Diff for /imach/src/imach.c between versions 1.42 and 1.137

version 1.42, 2002/05/21 18:44:41 version 1.137, 2010/04/29 18:11:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.137  2010/04/29 18:11:38  brouard
      (Module): Checking covariates for more complex models
   This program computes Healthy Life Expectancies from    than V1+V2. A lot of change to be done. Unstable.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.136  2010/04/26 20:30:53  brouard
   interviewed on their health status or degree of disability (in the    (Module): merging some libgsl code. Fixing computation
   case of a health survey which is our main interest) -2- at least a    of likelione (using inter/intrapolation if mle = 0) in order to
   second wave of interviews ("longitudinal") which measure each change    get same likelihood as if mle=1.
   (if any) in individual health status.  Health expectancies are    Some cleaning of code and comments added.
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.135  2009/10/29 15:33:14  brouard
   Maximum Likelihood of the parameters involved in the model.  The    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.134  2009/10/29 13:18:53  brouard
   conditional to be observed in state i at the first wave. Therefore    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.133  2009/07/06 10:21:25  brouard
   complex model than "constant and age", you should modify the program    just nforces
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.132  2009/07/06 08:22:05  brouard
   convergence.    Many tings
   
   The advantage of this computer programme, compared to a simple    Revision 1.131  2009/06/20 16:22:47  brouard
   multinomial logistic model, is clear when the delay between waves is not    Some dimensions resccaled
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.130  2009/05/26 06:44:34  brouard
   account using an interpolation or extrapolation.      (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
   hPijx is the probability to be observed in state i at age x+h    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.129  2007/08/31 13:49:27  lievre
   states. This elementary transition (by month or quarter trimester,    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.128  2006/06/30 13:02:05  brouard
   and the contribution of each individual to the likelihood is simply    (Module): Clarifications on computing e.j
   hPijx.  
     Revision 1.127  2006/04/28 18:11:50  brouard
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Yes the sum of survivors was wrong since
   of the life expectancies. It also computes the prevalence limits.    imach-114 because nhstepm was no more computed in the age
      loop. Now we define nhstepma in the age loop.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): In order to speed up (in case of numerous covariates) we
            Institut national d'études démographiques, Paris.    compute health expectancies (without variances) in a first step
   This software have been partly granted by Euro-REVES, a concerted action    and then all the health expectancies with variances or standard
   from the European Union.    deviation (needs data from the Hessian matrices) which slows the
   It is copyrighted identically to a GNU software product, ie programme and    computation.
   software can be distributed freely for non commercial use. Latest version    In the future we should be able to stop the program is only health
   can be accessed at http://euroreves.ined.fr/imach .    expectancies and graph are needed without standard deviations.
   **********************************************************************/  
      Revision 1.126  2006/04/28 17:23:28  brouard
 #include <math.h>    (Module): Yes the sum of survivors was wrong since
 #include <stdio.h>    imach-114 because nhstepm was no more computed in the age
 #include <stdlib.h>    loop. Now we define nhstepma in the age loop.
 #include <unistd.h>    Version 0.98h
   
 #define MAXLINE 256    Revision 1.125  2006/04/04 15:20:31  lievre
 #define GNUPLOTPROGRAM "gnuplot"    Errors in calculation of health expectancies. Age was not initialized.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Forecasting file added.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.124  2006/03/22 17:13:53  lievre
 #define windows    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    The log-likelihood is printed in the log file
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.123  2006/03/20 10:52:43  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    * imach.c (Module): <title> changed, corresponds to .htm file
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    name. <head> headers where missing.
   
 #define NINTERVMAX 8    * imach.c (Module): Weights can have a decimal point as for
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    English (a comma might work with a correct LC_NUMERIC environment,
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    otherwise the weight is truncated).
 #define NCOVMAX 8 /* Maximum number of covariates */    Modification of warning when the covariates values are not 0 or
 #define MAXN 20000    1.
 #define YEARM 12. /* Number of months per year */    Version 0.98g
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 int erreur; /* Error number */    otherwise the weight is truncated).
 int nvar;    Modification of warning when the covariates values are not 0 or
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    1.
 int npar=NPARMAX;    Version 0.98g
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.121  2006/03/16 17:45:01  lievre
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Module): Comments concerning covariates added
 int popbased=0;  
     * imach.c (Module): refinements in the computation of lli if
 int *wav; /* Number of waves for this individuual 0 is possible */    status=-2 in order to have more reliable computation if stepm is
 int maxwav; /* Maxim number of waves */    not 1 month. Version 0.98f
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.120  2006/03/16 15:10:38  lievre
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): refinements in the computation of lli if
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    status=-2 in order to have more reliable computation if stepm is
 double jmean; /* Mean space between 2 waves */    not 1 month. Version 0.98f
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.119  2006/03/15 17:42:26  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Bug if status = -2, the loglikelihood was
 FILE *ficgp,*ficresprob,*ficpop;    computed as likelihood omitting the logarithm. Version O.98e
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.118  2006/03/14 18:20:07  brouard
  FILE  *ficresvij;    (Module): varevsij Comments added explaining the second
   char fileresv[FILENAMELENGTH];    table of variances if popbased=1 .
  FILE  *ficresvpl;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   char fileresvpl[FILENAMELENGTH];    (Module): Function pstamp added
     (Module): Version 0.98d
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.117  2006/03/14 17:16:22  brouard
 #define FTOL 1.0e-10    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 #define NRANSI    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define ITMAX 200    (Module): Function pstamp added
     (Module): Version 0.98d
 #define TOL 2.0e-4  
     Revision 1.116  2006/03/06 10:29:27  brouard
 #define CGOLD 0.3819660    (Module): Variance-covariance wrong links and
 #define ZEPS 1.0e-10    varian-covariance of ej. is needed (Saito).
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.115  2006/02/27 12:17:45  brouard
 #define GOLD 1.618034    (Module): One freematrix added in mlikeli! 0.98c
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
 static double maxarg1,maxarg2;    filename with strsep.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.113  2006/02/24 14:20:24  brouard
      (Module): Memory leaks checks with valgrind and:
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    datafile was not closed, some imatrix were not freed and on matrix
 #define rint(a) floor(a+0.5)    allocation too.
   
 static double sqrarg;    Revision 1.112  2006/01/30 09:55:26  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.111  2006/01/25 20:38:18  brouard
 int imx;    (Module): Lots of cleaning and bugs added (Gompertz)
 int stepm;    (Module): Comments can be added in data file. Missing date values
 /* Stepm, step in month: minimum step interpolation*/    can be a simple dot '.'.
   
 int estepm;    Revision 1.110  2006/01/25 00:51:50  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (Module): Lots of cleaning and bugs added (Gompertz)
   
 int m,nb;    Revision 1.109  2006/01/24 19:37:15  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Comments (lines starting with a #) are allowed in data.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.108  2006/01/19 18:05:42  lievre
 double dateintmean=0;    Gnuplot problem appeared...
     To be fixed
 double *weight;  
 int **s; /* Status */    Revision 1.107  2006/01/19 16:20:37  brouard
 double *agedc, **covar, idx;    Test existence of gnuplot in imach path
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.106  2006/01/19 13:24:36  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Some cleaning and links added in html output
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.105  2006/01/05 20:23:19  lievre
 /**************** split *************************/    *** empty log message ***
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.104  2005/09/30 16:11:43  lievre
    char *s;                             /* pointer */    (Module): sump fixed, loop imx fixed, and simplifications.
    int  l1, l2;                         /* length counters */    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
    l1 = strlen( path );                 /* length of path */    (instead of missing=-1 in earlier versions) and his/her
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    contributions to the likelihood is 1 - Prob of dying from last
 #ifdef windows    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    s = strrchr( path, '\\' );           /* find last / */    the healthy state at last known wave). Version is 0.98
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.103  2005/09/30 15:54:49  lievre
 #endif    (Module): sump fixed, loop imx fixed, and simplifications.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.102  2004/09/15 17:31:30  brouard
       extern char       *getwd( );    Add the possibility to read data file including tab characters.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.101  2004/09/15 10:38:38  brouard
 #else    Fix on curr_time
       extern char       *getcwd( );  
     Revision 1.100  2004/07/12 18:29:06  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Add version for Mac OS X. Just define UNIX in Makefile
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.99  2004/06/05 08:57:40  brouard
       }    *** empty log message ***
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.98  2004/05/16 15:05:56  brouard
       s++;                              /* after this, the filename */    New version 0.97 . First attempt to estimate force of mortality
       l2 = strlen( s );                 /* length of filename */    directly from the data i.e. without the need of knowing the health
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    state at each age, but using a Gompertz model: log u =a + b*age .
       strcpy( name, s );                /* save file name */    This is the basic analysis of mortality and should be done before any
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    other analysis, in order to test if the mortality estimated from the
       dirc[l1-l2] = 0;                  /* add zero */    cross-longitudinal survey is different from the mortality estimated
    }    from other sources like vital statistic data.
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    The same imach parameter file can be used but the option for mle should be -3.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Agnès, who wrote this part of the code, tried to keep most of the
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    former routines in order to include the new code within the former code.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    The output is very simple: only an estimate of the intercept and of
    s++;    the slope with 95% confident intervals.
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Current limitations:
    l2= strlen( s)+1;    A) Even if you enter covariates, i.e. with the
    strncpy( finame, name, l1-l2);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    finame[l1-l2]= 0;    B) There is no computation of Life Expectancy nor Life Table.
    return( 0 );                         /* we're done */  
 }    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 /******************************************/  
     Revision 1.96  2003/07/15 15:38:55  brouard
 void replace(char *s, char*t)    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 {    rewritten within the same printf. Workaround: many printfs.
   int i;  
   int lg=20;    Revision 1.95  2003/07/08 07:54:34  brouard
   i=0;    * imach.c (Repository):
   lg=strlen(t);    (Repository): Using imachwizard code to output a more meaningful covariance
   for(i=0; i<= lg; i++) {    matrix (cov(a12,c31) instead of numbers.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.94  2003/06/27 13:00:02  brouard
   }    Just cleaning
 }  
     Revision 1.93  2003/06/25 16:33:55  brouard
 int nbocc(char *s, char occ)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int i,j=0;    (Module): Version 0.96b
   int lg=20;  
   i=0;    Revision 1.92  2003/06/25 16:30:45  brouard
   lg=strlen(s);    (Module): On windows (cygwin) function asctime_r doesn't
   for(i=0; i<= lg; i++) {    exist so I changed back to asctime which exists.
   if  (s[i] == occ ) j++;  
   }    Revision 1.91  2003/06/25 15:30:29  brouard
   return j;    * imach.c (Repository): Duplicated warning errors corrected.
 }    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 void cutv(char *u,char *v, char*t, char occ)    is stamped in powell.  We created a new html file for the graphs
 {    concerning matrix of covariance. It has extension -cov.htm.
   int i,lg,j,p=0;  
   i=0;    Revision 1.90  2003/06/24 12:34:15  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Some bugs corrected for windows. Also, when
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
   
   lg=strlen(t);    Revision 1.89  2003/06/24 12:30:52  brouard
   for(j=0; j<p; j++) {    (Module): Some bugs corrected for windows. Also, when
     (u[j] = t[j]);    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
      u[p]='\0';  
     Revision 1.88  2003/06/23 17:54:56  brouard
    for(j=0; j<= lg; j++) {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.87  2003/06/18 12:26:01  brouard
 }    Version 0.96
   
 /********************** nrerror ********************/    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 void nrerror(char error_text[])    routine fileappend.
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.85  2003/06/17 13:12:43  brouard
   fprintf(stderr,"%s\n",error_text);    * imach.c (Repository): Check when date of death was earlier that
   exit(1);    current date of interview. It may happen when the death was just
 }    prior to the death. In this case, dh was negative and likelihood
 /*********************** vector *******************/    was wrong (infinity). We still send an "Error" but patch by
 double *vector(int nl, int nh)    assuming that the date of death was just one stepm after the
 {    interview.
   double *v;    (Repository): Because some people have very long ID (first column)
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    we changed int to long in num[] and we added a new lvector for
   if (!v) nrerror("allocation failure in vector");    memory allocation. But we also truncated to 8 characters (left
   return v-nl+NR_END;    truncation)
 }    (Repository): No more line truncation errors.
   
