;*/
           fprintf(ficrespij,"\n");    double **dnewm,**doldm;
           for (h=0; h<=nhstepm; h++){    double **dnewmp,**doldmp;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    int i, j, nhstepm, hstepm, h, nstepm ;
             for(i=1; i<=nlstate;i++)    int k, cptcode;
               for(j=1; j<=nlstate+ndeath;j++)    double *xp;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    double **gp, **gm;  /* for var eij */
             fprintf(ficrespij,"\n");    double ***gradg, ***trgradg; /*for var eij */
           }    double **gradgp, **trgradgp; /* for var p point j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *gpp, *gmp; /* for var p point j */
           fprintf(ficrespij,"\n");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         }    double ***p3mat;
     }    double age,agelim, hf;
   }    double ***mobaverage;
     int theta;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    char digit[4];
     char digitp[25];
   fclose(ficrespij);  
     char fileresprobmorprev[FILENAMELENGTH];
   if(stepm == 1) {  
   /*---------- Forecasting ------------------*/    if(popbased==1){
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
   /*printf("calage= %f", calagedate);*/      else strcpy(digitp,"-populbased-nomobil-");
      }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    else 
       strcpy(digitp,"-stablbased-");
   
   strcpy(fileresf,"f");    if (mobilav!=0) {
   strcat(fileresf,fileres);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficresf=fopen(fileresf,"w"))==NULL) {      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   printf("Computing forecasting: result on file '%s' \n", fileresf);      }
     }
   free_matrix(mint,1,maxwav,1,n);  
   free_matrix(anint,1,maxwav,1,n);    strcpy(fileresprobmorprev,"prmorprev"); 
   free_matrix(agev,1,maxwav,1,imx);    sprintf(digit,"%-d",ij);
   /* Mobile average */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
   if (mobilav==1) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for (i=1; i<=nlstate;i++)    }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           mobaverage[(int)agedeb][i][cptcod]=0.;   
        fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    pstamp(ficresprobmorprev);
       for (i=1; i<=nlstate;i++){    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);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           for (cpt=0;cpt<=4;cpt++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      fprintf(ficresprobmorprev," p.%-d SE",j);
           }      for(i=1; i<=nlstate;i++)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        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");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   if (stepm<=12) stepsize=1;  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   agelim=AGESUP;    pstamp(ficresvij);
   /*hstepm=stepsize*YEARM; *//* Every year of age */    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   hstepm=1;    if(popbased==1)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   yp1=modf(dateintmean,&yp);    else
   anprojmean=yp;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   yp2=modf((yp1*12),&yp);    fprintf(ficresvij,"# Age");
   mprojmean=yp;    for(i=1; i<=nlstate;i++)
   yp1=modf((yp2*30.5),&yp);      for(j=1; j<=nlstate;j++)
   jprojmean=yp;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   if(jprojmean==0) jprojmean=1;    fprintf(ficresvij,"\n");
   if(mprojmean==0) jprojmean=1;  
     xp=vector(1,npar);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   if (popforecast==1) {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     if((ficpop=fopen(popfile,"r"))==NULL)    {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       printf("Problem with population file : %s\n",popfile);goto end;  
     }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     popage=ivector(0,AGESUP);    gpp=vector(nlstate+1,nlstate+ndeath);
     popeffectif=vector(0,AGESUP);    gmp=vector(nlstate+1,nlstate+ndeath);
     popcount=vector(0,AGESUP);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     i=1;      if(estepm < stepm){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      printf ("Problem %d lower than %d\n",estepm, stepm);
       {    }
         i=i+1;    else  hstepm=estepm;   
       }    /* For example we decided to compute the life expectancy with the smallest unit */
     imx=i;    /* 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 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       nstepm is the number of stepm from age to agelin. 
   }       Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   for(cptcov=1;cptcov<=i1;cptcov++){       survival function given by stepm (the optimization length). Unfortunately it