 /************************ free vector ******************/    Revision 1.84  2003/06/13 21:44:43  brouard
 void free_vector(double*v, int nl, int nh)    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   free((FREE_ARG)(v+nl-NR_END));    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.82  2003/06/05 15:57:20  brouard
   if (!v) nrerror("allocation failure in ivector");    Add log in  imach.c and  fullversion number is now printed.
   return v-nl+NR_END;  
 }  */
   /*
 /******************free ivector **************************/     Interpolated Markov Chain
 void free_ivector(int *v, long nl, long 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
 /******************* imatrix *******************************/    first survey ("cross") where individuals from different ages are
 int **imatrix(long nrl, long nrh, long ncl, long nch)    interviewed on their health status or degree of disability (in the
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    case of a health survey which is our main interest) -2- at least a
 {    second wave of interviews ("longitudinal") which measure each change
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (if any) in individual health status.  Health expectancies are
   int **m;    computed from the time spent in each health state according to a
      model. More health states you consider, more time is necessary to reach the
   /* allocate pointers to rows */    Maximum Likelihood of the parameters involved in the model.  The
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    simplest model is the multinomial logistic model where pij is the
   if (!m) nrerror("allocation failure 1 in matrix()");    probability to be observed in state j at the second wave
   m += NR_END;    conditional to be observed in state i at the first wave. Therefore
   m -= nrl;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
      'age' is age and 'sex' is a covariate. If you want to have a more
      complex model than "constant and age", you should modify the program
   /* allocate rows and set pointers to them */    where the markup *Covariates have to be included here again* invites
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    you to do it.  More covariates you add, slower the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    convergence.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    The advantage of this computer programme, compared to a simple
      multinomial logistic model, is clear when the delay between waves is not
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
   /* return pointer to array of pointers to rows */    account using an interpolation or extrapolation.  
   return m;  
 }    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
 /****************** free_imatrix *************************/    split into an exact number (nh*stepm) of unobserved intermediate
 void free_imatrix(m,nrl,nrh,ncl,nch)    states. This elementary transition (by month, quarter,
       int **m;    semester or year) is modelled as a multinomial logistic.  The hPx
       long nch,ncl,nrh,nrl;    matrix is simply the matrix product of nh*stepm elementary matrices
      /* free an int matrix allocated by imatrix() */    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /******************* matrix *******************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 double **matrix(long nrl, long nrh, long ncl, long nch)             Institut national d'études démographiques, Paris.
 {    This software have been partly granted by Euro-REVES, a concerted action
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    from the European Union.
   double **m;    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    can be accessed at http://euroreves.ined.fr/imach .
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   m -= nrl;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    **********************************************************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /*
   m[nrl] += NR_END;    main
   m[nrl] -= ncl;    read parameterfile
     read datafile
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    concatwav
   return m;    freqsummary
 }    if (mle >= 1)
       mlikeli
 /*************************free matrix ************************/    print results files
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    if mle==1 
 {       computes hessian
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    read end of parameter file: agemin, agemax, bage, fage, estepm
   free((FREE_ARG)(m+nrl-NR_END));        begin-prev-date,...
 }    open gnuplot file
     open html file
 /******************* ma3x *******************************/    period (stable) prevalence
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)     for age prevalim()
 {    h Pij x
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    variance of p varprob
   double ***m;    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Variance-covariance of DFLE
   if (!m) nrerror("allocation failure 1 in matrix()");    prevalence()
   m += NR_END;     movingaverage()
   m -= nrl;    varevsij() 
     if popbased==1 varevsij(,popbased)
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    total life expectancies
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Variance of period (stable) prevalence
   m[nrl] += NR_END;   end
   m[nrl] -= ncl;  */
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));   
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #include <math.h>
   m[nrl][ncl] += NR_END;  #include <stdio.h>
   m[nrl][ncl] -= nll;  #include <stdlib.h>
   for (j=ncl+1; j<=nch; j++)  #include <string.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #include <unistd.h>
    
   for (i=nrl+1; i<=nrh; i++) {  #include <limits.h>
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #include <sys/types.h>
     for (j=ncl+1; j<=nch; j++)  #include <sys/stat.h>
       m[i][j]=m[i][j-1]+nlay;  #include <errno.h>
   }  extern int errno;
   return m;  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /*************************free ma3x ************************/  #include "timeval.h"
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #ifdef GSL
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #include <gsl/gsl_errno.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <gsl/gsl_multimin.h>
   free((FREE_ARG)(m+nrl-NR_END));  #endif
 }  
   /* #include <libintl.h> */
 /***************** f1dim *************************/  /* #define _(String) gettext (String) */
 extern int ncom;  
 extern double *pcom,*xicom;  #define MAXLINE 256
 extern double (*nrfunc)(double []);  
    #define GNUPLOTPROGRAM "gnuplot"
 double f1dim(double x)  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 {  #define FILENAMELENGTH 132
   int j;  
   double f;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   double *xt;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
   xt=vector(1,ncom);  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  #define NINTERVMAX 8
   return f;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 20 /* Maximum number of covariates */
 /*****************brent *************************/  #define MAXN 20000
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   int iter;  #define AGEBASE 40
   double a,b,d,etemp;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   double fu,fv,fw,fx;  #ifdef UNIX
   double ftemp;  #define DIRSEPARATOR '/'
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define CHARSEPARATOR "/"
   double e=0.0;  #define ODIRSEPARATOR '\\'
    #else
   a=(ax < cx ? ax : cx);  #define DIRSEPARATOR '\\'
   b=(ax > cx ? ax : cx);  #define CHARSEPARATOR "\\"
   x=w=v=bx;  #define ODIRSEPARATOR '/'
   fw=fv=fx=(*f)(x);  #endif
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  /* $Id$ */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /* $State$ */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
 #ifdef DEBUG  char fullversion[]="$Revision$ $Date$"; 
     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);  char strstart[80];
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 #endif  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int nvar=0, nforce=0; /* Number of variables, number of forces */
       *xmin=x;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
       return fx;  int npar=NPARMAX;
     }  int nlstate=2; /* Number of live states */
     ftemp=fu;  int ndeath=1; /* Number of dead states */
     if (fabs(e) > tol1) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       r=(x-w)*(fx-fv);  int popbased=0;
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  int *wav; /* Number of waves for this individuual 0 is possible */
       q=2.0*(q-r);  int maxwav=0; /* Maxim number of waves */
       if (q > 0.0) p = -p;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       q=fabs(q);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       etemp=e;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       e=d;                     to the likelihood and the sum of weights (done by funcone)*/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int mle=1, weightopt=0;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       else {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
         d=p/q;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         u=x+d;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         if (u-a < tol2 || b-u < tol2)  double jmean=1; /* Mean space between 2 waves */
           d=SIGN(tol1,xm-x);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     } else {  /*FILE *fic ; */ /* Used in readdata only */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     }  FILE *ficlog, *ficrespow;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int globpr=0; /* Global variable for printing or not */
     fu=(*f)(u);  double fretone; /* Only one call to likelihood */
     if (fu <= fx) {  long ipmx=0; /* Number of contributions */
       if (u >= x) a=x; else b=x;  double sw; /* Sum of weights */
       SHFT(v,w,x,u)  char filerespow[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         } else {  FILE *ficresilk;
           if (u < x) a=u; else b=u;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
           if (fu <= fw || w == x) {  FILE *ficresprobmorprev;
             v=w;  FILE *fichtm, *fichtmcov; /* Html File */
             w=u;  FILE *ficreseij;
             fv=fw;  char filerese[FILENAMELENGTH];
             fw=fu;  FILE *ficresstdeij;
           } else if (fu <= fv || v == x || v == w) {  char fileresstde[FILENAMELENGTH];
             v=u;  FILE *ficrescveij;
             fv=fu;  char filerescve[FILENAMELENGTH];
           }  FILE  *ficresvij;
         }  char fileresv[FILENAMELENGTH];
   }  FILE  *ficresvpl;
   nrerror("Too many iterations in brent");  char fileresvpl[FILENAMELENGTH];
   *xmin=x;  char title[MAXLINE];
   return fx;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 /****************** mnbrak ***********************/  char command[FILENAMELENGTH];
   int  outcmd=0;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 {  
   double ulim,u,r,q, dum;  char filelog[FILENAMELENGTH]; /* Log file */
   double fu;  char filerest[FILENAMELENGTH];
    char fileregp[FILENAMELENGTH];
   *fa=(*func)(*ax);  char popfile[FILENAMELENGTH];
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       }  struct timezone tzp;
   *cx=(*bx)+GOLD*(*bx-*ax);  extern int gettimeofday();
   *fc=(*func)(*cx);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   while (*fb > *fc) {  long time_value;
     r=(*bx-*ax)*(*fb-*fc);  extern long time();
     q=(*bx-*cx)*(*fb-*fa);  char strcurr[80], strfor[80];
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  char *endptr;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  long lval;
     if ((*bx-u)*(u-*cx) > 0.0) {  double dval;
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define NR_END 1
       fu=(*func)(u);  #define FREE_ARG char*
       if (fu < *fc) {  #define FTOL 1.0e-10
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  #define NRANSI 
           }  #define ITMAX 200 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #define TOL 2.0e-4 
       fu=(*func)(u);  
     } else {  #define CGOLD 0.3819660 
       u=(*cx)+GOLD*(*cx-*bx);  #define ZEPS 1.0e-10 
       fu=(*func)(u);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     }  
     SHFT(*ax,*bx,*cx,u)  #define GOLD 1.618034 
       SHFT(*fa,*fb,*fc,fu)  #define GLIMIT 100.0 
       }  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /*************** linmin ************************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 int ncom;    
 double *pcom,*xicom;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double (*nrfunc)(double []);  #define rint(a) floor(a+0.5)
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double brent(double ax, double bx, double cx,  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                double (*f)(double), double tol, double *xmin);  int agegomp= AGEGOMP;
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int imx; 
               double *fc, double (*func)(double));  int stepm=1;
   int j;  /* Stepm, step in month: minimum step interpolation*/
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   ncom=n;  
   pcom=vector(1,n);  int m,nb;
   xicom=vector(1,n);  long *num;
   nrfunc=func;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   for (j=1;j<=n;j++) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     pcom[j]=p[j];  double **pmmij, ***probs;
     xicom[j]=xi[j];  double *ageexmed,*agecens;
   }  double dateintmean=0;
   ax=0.0;  
   xx=1.0;  double *weight;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int **s; /* Status */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double *agedc, **covar, idx;
 #ifdef DEBUG  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double *lsurv, *lpop, *tpop;
 #endif  
   for (j=1;j<=n;j++) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     xi[j] *= xmin;  double ftolhess; /* Tolerance for computing hessian */
     p[j] += xi[j];  
   }  /**************** split *************************/
   free_vector(xicom,1,n);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   free_vector(pcom,1,n);  {
 }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
 /*************** powell ************************/    */ 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    char  *ss;                            /* pointer */
             double (*func)(double []))    int   l1, l2;                         /* length counters */
 {  
   void linmin(double p[], double xi[], int n, double *fret,    l1 = strlen(path );                   /* length of path */
               double (*func)(double []));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,ibig,j;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   double del,t,*pt,*ptt,*xit;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double fp,fptt;      strcpy( name, path );               /* we got the fullname name because no directory */
   double *xits;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   pt=vector(1,n);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   ptt=vector(1,n);      /* get current working directory */
   xit=vector(1,n);      /*    extern  char* getcwd ( char *buf , int len);*/
   xits=vector(1,n);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   *fret=(*func)(p);        return( GLOCK_ERROR_GETCWD );
   for (j=1;j<=n;j++) pt[j]=p[j];      }
   for (*iter=1;;++(*iter)) {      /* got dirc from getcwd*/
     fp=(*fret);      printf(" DIRC = %s \n",dirc);
     ibig=0;    } else {                              /* strip direcotry from path */
     del=0.0;      ss++;                               /* after this, the filename */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      l2 = strlen( ss );                  /* length of filename */
     for (i=1;i<=n;i++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       printf(" %d %.12f",i, p[i]);      strcpy( name, ss );         /* save file name */
     printf("\n");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     for (i=1;i<=n;i++) {      dirc[l1-l2] = 0;                    /* add zero */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      printf(" DIRC2 = %s \n",dirc);
       fptt=(*fret);    }
 #ifdef DEBUG    /* We add a separator at the end of dirc if not exists */
       printf("fret=%lf \n",*fret);    l1 = strlen( dirc );                  /* length of directory */
 #endif    if( dirc[l1-1] != DIRSEPARATOR ){
       printf("%d",i);fflush(stdout);      dirc[l1] =  DIRSEPARATOR;
       linmin(p,xit,n,fret,func);      dirc[l1+1] = 0; 
       if (fabs(fptt-(*fret)) > del) {      printf(" DIRC3 = %s \n",dirc);
         del=fabs(fptt-(*fret));    }
         ibig=i;    ss = strrchr( name, '.' );            /* find last / */
       }    if (ss >0){
 #ifdef DEBUG      ss++;
       printf("%d %.12e",i,(*fret));      strcpy(ext,ss);                     /* save extension */
       for (j=1;j<=n;j++) {      l1= strlen( name);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      l2= strlen(ss)+1;
         printf(" x(%d)=%.12e",j,xit[j]);      strncpy( finame, name, l1-l2);
       }      finame[l1-l2]= 0;
       for(j=1;j<=n;j++)    }
         printf(" p=%.12e",p[j]);  
       printf("\n");    return( 0 );                          /* we're done */
 #endif  }
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /******************************************/
       int k[2],l;  
       k[0]=1;  void replace_back_to_slash(char *s, char*t)
       k[1]=-1;  {
       printf("Max: %.12e",(*func)(p));    int i;
       for (j=1;j<=n;j++)    int lg=0;
         printf(" %.12e",p[j]);    i=0;
       printf("\n");    lg=strlen(t);
       for(l=0;l<=1;l++) {    for(i=0; i<= lg; i++) {
         for (j=1;j<=n;j++) {      (s[i] = t[i]);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      if (t[i]== '\\') s[i]='/';
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    }
         }  }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  char *trimbb(char *out, char *in)
 #endif  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
     s=out;
       free_vector(xit,1,n);    while (*in != '\0'){
       free_vector(xits,1,n);      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       free_vector(ptt,1,n);        in++;
       free_vector(pt,1,n);      }
       return;      *out++ = *in++;
     }    }
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    *out='\0';
     for (j=1;j<=n;j++) {    return s;
       ptt[j]=2.0*p[j]-pt[j];  }
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  char *cutv(char *blocc, char *alocc, char *in, char occ)
     }  {
     fptt=(*func)(ptt);    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     if (fptt < fp) {       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);       gives blocc="abcdef2ghi" and alocc="j".
       if (t < 0.0) {       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         linmin(p,xit,n,fret,func);    */
         for (j=1;j<=n;j++) {    char *s, *t;
           xi[j][ibig]=xi[j][n];    t=in;s=in;
           xi[j][n]=xit[j];    while (*in != '\0'){
         }      while( *in == occ){
 #ifdef DEBUG        *blocc++ = *in++;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        s=in;
         for(j=1;j<=n;j++)      }
           printf(" %.12e",xit[j]);      *blocc++ = *in++;
         printf("\n");    }
 #endif    if (s == t) /* occ not found */
       }      *(blocc-(in-s))='\0';
     }    else
   }      *(blocc-(in-s)-1)='\0';
 }    in=s;
     while ( *in != '\0'){
 /**** Prevalence limit ****************/      *alocc++ = *in++;
     }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    *alocc='\0';
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    return s;
      matrix by transitions matrix until convergence is reached */  }
   
   int i, ii,j,k;  int nbocc(char *s, char occ)
   double min, max, maxmin, maxmax,sumnew=0.;  {
   double **matprod2();    int i,j=0;
   double **out, cov[NCOVMAX], **pmij();    int lg=20;
   double **newm;    i=0;
   double agefin, delaymax=50 ; /* Max number of years to converge */    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   for (ii=1;ii<=nlstate+ndeath;ii++)    if  (s[i] == occ ) j++;
     for (j=1;j<=nlstate+ndeath;j++){    }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return j;
     }  }
   
    cov[1]=1.;  /* void cutv(char *u,char *v, char*t, char occ) */
    /* { */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     newm=savm;  /*      gives u="abcdef2ghi" and v="j" *\/ */
     /* Covariates have to be included here again */  /*   int i,lg,j,p=0; */
      cov[2]=agefin;  /*   i=0; */
    /*   lg=strlen(t); */
       for (k=1; k<=cptcovn;k++) {  /*   for(j=0; j<=lg-1; j++) { */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  /*   } */
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*   for(j=0; j<p; j++) { */
       for (k=1; k<=cptcovprod;k++)  /*     (u[j] = t[j]); */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*   } */
   /*      u[p]='\0'; */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /*    for(j=0; j<= lg; j++) { */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /*   } */
   /* } */
     savm=oldm;  
     oldm=newm;  /********************** nrerror ********************/
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  void nrerror(char error_text[])
       min=1.;  {
       max=0.;    fprintf(stderr,"ERREUR ...\n");
       for(i=1; i<=nlstate; i++) {    fprintf(stderr,"%s\n",error_text);
         sumnew=0;    exit(EXIT_FAILURE);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  }
         prlim[i][j]= newm[i][j]/(1-sumnew);  /*********************** vector *******************/
         max=FMAX(max,prlim[i][j]);  double *vector(int nl, int nh)
         min=FMIN(min,prlim[i][j]);  {
       }    double *v;
       maxmin=max-min;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       maxmax=FMAX(maxmax,maxmin);    if (!v) nrerror("allocation failure in vector");
     }    return v-nl+NR_END;
     if(maxmax < ftolpl){  }
       return prlim;  
     }  /************************ free vector ******************/
   }  void free_vector(double*v, int nl, int nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /*************** transition probabilities ***************/  }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /************************ivector *******************************/
 {  int *ivector(long nl,long nh)
   double s1, s2;  {
   /*double t34;*/    int *v;
   int i,j,j1, nc, ii, jj;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
     for(i=1; i<= nlstate; i++){    return v-nl+NR_END;
     for(j=1; j<i;j++){  }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /******************free ivector **************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  void free_ivector(int *v, long nl, long nh)
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    free((FREE_ARG)(v+nl-NR_END));
       ps[i][j]=s2;  }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  /************************lvector *******************************/
     for(j=i+1; j<=nlstate+ndeath;j++){  long *lvector(long nl,long nh)
       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 *v;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       }    if (!v) nrerror("allocation failure in ivector");
       ps[i][j]=s2;    return v-nl+NR_END;
     }  }
   }  
     /*ps[3][2]=1;*/  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
   for(i=1; i<= nlstate; i++){  {
      s1=0;    free((FREE_ARG)(v+nl-NR_END));
     for(j=1; j<i; j++)  }
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  /******************* imatrix *******************************/
       s1+=exp(ps[i][j]);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     ps[i][i]=1./(s1+1.);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for(j=1; j<i; j++)  { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     for(j=i+1; j<=nlstate+ndeath; j++)    int **m; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    /* allocate pointers to rows */ 
   } /* end i */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    m += NR_END; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    m -= nrl; 
       ps[ii][jj]=0;    
       ps[ii][ii]=1;    
     }    /* 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; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    m[nrl] -= ncl; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    
      printf("%lf ",ps[ii][jj]);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
    }    
     printf("\n ");    /* return pointer to array of pointers to rows */ 
     }    return m; 
     printf("\n ");printf("%lf ",cov[2]);*/  } 
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /****************** free_imatrix *************************/
   goto end;*/  void free_imatrix(m,nrl,nrh,ncl,nch)
     return ps;        int **m;
 }        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 /**************** Product of 2 matrices ******************/  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    free((FREE_ARG) (m+nrl-NR_END)); 
 {  } 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /******************* matrix *******************************/
   /* in, b, out are matrice of pointers which should have been initialized  double **matrix(long nrl, long nrh, long ncl, long nch)
      before: only the contents of out is modified. The function returns  {
      a pointer to pointers identical to out */    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   long i, j, k;    double **m;
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    if (!m) nrerror("allocation failure 1 in matrix()");
         out[i][k] +=in[i][j]*b[j][k];    m += NR_END;
     m -= nrl;
   return out;  
 }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /************* Higher Matrix Product ***************/    m[nrl] -= ncl;
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {    return m;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      duration (i.e. until     */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  }
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).  /*************************free matrix ************************/
      Model is determined by parameters x and covariates have to be  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
      included manually here.  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
      */    free((FREE_ARG)(m+nrl-NR_END));
   }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  /******************* ma3x *******************************/
   double **newm;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
   /* Hstepm could be zero and should return the unit matrix */    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (i=1;i<=nlstate+ndeath;i++)    double ***m;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       po[i][j][0]=(i==j ? 1.0 : 0.0);    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m -= nrl;
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       newm=savm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       /* Covariates have to be included here again */    m[nrl] += NR_END;
       cov[1]=1.;    m[nrl] -= ncl;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       for (k=1; k<=cptcovprod;k++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      m[nrl][j]=m[nrl][j-1]+nlay;
       /*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,    for (i=nrl+1; i<=nrh; i++) {
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       savm=oldm;      for (j=ncl+1; j<=nch; j++) 
       oldm=newm;        m[i][j]=m[i][j-1]+nlay;
     }    }
     for(i=1; i<=nlstate+ndeath; i++)    return m; 
       for(j=1;j<=nlstate+ndeath;j++) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         po[i][j][h]=newm[i][j];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    */
          */  }
       }  
   } /* end h */  /*************************free ma3x ************************/
   return po;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /*************** log-likelihood *************/    free((FREE_ARG)(m+nrl-NR_END));
 double func( double *x)  }
 {  
   int i, ii, j, k, mi, d, kk;  /*************** function subdirf ***********/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  char *subdirf(char fileres[])
   double **out;  {
   double sw; /* Sum of weights */    /* Caution optionfilefiname is hidden */
   double lli; /* Individual log likelihood */    strcpy(tmpout,optionfilefiname);
   long ipmx;    strcat(tmpout,"/"); /* Add to the right */
   /*extern weight */    strcat(tmpout,fileres);
   /* We are differentiating ll according to initial status */    return tmpout;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  }
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  /*************** function subdirf2 ***********/
   */  char *subdirf2(char fileres[], char *preop)
   cov[1]=1.;  {
     