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       means that if the survival funtion is printed every two years of age and if
       k=k+1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficresf,"\n#******");       results. So we changed our mind and took the option of the best precision.
       for(j=1;j<=cptcoveff;j++) {    */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }    agelim = AGESUP;
       fprintf(ficresf,"******\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficresf,"# StartingAge FinalAge");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       if (popforecast==1)  fprintf(ficresf," [Population]");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       for (cpt=0; cpt<4;cpt++) {      gp=matrix(0,nhstepm,1,nlstate);
         fprintf(ficresf,"\n");      gm=matrix(0,nhstepm,1,nlstate);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */      for(theta=1; theta <=npar; theta++){
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         nhstepm = nhstepm/hstepm;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         oldm=oldms;savm=savms;  
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          if (popbased==1) {
                  if(mobilav ==0){
         for (h=0; h<=nhstepm; h++){            for(i=1; i<=nlstate;i++)
           if (h==(int) (calagedate+YEARM*cpt)) {              prlim[i][i]=probs[(int)age][i][ij];
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);          }else{ /* mobilav */ 
           }            for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++) {              prlim[i][i]=mobaverage[(int)age][i][ij];
             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];        for(j=1; j<= nlstate; j++){
               else {          for(h=0; h<=nhstepm; h++){
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
               }          }
         }
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];        /* This for computing probability of death (h=1 means
             }           computed over hstepm matrices product = hstepm*stepm months) 
                     as a weighted average of prlim.
             if (h==(int)(calagedate+12*cpt)){        */
               fprintf(ficresf," %.3f", kk1);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
                        for(i=1,gpp[j]=0.; i<= nlstate; i++)
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
             }        }    
           }        /* end probability of death */
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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 (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if (popbased==1) {
   if (popforecast==1) {          if(mobilav ==0){
     free_ivector(popage,0,AGESUP);            for(i=1; i<=nlstate;i++)
     free_vector(popeffectif,0,AGESUP);              prlim[i][i]=probs[(int)age][i][ij];
     free_vector(popcount,0,AGESUP);          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
   free_imatrix(s,1,maxwav+1,1,n);              prlim[i][i]=mobaverage[(int)age][i][ij];
   free_vector(weight,1,n);          }
   fclose(ficresf);        }
   }/* End forecasting */  
   else{        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     erreur=108;          for(h=0; h<=nhstepm; h++){
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   /*---------- Health expectancies and variances ------------*/        }
         /* This for computing probability of death (h=1 means
   strcpy(filerest,"t");           computed over hstepm matrices product = hstepm*stepm months) 
   strcat(filerest,fileres);           as a weighted average of prlim.
   if((ficrest=fopen(filerest,"w"))==NULL) {        */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   printf("Computing Total LEs with variances: file '%s' \n", filerest);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   strcpy(filerese,"e");  
   strcat(filerese,fileres);        for(j=1; j<= nlstate; j++) /* vareij */
   if((ficreseij=fopen(filerese,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
  strcpy(fileresv,"v");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   strcat(fileresv,fileres);        }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      } /* End theta */
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
   k=0;      for(h=0; h<=nhstepm; h++) /* veij */
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=1; j<=nlstate;j++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for(theta=1; theta <=npar; theta++)
       k=k+1;            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(theta=1; theta <=npar; theta++)
       fprintf(ficrest,"******\n");          trgradgp[j][theta]=gradgp[theta][j];
     