   for(k=1; k<=nlstate; k++) ll[k]=0.;    /* Caution optionfilefiname is hidden */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    strcpy(tmpout,optionfilefiname);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    strcat(tmpout,"/");
     for(mi=1; mi<= wav[i]-1; mi++){    strcat(tmpout,preop);
       for (ii=1;ii<=nlstate+ndeath;ii++)    strcat(tmpout,fileres);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return tmpout;
       for(d=0; d<dh[mi][i]; d++){  }
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*************** function subdirf3 ***********/
         for (kk=1; kk<=cptcovage;kk++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  {
         }    
            /* Caution optionfilefiname is hidden */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    strcpy(tmpout,optionfilefiname);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    strcat(tmpout,"/");
         savm=oldm;    strcat(tmpout,preop);
         oldm=newm;    strcat(tmpout,preop2);
            strcat(tmpout,fileres);
            return tmpout;
       } /* end mult */  }
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /***************** f1dim *************************/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  extern int ncom; 
       ipmx +=1;  extern double *pcom,*xicom;
       sw += weight[i];  extern double (*nrfunc)(double []); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;   
     } /* end of wave */  double f1dim(double x) 
   } /* end of individual */  { 
     int j; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double f;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    double *xt; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */   
   return -l;    xt=vector(1,ncom); 
 }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
 /*********** Maximum Likelihood Estimation ***************/    return f; 
   } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  /*****************brent *************************/
   int i,j, iter;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double **xi,*delti;  { 
   double fret;    int iter; 
   xi=matrix(1,npar,1,npar);    double a,b,d,etemp;
   for (i=1;i<=npar;i++)    double fu,fv,fw,fx;
     for (j=1;j<=npar;j++)    double ftemp;
       xi[i][j]=(i==j ? 1.0 : 0.0);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   printf("Powell\n");    double e=0.0; 
   powell(p,xi,npar,ftol,&iter,&fret,func);   
     a=(ax < cx ? ax : cx); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    b=(ax > cx ? ax : cx); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 }    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 /**** Computes Hessian and covariance matrix ***/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 {      printf(".");fflush(stdout);
   double  **a,**y,*x,pd;      fprintf(ficlog,".");fflush(ficlog);
   double **hess;  #ifdef DEBUG
   int i, j,jk;      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 *indx;      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)))) { */
   double hessii(double p[], double delta, int theta, double delti[]);  #endif
   double hessij(double p[], double delti[], int i, int j);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        *xmin=x; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        return fx; 
       } 
   hess=matrix(1,npar,1,npar);      ftemp=fu;
       if (fabs(e) > tol1) { 
   printf("\nCalculation of the hessian matrix. Wait...\n");        r=(x-w)*(fx-fv); 
   for (i=1;i<=npar;i++){        q=(x-v)*(fx-fw); 
     printf("%d",i);fflush(stdout);        p=(x-v)*q-(x-w)*r; 
     hess[i][i]=hessii(p,ftolhess,i,delti);        q=2.0*(q-r); 
     /*printf(" %f ",p[i]);*/        if (q > 0.0) p = -p; 
     /*printf(" %lf ",hess[i][i]);*/        q=fabs(q); 
   }        etemp=e; 
          e=d; 
   for (i=1;i<=npar;i++) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for (j=1;j<=npar;j++)  {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       if (j>i) {        else { 
         printf(".%d%d",i,j);fflush(stdout);          d=p/q; 
         hess[i][j]=hessij(p,delti,i,j);          u=x+d; 
         hess[j][i]=hess[i][j];              if (u-a < tol2 || b-u < tol2) 
         /*printf(" %lf ",hess[i][j]);*/            d=SIGN(tol1,xm-x); 
       }        } 
     }      } else { 
   }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   printf("\n");      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      fu=(*f)(u); 
        if (fu <= fx) { 
   a=matrix(1,npar,1,npar);        if (u >= x) a=x; else b=x; 
   y=matrix(1,npar,1,npar);        SHFT(v,w,x,u) 
   x=vector(1,npar);          SHFT(fv,fw,fx,fu) 
   indx=ivector(1,npar);          } else { 
   for (i=1;i<=npar;i++)            if (u < x) a=u; else b=u; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];            if (fu <= fw || w == x) { 
   ludcmp(a,npar,indx,&pd);              v=w; 
               w=u; 
   for (j=1;j<=npar;j++) {              fv=fw; 
     for (i=1;i<=npar;i++) x[i]=0;              fw=fu; 
     x[j]=1;            } else if (fu <= fv || v == x || v == w) { 
     lubksb(a,npar,indx,x);              v=u; 
     for (i=1;i<=npar;i++){              fv=fu; 
       matcov[i][j]=x[i];            } 
     }          } 
   }    } 
     nrerror("Too many iterations in brent"); 
   printf("\n#Hessian matrix#\n");    *xmin=x; 
   for (i=1;i<=npar;i++) {    return fx; 
     for (j=1;j<=npar;j++) {  } 
       printf("%.3e ",hess[i][j]);  
     }  /****************** mnbrak ***********************/
     printf("\n");  
   }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   /* Recompute Inverse */  { 
   for (i=1;i<=npar;i++)    double ulim,u,r,q, dum;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double fu; 
   ludcmp(a,npar,indx,&pd);   
     *fa=(*func)(*ax); 
   /*  printf("\n#Hessian matrix recomputed#\n");    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
   for (j=1;j<=npar;j++) {      SHFT(dum,*ax,*bx,dum) 
     for (i=1;i<=npar;i++) x[i]=0;        SHFT(dum,*fb,*fa,dum) 
     x[j]=1;        } 
     lubksb(a,npar,indx,x);    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (i=1;i<=npar;i++){    *fc=(*func)(*cx); 
       y[i][j]=x[i];    while (*fb > *fc) { 
       printf("%.3e ",y[i][j]);      r=(*bx-*ax)*(*fb-*fc); 
     }      q=(*bx-*cx)*(*fb-*fa); 
     printf("\n");      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
   free_matrix(a,1,npar,1,npar);        fu=(*func)(u); 
   free_matrix(y,1,npar,1,npar);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   free_vector(x,1,npar);        fu=(*func)(u); 
   free_ivector(indx,1,npar);        if (fu < *fc) { 
   free_matrix(hess,1,npar,1,npar);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
 }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
 /*************** hessian matrix ****************/        fu=(*func)(u); 
 double hessii( double x[], double delta, int theta, double delti[])      } else { 
 {        u=(*cx)+GOLD*(*cx-*bx); 
   int i;        fu=(*func)(u); 
   int l=1, lmax=20;      } 
   double k1,k2;      SHFT(*ax,*bx,*cx,u) 
   double p2[NPARMAX+1];        SHFT(*fa,*fb,*fc,fu) 
   double res;        } 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  } 
   double fx;  
   int k=0,kmax=10;  /*************** linmin ************************/
   double l1;  
   int ncom; 
   fx=func(x);  double *pcom,*xicom;
   for (i=1;i<=npar;i++) p2[i]=x[i];  double (*nrfunc)(double []); 
   for(l=0 ; l <=lmax; l++){   
     l1=pow(10,l);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     delts=delt;  { 
     for(k=1 ; k <kmax; k=k+1){    double brent(double ax, double bx, double cx, 
       delt = delta*(l1*k);                 double (*f)(double), double tol, double *xmin); 
       p2[theta]=x[theta] +delt;    double f1dim(double x); 
       k1=func(p2)-fx;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       p2[theta]=x[theta]-delt;                double *fc, double (*func)(double)); 
       k2=func(p2)-fx;    int j; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double xx,xmin,bx,ax; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double fx,fb,fa;
         
 #ifdef DEBUG    ncom=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);    pcom=vector(1,n); 
 #endif    xicom=vector(1,n); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    nrfunc=func; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (j=1;j<=n;j++) { 
         k=kmax;      pcom[j]=p[j]; 
       }      xicom[j]=xi[j]; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    } 
         k=kmax; l=lmax*10.;    ax=0.0; 
       }    xx=1.0; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         delts=delt;    *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);
   delti[theta]=delts;  #endif
   return res;    for (j=1;j<=n;j++) { 
        xi[j] *= xmin; 
 }      p[j] += xi[j]; 
     } 
 double hessij( double x[], double delti[], int thetai,int thetaj)    free_vector(xicom,1,n); 
 {    free_vector(pcom,1,n); 
   int i;  } 
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  char *asc_diff_time(long time_sec, char ascdiff[])
   double p2[NPARMAX+1];  {
   int k;    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
   fx=func(x);    sec_left = (time_sec) % (60*60*24);
   for (k=1; k<=2; k++) {    hours = (sec_left) / (60*60) ;
     for (i=1;i<=npar;i++) p2[i]=x[i];    sec_left = (sec_left) %(60*60);
     p2[thetai]=x[thetai]+delti[thetai]/k;    minutes = (sec_left) /60;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    sec_left = (sec_left) % (60);
     k1=func(p2)-fx;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
      return ascdiff;
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  /*************** powell ************************/
    void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     p2[thetai]=x[thetai]-delti[thetai]/k;              double (*func)(double [])) 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  { 
     k3=func(p2)-fx;    void linmin(double p[], double xi[], int n, double *fret, 
                  double (*func)(double [])); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    int i,ibig,j; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double del,t,*pt,*ptt,*xit;
     k4=func(p2)-fx;    double fp,fptt;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double *xits;
 #ifdef DEBUG    int niterf, itmp;
     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);  
 #endif    pt=vector(1,n); 
   }    ptt=vector(1,n); 
   return res;    xit=vector(1,n); 
 }    xits=vector(1,n); 
     *fret=(*func)(p); 
 /************** Inverse of matrix **************/    for (j=1;j<=n;j++) pt[j]=p[j]; 
 void ludcmp(double **a, int n, int *indx, double *d)    for (*iter=1;;++(*iter)) { 
 {      fp=(*fret); 
   int i,imax,j,k;      ibig=0; 
   double big,dum,sum,temp;      del=0.0; 
   double *vv;      last_time=curr_time;
        (void) gettimeofday(&curr_time,&tzp);
   vv=vector(1,n);      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);
   *d=1.0;      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);
   for (i=1;i<=n;i++) {  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     big=0.0;     for (i=1;i<=n;i++) {
     for (j=1;j<=n;j++)        printf(" %d %.12f",i, p[i]);
       if ((temp=fabs(a[i][j])) > big) big=temp;        fprintf(ficlog," %d %.12lf",i, p[i]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        fprintf(ficrespow," %.12lf", p[i]);
     vv[i]=1.0/big;      }
   }      printf("\n");
   for (j=1;j<=n;j++) {      fprintf(ficlog,"\n");
     for (i=1;i<j;i++) {      fprintf(ficrespow,"\n");fflush(ficrespow);
       sum=a[i][j];      if(*iter <=3){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        tm = *localtime(&curr_time.tv_sec);
       a[i][j]=sum;        strcpy(strcurr,asctime(&tm));
     }  /*       asctime_r(&tm,strcurr); */
     big=0.0;        forecast_time=curr_time; 
     for (i=j;i<=n;i++) {        itmp = strlen(strcurr);
       sum=a[i][j];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       for (k=1;k<j;k++)          strcurr[itmp-1]='\0';
         sum -= a[i][k]*a[k][j];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       a[i][j]=sum;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(niterf=10;niterf<=30;niterf+=10){
         big=dum;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         imax=i;          tmf = *localtime(&forecast_time.tv_sec);
       }  /*      asctime_r(&tmf,strfor); */
     }          strcpy(strfor,asctime(&tmf));
     if (j != imax) {          itmp = strlen(strfor);
       for (k=1;k<=n;k++) {          if(strfor[itmp-1]=='\n')
         dum=a[imax][k];          strfor[itmp-1]='\0';
         a[imax][k]=a[j][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);
         a[j][k]=dum;          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);
       }        }
       *d = -(*d);      }
       vv[imax]=vv[j];      for (i=1;i<=n;i++) { 
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     indx[j]=imax;        fptt=(*fret); 
     if (a[j][j] == 0.0) a[j][j]=TINY;  #ifdef DEBUG
     if (j != n) {        printf("fret=%lf \n",*fret);
       dum=1.0/(a[j][j]);        fprintf(ficlog,"fret=%lf \n",*fret);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  #endif
     }        printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
   free_vector(vv,1,n);  /* Doesn't work */        linmin(p,xit,n,fret,func); 
 ;        if (fabs(fptt-(*fret)) > del) { 
 }          del=fabs(fptt-(*fret)); 
           ibig=i; 
 void lubksb(double **a, int n, int *indx, double b[])        } 
 {  #ifdef DEBUG
   int i,ii=0,ip,j;        printf("%d %.12e",i,(*fret));
   double sum;        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
   for (i=1;i<=n;i++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     ip=indx[i];          printf(" x(%d)=%.12e",j,xit[j]);
     sum=b[ip];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     b[ip]=b[i];        }
     if (ii)        for(j=1;j<=n;j++) {
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          printf(" p=%.12e",p[j]);
     else if (sum) ii=i;          fprintf(ficlog," p=%.12e",p[j]);
     b[i]=sum;        }
   }        printf("\n");
   for (i=n;i>=1;i--) {        fprintf(ficlog,"\n");
     sum=b[i];  #endif
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      } 
     b[i]=sum/a[i][i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   }  #ifdef DEBUG
 }        int k[2],l;
         k[0]=1;
 /************ Frequencies ********************/        k[1]=-1;
 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,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        printf("Max: %.12e",(*func)(p));
 {  /* Some frequencies */        fprintf(ficlog,"Max: %.12e",(*func)(p));
          for (j=1;j<=n;j++) {
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          printf(" %.12e",p[j]);
   double ***freq; /* Frequencies */          fprintf(ficlog," %.12e",p[j]);
   double *pp;        }
   double pos, k2, dateintsum=0,k2cpt=0;        printf("\n");
   FILE *ficresp;        fprintf(ficlog,"\n");
   char fileresp[FILENAMELENGTH];        for(l=0;l<=1;l++) {
            for (j=1;j<=n;j++) {
   pp=vector(1,nlstate);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   strcpy(fileresp,"p");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   strcat(fileresp,fileres);          }
   if((ficresp=fopen(fileresp,"w"))==NULL) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     printf("Problem with prevalence resultfile: %s\n", fileresp);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     exit(0);        }
   }  #endif
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  
          free_vector(xit,1,n); 
   j=cptcoveff;        free_vector(xits,1,n); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
   for(k1=1; k1<=j;k1++){        return; 
     for(i1=1; i1<=ncodemax[k1];i1++){      } 
       j1++;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      for (j=1;j<=n;j++) { 
         scanf("%d", i);*/        ptt[j]=2.0*p[j]-pt[j]; 
       for (i=-1; i<=nlstate+ndeath; i++)          xit[j]=p[j]-pt[j]; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          pt[j]=p[j]; 
           for(m=agemin; m <= agemax+3; m++)      } 
             freq[i][jk][m]=0;      fptt=(*func)(ptt); 
            if (fptt < fp) { 
       dateintsum=0;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       k2cpt=0;        if (t < 0.0) { 
       for (i=1; i<=imx; i++) {          linmin(p,xit,n,fret,func); 
         bool=1;          for (j=1;j<=n;j++) { 
         if  (cptcovn>0) {            xi[j][ibig]=xi[j][n]; 
           for (z1=1; z1<=cptcoveff; z1++)            xi[j][n]=xit[j]; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          }
               bool=0;  #ifdef DEBUG
         }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         if (bool==1) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(m=firstpass; m<=lastpass; m++){          for(j=1;j<=n;j++){
             k2=anint[m][i]+(mint[m][i]/12.);            printf(" %.12e",xit[j]);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            fprintf(ficlog," %.12e",xit[j]);
               if(agev[m][i]==0) agev[m][i]=agemax+1;          }
               if(agev[m][i]==1) agev[m][i]=agemax+2;          printf("\n");
               if (m<lastpass) {          fprintf(ficlog,"\n");
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  #endif
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        }
               }      } 
                  } 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  } 
                 dateintsum=dateintsum+k2;  
                 k2cpt++;  /**** Prevalence limit (stable or period prevalence)  ****************/
               }  
             }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           }  {
         }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
       if  (cptcovn>0) {    double **matprod2();
         fprintf(ficresp, "\n#********** Variable ");    double **out, cov[NCOVMAX+1], **pmij();
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double **newm;
         fprintf(ficresp, "**********\n#");    double agefin, delaymax=50 ; /* Max number of years to converge */
       }  
       for(i=1; i<=nlstate;i++)    for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficresp, "\n");        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3)     cov[1]=1.;
           printf("Total");   
         else   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           printf("Age %d", i);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         for(jk=1; jk <=nlstate ; jk++){      newm=savm;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      /* Covariates have to be included here again */
             pp[jk] += freq[jk][m][i];       cov[2]=agefin;
         }    
         for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) {
           for(m=-1, pos=0; m <=0 ; m++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             pos += freq[jk][m][i];          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
           if(pp[jk]>=1.e-10)        }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           else        for (k=1; k<=cptcovprod;k++)
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         }  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         for(jk=1; jk <=nlstate ; jk++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
             pp[jk] += freq[jk][m][i];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         }  
       savm=oldm;
         for(jk=1,pos=0; jk <=nlstate ; jk++)      oldm=newm;
           pos += pp[jk];      maxmax=0.;
         for(jk=1; jk <=nlstate ; jk++){      for(j=1;j<=nlstate;j++){
           if(pos>=1.e-5)        min=1.;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        max=0.;
           else        for(i=1; i<=nlstate; i++) {
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          sumnew=0;
           if( i <= (int) agemax){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
             if(pos>=1.e-5){          prlim[i][j]= newm[i][j]/(1-sumnew);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          max=FMAX(max,prlim[i][j]);
               probs[i][jk][j1]= pp[jk]/pos;          min=FMIN(min,prlim[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]);*/        }
             }        maxmin=max-min;
             else        maxmax=FMAX(maxmax,maxmin);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      }
           }      if(maxmax < ftolpl){
         }        return prlim;
              }
         for(jk=-1; jk <=nlstate+ndeath; jk++)    }
           for(m=-1; m <=nlstate+ndeath; m++)  }
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
         if(i <= (int) agemax)  /*************** transition probabilities ***************/ 
           fprintf(ficresp,"\n");  
         printf("\n");  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       }  {
     }    double s1, s2;
   }    /*double t34;*/
   dateintmean=dateintsum/k2cpt;    int i,j,j1, nc, ii, jj;
    