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      for(i=1;i<=nlstate;i++)
       fprintf(ficreseij,"******\n");        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      for(h=0;h<=nhstepm;h++){
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        for(k=0;k<=nhstepm;k++){
       fprintf(ficresvij,"******\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for(i=1;i<=nlstate;i++)
       oldm=oldms;savm=savms;            for(j=1;j<=nlstate;j++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }
       oldm=oldms;savm=savms;      }
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    
            /* pptj */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficrest,"\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
                for(i=nlstate+1;i<=nlstate+ndeath;i++)
       hf=1;          varppt[j][i]=doldmp[j][i];
       if (stepm >= YEARM) hf=stepm/YEARM;      /* end ppptj */
       epj=vector(1,nlstate+1);      /*  x centered again */
       for(age=bage; age <=fage ;age++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         if (popbased==1) {   
           for(i=1; i<=nlstate;i++)      if (popbased==1) {
             prlim[i][i]=probs[(int)age][i][k];        if(mobilav ==0){
         }          for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficrest," %.0f",age);        }else{ /* mobilav */ 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(i=1; i<=nlstate;i++)
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        }
           }      }
           epj[nlstate+1] +=epj[j];               
         }      /* This for computing probability of death (h=1 means
         for(i=1, vepp=0.;i <=nlstate;i++)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           for(j=1;j <=nlstate;j++)         as a weighted average of prlim.
             vepp += vareij[i][j][(int)age];      */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(j=1;j <=nlstate;j++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         }      }    
         fprintf(ficrest,"\n");      /* 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]);
         }
  fclose(ficreseij);      } 
  fclose(ficresvij);      fprintf(ficresprobmorprev,"\n");
   fclose(ficrest);  
   fclose(ficpar);      fprintf(ficresvij,"%.0f ",age );
   free_vector(epj,1,nlstate+1);      for(i=1; i<=nlstate;i++)
   /*  scanf("%d ",i); */        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   /*------- Variance limit prevalence------*/          }
       fprintf(ficresvij,"\n");
 strcpy(fileresvpl,"vpl");      free_matrix(gp,0,nhstepm,1,nlstate);
   strcat(fileresvpl,fileres);      free_matrix(gm,0,nhstepm,1,nlstate);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     exit(0);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    } /* End age */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
  k=0;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
  for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
      k=k+1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      fprintf(ficresvpl,"\n#****** ");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      for(j=1;j<=cptcoveff;j++)  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficresvpl,"******\n");  /*   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));
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
      oldm=oldms;savm=savms;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    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);
   */
   fclose(ficresvpl);  /*   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);
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,nlstate);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_matrix(dnewm,1,nlstate,1,npar);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    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);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    fclose(ficresprobmorprev);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    fflush(ficgp);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fflush(fichtm); 
    }  /* end varevsij */
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);  /************ 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[])
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  {
     /* Variance of prevalence limit */
   if(erreur >0)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     printf("End of Imach with error %d\n",erreur);    double **newm;
   else   printf("End of Imach\n");    double **dnewm,**doldm;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int i, j, nhstepm, hstepm;
      int k, cptcode;
   /* 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);*/    double *xp;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double *gp, *gm;
   /*------ End -----------*/    double **gradg, **trgradg;
     double age,agelim;
     int theta;
  end:    
 #ifdef windows    pstamp(ficresvpl);
   /* chdir(pathcd);*/    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
 #endif    fprintf(ficresvpl,"# Age");
  /*system("wgnuplot graph.plt");*/    for(i=1; i<=nlstate;i++)
  /*system("../gp37mgw/wgnuplot graph.plt");*/        fprintf(ficresvpl," %1d-%1d",i,i);
  /*system("cd ../gp37mgw");*/    fprintf(ficresvpl,"\n");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    xp=vector(1,npar);
  strcat(plotcmd," ");    dnewm=matrix(1,nlstate,1,npar);
  strcat(plotcmd,optionfilegnuplot);    doldm=matrix(1,nlstate,1,nlstate);
  system(plotcmd);    
     hstepm=1*YEARM; /* Every year of age */
 #ifdef windows    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   while (z[0] != 'q') {    agelim = AGESUP;
     chdir(path);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     scanf("%s",z);      if (stepm >= YEARM) hstepm=1;
     if (z[0] == 'c') system("./imach");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     else if (z[0] == 'e') {      gradg=matrix(1,npar,1,nlstate);
       chdir(path);      gp=vector(1,nlstate);
       system(optionfilehtm);      gm=vector(1,nlstate);
     }  
     else if (z[0] == 'q') exit(0);      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ /* Computes gradient */
 #endif          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,"\nunset parametric;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, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              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), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, 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). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* 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 m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   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;
     int vpopbased=0;
   
     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 linetmp[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;
     /* where is ncovprod ?*/
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforces= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     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++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       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); /* s[i][j] health state for wave i and individual j */ 
     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;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           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 '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             goto end;
           }
         }
         s[j][i]=lval;
         
         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 for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           goto end;
         }
         anint[j][i]= (double) year; 
         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 for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       andc[i]=(double) year; 
       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);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);fflush(ficlog);
           goto end;
       }
       annais[i]=(double)(year);
       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);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         goto end;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             goto end;
           }
         }
         if(lval <-1 || lval >1){
           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);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           goto end;
         }
         covar[j][i]=(double)(lval);
         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,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     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; /* Number of covariates V1+V2+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       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);fflush(ficlog);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sums the number of covariates including age as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*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 V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             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);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*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 */
   
     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++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             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 codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][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 */
       globpr=0;/* debug */
       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;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           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);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==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 */
    endfree:
     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_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);
     }
   }
   
   
   

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changed lines
  Added in v.1.132


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