   fclose(ficresp);      for(i=1; i<= nlstate; i++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(j=1; j<i;j++){
   free_vector(pp,1,nlstate);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
              /*s2 += param[i][j][nc]*cov[nc];*/
   /* End of Freq */            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); */
           }
 /************ Prevalence ********************/          ps[i][j]=s2;
 void prevalence(int agemin, float 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)  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
 {  /* Some frequencies */        }
          for(j=i+1; j<=nlstate+ndeath;j++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double ***freq; /* Frequencies */            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double *pp;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   double pos, k2;          }
           ps[i][j]=s2;
   pp=vector(1,nlstate);        }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
        /*ps[3][2]=1;*/
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      
   j1=0;      for(i=1; i<= nlstate; i++){
          s1=0;
   j=cptcoveff;        for(j=1; j<i; j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          s1+=exp(ps[i][j]);
            /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   for(k1=1; k1<=j;k1++){        }
     for(i1=1; i1<=ncodemax[k1];i1++){        for(j=i+1; j<=nlstate+ndeath; j++){
       j1++;          s1+=exp(ps[i][j]);
                /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       for (i=-1; i<=nlstate+ndeath; i++)          }
         for (jk=-1; jk<=nlstate+ndeath; jk++)          ps[i][i]=1./(s1+1.);
           for(m=agemin; m <= agemax+3; m++)        for(j=1; j<i; j++)
             freq[i][jk][m]=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
              for(j=i+1; j<=nlstate+ndeath; j++)
       for (i=1; i<=imx; i++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
         bool=1;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         if  (cptcovn>0) {      } /* end i */
           for (z1=1; z1<=cptcoveff; z1++)      
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
               bool=0;        for(jj=1; jj<= nlstate+ndeath; jj++){
         }          ps[ii][jj]=0;
         if (bool==1) {          ps[ii][ii]=1;
           for(m=firstpass; m<=lastpass; m++){        }
             k2=anint[m][i]+(mint[m][i]/12.);      }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
               if (m<lastpass) {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
                 if (calagedate>0)  /*         printf("ddd %lf ",ps[ii][jj]); */
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  /*       } */
                 else  /*       printf("\n "); */
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*        } */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  /*        printf("\n ");printf("%lf ",cov[2]); */
               }         /*
             }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           }        goto end;*/
         }      return ps;
       }  }
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         for(jk=1; jk <=nlstate ; jk++){  /**************** Product of 2 matrices ******************/
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         }  {
         for(jk=1; jk <=nlstate ; jk++){    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           for(m=-1, pos=0; m <=0 ; m++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
             pos += freq[jk][m][i];    /* in, b, out are matrice of pointers which should have been initialized 
         }       before: only the contents of out is modified. The function returns
               a pointer to pointers identical to out */
         for(jk=1; jk <=nlstate ; jk++){    long i, j, k;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    for(i=nrl; i<= nrh; i++)
             pp[jk] += freq[jk][m][i];      for(k=ncolol; k<=ncoloh; k++)
         }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                  out[i][k] +=in[i][j]*b[j][k];
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
            return out;
         for(jk=1; jk <=nlstate ; jk++){      }
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  
               probs[i][jk][j1]= pp[jk]/pos;  /************* Higher Matrix Product ***************/
             }  
           }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         }  {
            /* Computes the transition matrix starting at age 'age' over 
       }       'nhstepm*hstepm*stepm' months (i.e. until
     }       age (in years)  age+nhstepm*hstepm*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 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       for the memory).
   free_vector(pp,1,nlstate);       Model is determined by parameters x and covariates have to be 
         included manually here. 
 }  /* End of Freq */  
        */
 /************* Waves Concatenation ***************/  
     int i, j, d, h, k;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    double **out, cov[NCOVMAX+1];
 {    double **newm;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).    /* Hstepm could be zero and should return the unit matrix */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    for (i=1;i<=nlstate+ndeath;i++)
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (j=1;j<=nlstate+ndeath;j++){
      and mw[mi+1][i]. dh depends on stepm.        oldm[i][j]=(i==j ? 1.0 : 0.0);
      */        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   int i, mi, m;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    for(h=1; h <=nhstepm; h++){
      double sum=0., jmean=0.;*/      for(d=1; d <=hstepm; d++){
         newm=savm;
   int j, k=0,jk, ju, jl;        /* Covariates have to be included here again */
   double sum=0.;        cov[1]=1.;
   jmin=1e+5;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   jmax=-1;        for (k=1; k<=cptcovn;k++) 
   jmean=0.;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for(i=1; i<=imx; i++){        for (k=1; k<=cptcovage;k++)
     mi=0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     m=firstpass;        for (k=1; k<=cptcovprod;k++)
     while(s[m][i] <= nlstate){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if(s[m][i]>=1)  
         mw[++mi][i]=m;  
       if(m >=lastpass)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         break;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       else        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         m++;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }/* end while */        savm=oldm;
     if (s[m][i] > nlstate){        oldm=newm;
       mi++;     /* Death is another wave */      }
       /* if(mi==0)  never been interviewed correctly before death */      for(i=1; i<=nlstate+ndeath; i++)
          /* Only death is a correct wave */        for(j=1;j<=nlstate+ndeath;j++) {
       mw[mi][i]=m;          po[i][j][h]=newm[i][j];
     }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
     wav[i]=mi;      /*printf("h=%d ",h);*/
     if(mi==0)    } /* end h */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  /*     printf("\n H=%d \n",h); */
   }    return po;
   }
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  /*************** log-likelihood *************/
         dh[mi][i]=1;  double func( double *x)
       else{  {
         if (s[mw[mi+1][i]][i] > nlstate) {    int i, ii, j, k, mi, d, kk;
           if (agedc[i] < 2*AGESUP) {    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    double **out;
           if(j==0) j=1;  /* Survives at least one month after exam */    double sw; /* Sum of weights */
           k=k+1;    double lli; /* Individual log likelihood */
           if (j >= jmax) jmax=j;    int s1, s2;
           if (j <= jmin) jmin=j;    double bbh, survp;
           sum=sum+j;    long ipmx;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    /*extern weight */
           }    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         else{    /*for(i=1;i<imx;i++) 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      printf(" %d\n",s[4][i]);
           k=k+1;    */
           if (j >= jmax) jmax=j;    cov[1]=1.;
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    for(k=1; k<=nlstate; k++) ll[k]=0.;
           sum=sum+j;  
         }    if(mle==1){
         jk= j/stepm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         jl= j -jk*stepm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         ju= j -(jk+1)*stepm;        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
         if(jl <= -ju)           is 6, Tvar[3=age*V3] should not been computed because of age Tvar[4=V3*V2] 
           dh[mi][i]=jk;           has been calculated etc */
         else        for(mi=1; mi<= wav[i]-1; mi++){
           dh[mi][i]=jk+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(dh[mi][i]==0)            for (j=1;j<=nlstate+ndeath;j++){
           dh[mi][i]=1; /* At least one step */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
   }          for(d=0; d<dh[mi][i]; d++){
   jmean=sum/k;            newm=savm;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  }            for (kk=1; kk<=cptcovage;kk++) {
 /*********** Tricode ****************************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
 void tricode(int *Tvar, int **nbcode, int imx)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int Ndum[20],ij=1, k, j, i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int cptcode=0;            savm=oldm;
   cptcoveff=0;            oldm=newm;
            } /* end mult */
   for (k=0; k<19; k++) Ndum[k]=0;        
   for (k=1; k<=7; k++) ncodemax[k]=0;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1; i<=imx; i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
       ij=(int)(covar[Tvar[j]][i]);           * the nearest (and in case of equal distance, to the lowest) interval but now
       Ndum[ij]++;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       if (ij > cptcode) cptcode=ij;           * probability in order to take into account the bias as a fraction of the way
     }           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
     for (i=0; i<=cptcode; i++) {           * For stepm=1 the results are the same as for previous versions of Imach.
       if(Ndum[i]!=0) ncodemax[j]++;           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
     ij=1;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
     for (i=1; i<=ncodemax[j]; i++) {          /* bias bh is positive if real duration
       for (k=0; k<=19; k++) {           * is higher than the multiple of stepm and negative otherwise.
         if (Ndum[k] != 0) {           */
           nbcode[Tvar[j]][ij]=k;          /* 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){ 
           ij++;            /* i.e. if s2 is a death state and if the date of death is known 
         }               then the contribution to the likelihood is the probability to 
         if (ij > ncodemax[j]) break;               die between last step unit time and current  step unit time, 
       }                 which is also equal to probability to die before dh 
     }               minus probability to die before dh-stepm . 
   }                 In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
  for (k=0; k<19; k++) Ndum[k]=0;          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
  for (i=1; i<=ncovmodel-2; i++) {          to consider that at each interview the state was recorded
       ij=Tvar[i];          (healthy, disable or death) and IMaCh was corrected; but when we
       Ndum[ij]++;          introduced the exact date of death then we should have modified
     }          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
  ij=1;          stepm. It is no more the probability to die between last interview
  for (i=1; i<=10; i++) {          and month of death but the probability to survive from last
    if((Ndum[i]!=0) && (i<=ncovcol)){          interview up to one month before death multiplied by the
      Tvaraff[ij]=i;          probability to die within a month. Thanks to Chris
      ij++;          Jackson for correcting this bug.  Former versions increased
    }          mortality artificially. The bad side is that we add another loop
  }          which slows down the processing. The difference can be up to 10%
            lower mortality.
     cptcoveff=ij-1;            */
 }            lli=log(out[s1][s2] - savm[s1][s2]);
   
 /*********** Health Expectancies ****************/  
           } else if  (s2==-2) {
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )            for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 {            /*survp += out[s1][j]; */
   /* Health expectancies */            lli= log(survp);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          }
   double age, agelim, hf;          
   double ***p3mat,***varhe;          else if  (s2==-4) { 
   double **dnewm,**doldm;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double *xp;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double **gp, **gm;            lli= log(survp); 
   double ***gradg, ***trgradg;          } 
   int theta;  
           else if  (s2==-5) { 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            for (j=1,survp=0. ; j<=2; j++)  
   xp=vector(1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   dnewm=matrix(1,nlstate*2,1,npar);            lli= log(survp); 
   doldm=matrix(1,nlstate*2,1,nlstate*2);          } 
            
   fprintf(ficreseij,"# Health expectancies\n");          else{
   fprintf(ficreseij,"# Age");            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for(i=1; i<=nlstate;i++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     for(j=1; j<=nlstate;j++)          } 
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fprintf(ficreseij,"\n");          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   if(estepm < stepm){          ipmx +=1;
     printf ("Problem %d lower than %d\n",estepm, stepm);          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   else  hstepm=estepm;          } /* end of wave */
   /* We compute the life expectancy from trapezoids spaced every estepm months      } /* end of individual */
    * This is mainly to measure the difference between two models: for example    }  else if(mle==2){
    * if stepm=24 months pijx are given only every 2 years and by summing them      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    * we are calculating an estimate of the Life Expectancy assuming a linear        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
    * progression inbetween and thus overestimating or underestimating according        for(mi=1; mi<= wav[i]-1; mi++){
    * to the curvature of the survival function. If, for the same date, we          for (ii=1;ii<=nlstate+ndeath;ii++)
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            for (j=1;j<=nlstate+ndeath;j++){
    * to compare the new estimate of Life expectancy with the same linear              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    * hypothesis. A more precise result, taking into account a more precise              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    * curvature will be obtained if estepm is as small as stepm. */            }
           for(d=0; d<=dh[mi][i]; d++){
   /* For example we decided to compute the life expectancy with the smallest unit */            newm=savm;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      nhstepm is the number of hstepm from age to agelim            for (kk=1; kk<=cptcovage;kk++) {
      nstepm is the number of stepm from age to agelin.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      Look at hpijx to understand the reason of that which relies in memory size            }
      and note for a fixed period like estepm months */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      survival function given by stepm (the optimization length). Unfortunately it            savm=oldm;
      means that if the survival funtion is printed only each two years of age and if            oldm=newm;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          } /* end mult */
      results. So we changed our mind and took the option of the best precision.        
   */          s1=s[mw[mi][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   agelim=AGESUP;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ipmx +=1;
     /* nhstepm age range expressed in number of stepm */          sw += weight[i];
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        } /* end of wave */
     /* if (stepm >= YEARM) hstepm=1;*/      } /* end of individual */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    }  else if(mle==3){  /* exponential inter-extrapolation */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gp=matrix(0,nhstepm,1,nlstate*2);        for(mi=1; mi<= wav[i]-1; mi++){
     gm=matrix(0,nhstepm,1,nlstate*2);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              }
            for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     /* Computing Variances of health expectancies */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
      for(theta=1; theta <=npar; theta++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=npar; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            savm=oldm;
       }            oldm=newm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } /* end mult */
          
       cptj=0;          s1=s[mw[mi][i]][i];
       for(j=1; j<= nlstate; j++){          s2=s[mw[mi+1][i]][i];
         for(i=1; i<=nlstate; i++){          bbh=(double)bh[mi][i]/(double)stepm; 
           cptj=cptj+1;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          ipmx +=1;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          sw += weight[i];
           }          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 */
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<=npar; i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(mi=1; mi<= wav[i]-1; mi++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for (ii=1;ii<=nlstate+ndeath;ii++)
                  for (j=1;j<=nlstate+ndeath;j++){
       cptj=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(i=1;i<=nlstate;i++){            }
           cptj=cptj+1;          for(d=0; d<dh[mi][i]; d++){
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){            newm=savm;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
                
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<= nlstate*2; j++)            savm=oldm;
         for(h=0; h<=nhstepm-1; h++){            oldm=newm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          } /* end mult */
         }        
           s1=s[mw[mi][i]][i];
      }          s2=s[mw[mi+1][i]][i];
              if( s2 > nlstate){ 
 /* End theta */            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
      for(h=0; h<=nhstepm-1; h++)          ipmx +=1;
       for(j=1; j<=nlstate*2;j++)          sw += weight[i];
         for(theta=1; theta <=npar; theta++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         trgradg[h][j][theta]=gradg[h][theta][j];  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
       } /* end of individual */
      for(i=1;i<=nlstate*2;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(j=1;j<=nlstate*2;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         varhe[i][j][(int)age] =0.;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
      printf("%d||",(int)age);fflush(stdout);          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(h=0;h<=nhstepm-1;h++){            for (j=1;j<=nlstate+ndeath;j++){
       for(k=0;k<=nhstepm-1;k++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            }
         for(i=1;i<=nlstate*2;i++)          for(d=0; d<dh[mi][i]; d++){
           for(j=1;j<=nlstate*2;j++)            newm=savm;
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
                
     /* Computing expectancies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<=nlstate;j++)            savm=oldm;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){            oldm=newm;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          } /* end mult */
                  
 /* 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]);*/          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
         }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
     fprintf(ficreseij,"%3.0f",age );          sw += weight[i];
     cptj=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1; i<=nlstate;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]);*/
       for(j=1; j<=nlstate;j++){        } /* end of wave */
         cptj++;      } /* end of individual */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     fprintf(ficreseij,"\n");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
        l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_matrix(gm,0,nhstepm,1,nlstate*2);    return -l;
     free_matrix(gp,0,nhstepm,1,nlstate*2);  }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  /*************** log-likelihood *************/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  double funcone( double *x)
   }  {
   free_vector(xp,1,npar);    /* Same as likeli but slower because of a lot of printf and if */
   free_matrix(dnewm,1,nlstate*2,1,npar);    int i, ii, j, k, mi, d, kk;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    double **out;
 }    double lli; /* Individual log likelihood */
     double llt;
 /************ Variance ******************/    int s1, s2;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    double bbh, survp;
 {    /*extern weight */
   /* Variance of health expectancies */    /* We are differentiating ll according to initial status */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double **newm;    /*for(i=1;i<imx;i++) 
   double **dnewm,**doldm;      printf(" %d\n",s[4][i]);
   int i, j, nhstepm, hstepm, h, nstepm ;    */
   int k, cptcode;    cov[1]=1.;
   double *xp;  
   double **gp, **gm;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double ***gradg, ***trgradg;  
   double ***p3mat;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double age,agelim, hf;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int theta;      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
    fprintf(ficresvij,"# Covariances of life expectancies\n");          for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficresvij,"# Age");            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=nlstate;i++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<=nlstate;j++)          }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        for(d=0; d<dh[mi][i]; d++){
   fprintf(ficresvij,"\n");          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   xp=vector(1,npar);          for (kk=1; kk<=cptcovage;kk++) {
   dnewm=matrix(1,nlstate,1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   doldm=matrix(1,nlstate,1,nlstate);          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if(estepm < stepm){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf ("Problem %d lower than %d\n",estepm, stepm);          savm=oldm;
   }          oldm=newm;
   else  hstepm=estepm;          } /* end mult */
   /* 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.        s1=s[mw[mi][i]][i];
      nhstepm is the number of hstepm from age to agelim        s2=s[mw[mi+1][i]][i];
      nstepm is the number of stepm from age to agelin.        bbh=(double)bh[mi][i]/(double)stepm; 
      Look at hpijx to understand the reason of that which relies in memory size        /* bias is positive if real duration
      and note for a fixed period like k years */         * is higher than the multiple of stepm and negative otherwise.
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the         */
      survival function given by stepm (the optimization length). Unfortunately it        if( s2 > nlstate && (mle <5) ){  /* Jackson */
      means that if the survival funtion is printed only each two years of age and if          lli=log(out[s1][s2] - savm[s1][s2]);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        } else if  (s2==-2) {
      results. So we changed our mind and took the option of the best precision.          for (j=1,survp=0. ; j<=nlstate; j++) 
   */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          lli= log(survp);
   agelim = AGESUP;        }else if (mle==1){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } else if(mle==2){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } else if(mle==3){  /* exponential inter-extrapolation */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          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 */
     gp=matrix(0,nhstepm,1,nlstate);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     gm=matrix(0,nhstepm,1,nlstate);          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
     for(theta=1; theta <=npar; theta++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(i=1; i<=npar; i++){ /* Computes gradient */          /*lli=log(out[s1][s2]); */ /* Original formula */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } /* End of if */
       }        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) {        if(globpr){
         for(i=1; i<=nlstate;i++)          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
           prlim[i][i]=probs[(int)age][i][ij];   %11.6f %11.6f %11.6f ", \
       }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       for(j=1; j<= nlstate; j++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         for(h=0; h<=nhstepm; h++){            llt +=ll[k]*gipmx/gsw;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          }
         }          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
          } /* end of wave */
       for(i=1; i<=npar; i++) /* Computes gradient */    } /* end of individual */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    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 */
       if (popbased==1) {      gipmx=ipmx;
         for(i=1; i<=nlstate;i++)      gsw=sw;
           prlim[i][i]=probs[(int)age][i][ij];    }
       }    return -l;
   }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  /*************** function likelione ***********/
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         }  {
       }    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
       for(j=1; j<= nlstate; j++)       to check the exact contribution to the likelihood.
         for(h=0; h<=nhstepm; h++){       Plotting could be done.
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];     */
         }    int k;
     } /* End theta */  
     if(*globpri !=0){ /* Just counts and sums, no printings */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
     for(h=0; h<=nhstepm; h++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(j=1; j<=nlstate;j++)        printf("Problem with resultfile: %s\n", fileresilk);
         for(theta=1; theta <=npar; theta++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           trgradg[h][j][theta]=gradg[h][theta][j];      }
       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");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     for(i=1;i<=nlstate;i++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(j=1;j<=nlstate;j++)      for(k=1; k<=nlstate; k++) 
         vareij[i][j][(int)age] =0.;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for(h=0;h<=nhstepm;h++){    }
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    *fretone=(*funcone)(p);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    if(*globpri !=0){
         for(i=1;i<=nlstate;i++)      fclose(ficresilk);
           for(j=1;j<=nlstate;j++)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      fflush(fichtm); 
       }    } 
     }    return;
   }
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  /*********** Maximum Likelihood Estimation ***************/
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  
       }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     fprintf(ficresvij,"\n");  {
     free_matrix(gp,0,nhstepm,1,nlstate);    int i,j, iter;
     free_matrix(gm,0,nhstepm,1,nlstate);    double **xi;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double fret;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double fretone; /* Only one call to likelihood */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*  char filerespow[FILENAMELENGTH];*/
   } /* End age */    xi=matrix(1,npar,1,npar);
      for (i=1;i<=npar;i++)
   free_vector(xp,1,npar);      for (j=1;j<=npar;j++)
   free_matrix(doldm,1,nlstate,1,npar);        xi[i][j]=(i==j ? 1.0 : 0.0);
   free_matrix(dnewm,1,nlstate,1,nlstate);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
 }    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
 /************ Variance of prevlim ******************/      printf("Problem with resultfile: %s\n", filerespow);
 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)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 {    }
   /* Variance of prevalence limit */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=1;i<=nlstate;i++)
   double **newm;      for(j=1;j<=nlstate+ndeath;j++)
   double **dnewm,**doldm;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   int i, j, nhstepm, hstepm;    fprintf(ficrespow,"\n");
   int k, cptcode;  
   double *xp;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double *gp, *gm;  
   double **gradg, **trgradg;    free_matrix(xi,1,npar,1,npar);
   double age,agelim;    fclose(ficrespow);
   int theta;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
        fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)  }
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   xp=vector(1,npar);  {
   dnewm=matrix(1,nlstate,1,npar);    double  **a,**y,*x,pd;
   doldm=matrix(1,nlstate,1,nlstate);    double **hess;
      int i, j,jk;
   hstepm=1*YEARM; /* Every year of age */    int *indx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    void lubksb(double **a, int npar, int *indx, double b[]) ;
     if (stepm >= YEARM) hstepm=1;    void ludcmp(double **a, int npar, int *indx, double *d) ;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double gompertz(double p[]);
     gradg=matrix(1,npar,1,nlstate);    hess=matrix(1,npar,1,npar);
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++){
       for(i=1; i<=npar; i++){ /* Computes gradient */      printf("%d",i);fflush(stdout);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(ficlog,"%d",i);fflush(ficlog);
       }     
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(i=1;i<=nlstate;i++)      
         gp[i] = prlim[i][i];      /*  printf(" %f ",p[i]);
              printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[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<=npar;i++) {
       for(i=1;i<=nlstate;i++)      for (j=1;j<=npar;j++)  {
         gm[i] = prlim[i][i];        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
       for(i=1;i<=nlstate;i++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          hess[i][j]=hessij(p,delti,i,j,func,npar);
     } /* End theta */          
           hess[j][i]=hess[i][j];    
     trgradg =matrix(1,nlstate,1,npar);          /*printf(" %lf ",hess[i][j]);*/
         }
     for(j=1; j<=nlstate;j++)      }
       for(theta=1; theta <=npar; theta++)    }
         trgradg[j][theta]=gradg[theta][j];    printf("\n");
     fprintf(ficlog,"\n");
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    
     for(i=1;i<=nlstate;i++)    a=matrix(1,npar,1,npar);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     fprintf(ficresvpl,"%.0f ",age );    indx=ivector(1,npar);
     for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++)
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     fprintf(ficresvpl,"\n");    ludcmp(a,npar,indx,&pd);
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);    for (j=1;j<=npar;j++) {
     free_matrix(gradg,1,npar,1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
     free_matrix(trgradg,1,nlstate,1,npar);      x[j]=1;
   } /* End age */      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   free_vector(xp,1,npar);        matcov[i][j]=x[i];
   free_matrix(doldm,1,nlstate,1,npar);      }
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
   
 }    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
 /************ Variance of one-step probabilities  ******************/    for (i=1;i<=npar;i++) { 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)      for (j=1;j<=npar;j++) { 
 {        printf("%.3e ",hess[i][j]);
   int i, j, i1, k1, j1, z1;        fprintf(ficlog,"%.3e ",hess[i][j]);
   int k=0, cptcode;      }
   double **dnewm,**doldm;      printf("\n");
   double *xp;      fprintf(ficlog,"\n");
   double *gp, *gm;    }
   double **gradg, **trgradg;  
   double age,agelim, cov[NCOVMAX];    /* Recompute Inverse */
   int theta;    for (i=1;i<=npar;i++)
   char fileresprob[FILENAMELENGTH];      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);    /*  printf("\n#Hessian matrix recomputed#\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      x[j]=1;
        lubksb(a,npar,indx,x);
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");      for (i=1;i<=npar;i++){ 
   fprintf(ficresprob,"# Age");        y[i][j]=x[i];
   for(i=1; i<=nlstate;i++)        printf("%.3e ",y[i][j]);
     for(j=1; j<=(nlstate+ndeath);j++)        fprintf(ficlog,"%.3e ",y[i][j]);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      }
       printf("\n");
       fprintf(ficlog,"\n");
   fprintf(ficresprob,"\n");    }
     */
   
   xp=vector(1,npar);    free_matrix(a,1,npar,1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_matrix(y,1,npar,1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    free_vector(x,1,npar);
      free_ivector(indx,1,npar);
   cov[1]=1;    free_matrix(hess,1,npar,1,npar);
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   j1=0;  }
   for(k1=1; k1<=1;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  /*************** hessian matrix ****************/
     j1++;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
     if  (cptcovn>0) {    int i;
       fprintf(ficresprob, "\n#********** Variable ");    int l=1, lmax=20;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double k1,k2;
       fprintf(ficresprob, "**********\n#");    double p2[MAXPARM+1]; /* identical to x */
     }    double res;
        double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for (age=bage; age<=fage; age ++){    double fx;
         cov[2]=age;    int k=0,kmax=10;
         for (k=1; k<=cptcovn;k++) {    double l1;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  
              fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for(l=0 ; l <=lmax; l++){
         for (k=1; k<=cptcovprod;k++)      l1=pow(10,l);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      delts=delt;
              for(k=1 ; k <kmax; k=k+1){
         gradg=matrix(1,npar,1,9);        delt = delta*(l1*k);
         trgradg=matrix(1,9,1,npar);        p2[theta]=x[theta] +delt;
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        k1=func(p2)-fx;
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        p2[theta]=x[theta]-delt;
            k2=func(p2)-fx;
         for(theta=1; theta <=npar; theta++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
           for(i=1; i<=npar; i++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        
            #ifdef DEBUGHESS
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        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);
           k=0;  #endif
           for(i=1; i<= (nlstate+ndeath); i++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             for(j=1; j<=(nlstate+ndeath);j++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
               k=k+1;          k=kmax;
               gp[k]=pmmij[i][j];        }
             }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           }          k=kmax; l=lmax*10.;
                  }
           for(i=1; i<=npar; i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          delts=delt;
            }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      }
           k=0;    }
           for(i=1; i<=(nlstate+ndeath); i++){    delti[theta]=delts;
             for(j=1; j<=(nlstate+ndeath);j++){    return res; 
               k=k+1;    
               gm[k]=pmmij[i][j];  }
             }  
           }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
        {
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    int i;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      int l=1, l1, lmax=20;
         }    double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    int k;
           for(theta=1; theta <=npar; theta++)  
             trgradg[j][theta]=gradg[theta][j];    fx=func(x);
            for (k=1; k<=2; k++) {
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      for (i=1;i<=npar;i++) p2[i]=x[i];
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      p2[thetai]=x[thetai]+delti[thetai]/k;
              p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         pmij(pmmij,cov,ncovmodel,x,nlstate);      k1=func(p2)-fx;
            
         k=0;      p2[thetai]=x[thetai]+delti[thetai]/k;
         for(i=1; i<=(nlstate+ndeath); i++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           for(j=1; j<=(nlstate+ndeath);j++){      k2=func(p2)-fx;
             k=k+1;    
             gm[k]=pmmij[i][j];      p2[thetai]=x[thetai]-delti[thetai]/k;
           }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k3=func(p2)-fx;
          
      /*printf("\n%d ",(int)age);      p2[thetai]=x[thetai]-delti[thetai]/k;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      k4=func(p2)-fx;
      }*/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
         fprintf(ficresprob,"\n%d ",(int)age);      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);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)  #endif
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    }
      return res;
       }  }
     }  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  /************** Inverse of matrix **************/
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  void ludcmp(double **a, int n, int *indx, double *d) 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  { 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i,imax,j,k; 
   }    double big,dum,sum,temp; 
   free_vector(xp,1,npar);    double *vv; 
   fclose(ficresprob);   
      vv=vector(1,n); 
 }    *d=1.0; 
     for (i=1;i<=n;i++) { 
 /******************* Printing html file ***********/      big=0.0; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      for (j=1;j<=n;j++) 
  int lastpass, int stepm, int weightopt, char model[],\        if ((temp=fabs(a[i][j])) > big) big=temp; 
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      vv[i]=1.0/big; 
  char version[], int popforecast, int estepm ){    } 
   int jj1, k1, i1, cpt;    for (j=1;j<=n;j++) { 
   FILE *fichtm;      for (i=1;i<j;i++) { 
   /*char optionfilehtm[FILENAMELENGTH];*/        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   strcpy(optionfilehtm,optionfile);        a[i][j]=sum; 
   strcat(optionfilehtm,".htm");      } 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      big=0.0; 
     printf("Problem with %s \n",optionfilehtm), exit(0);      for (i=j;i<=n;i++) { 
   }        sum=a[i][j]; 
         for (k=1;k<j;k++) 
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          sum -= a[i][k]*a[k][j]; 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        a[i][j]=sum; 
 \n        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 Total number of observations=%d <br>\n          big=dum; 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          imax=i; 
 <hr  size=\"2\" color=\"#EC5E5E\">        } 
  <ul><li>Outputs files<br>\n      } 
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      if (j != imax) { 
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n        for (k=1;k<=n;k++) { 
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          dum=a[imax][k]; 
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          a[imax][k]=a[j][k]; 
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n          a[j][k]=dum; 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        } 
         *d = -(*d); 
  fprintf(fichtm,"\n        vv[imax]=vv[j]; 
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      } 
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      indx[j]=imax; 
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      if (a[j][j] == 0.0) a[j][j]=TINY; 
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      if (j != n) { 
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
  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    free_vector(vv,1,n);  /* Doesn't work */
         <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);  
 fprintf(fichtm," <li>Graphs</li><p>");  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
  m=cptcoveff;    int i,ii=0,ip,j; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double sum; 
    
  jj1=0;    for (i=1;i<=n;i++) { 
  for(k1=1; k1<=m;k1++){      ip=indx[i]; 
    for(i1=1; i1<=ncodemax[k1];i1++){      sum=b[ip]; 
        jj1++;      b[ip]=b[i]; 
        if (cptcovn > 0) {      if (ii) 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
          for (cpt=1; cpt<=cptcoveff;cpt++)      else if (sum) ii=i; 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      b[i]=sum; 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    } 
        }    for (i=n;i>=1;i--) { 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.png<br>      sum=b[i]; 
 <img src=\"pe%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        for(cpt=1; cpt<nlstate;cpt++){      b[i]=sum/a[i][i]; 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.png<br>    } 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  } 
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {  void pstamp(FILE *fichier)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  {
 interval) in state (%d): v%s%d%d.png <br>    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    }
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {  /************ Frequencies ********************/
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>  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[])
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  {  /* Some frequencies */
      }    
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    int i, m, jk, k1,i1, j1, bool, z1,j;
 health expectancies in states (1) and (2): e%s%d.png<br>    int first;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    double ***freq; /* Frequencies */
 fprintf(fichtm,"\n</body>");    double *pp, **prop;
    }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
    }    char fileresp[FILENAMELENGTH];
 fclose(fichtm);    
 }    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
 /******************* Gnuplot file **************/    strcpy(fileresp,"p");
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   strcpy(optionfilegnuplot,optionfilefiname);      exit(0);
   strcat(optionfilegnuplot,".gp.txt");    }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     printf("Problem with file %s",optionfilegnuplot);    j1=0;
   }    
     j=cptcoveff;
 #ifdef windows    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif    first=1;
 m=pow(2,cptcoveff);  
      for(k1=1; k1<=j;k1++){
  /* 1eme*/      for(i1=1; i1<=ncodemax[k1];i1++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {        j1++;
    for (k1=1; k1<= m ; k1 ++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
 #ifdef windows        for (i=-5; i<=nlstate+ndeath; i++)  
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            for(m=iagemin; m <= iagemax+3; m++)
 #endif              freq[i][jk][m]=0;
 #ifdef unix  
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);      for (i=1; i<=nlstate; i++)  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        for(m=iagemin; m <= iagemax+3; m++)
 #endif          prop[i][m]=0;
         
 for (i=1; i<= nlstate ; i ++) {        dateintsum=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        k2cpt=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (i=1; i<=imx; i++) {
 }          bool=1;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          if  (cptcovn>0) {
     for (i=1; i<= nlstate ; i ++) {            for (z1=1; z1<=cptcoveff; z1++) 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");                bool=0;
 }          }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          if (bool==1){
      for (i=1; i<= nlstate ; i ++) {            for(m=firstpass; m<=lastpass; m++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              k2=anint[m][i]+(mint[m][i]/12.);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 }                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 #ifdef unix                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");                if (m<lastpass) {
 #endif                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   }                }
   /*2 eme*/                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   for (k1=1; k1<= m ; k1 ++) {                  dateintsum=dateintsum+k2;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n\n",strtok(optionfile, "."),k1);                  k2cpt++;
     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,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {         
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");        pstamp(ficresp);
 }          if  (cptcovn>0) {
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          fprintf(ficresp, "\n#********** Variable "); 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficresp, "**********\n#");
       for (j=1; j<= nlstate+1 ; j ++) {        }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1; i<=nlstate;i++) 
         else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 }          fprintf(ficresp, "\n");
       fprintf(ficgp,"\" t\"\" w l 0,");        
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(i=iagemin; i <= iagemax+3; i++){
       for (j=1; j<= nlstate+1 ; j ++) {          if(i==iagemax+3){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficlog,"Total");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }else{
 }              if(first==1){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              first=0;
       else fprintf(ficgp,"\" t\"\" w l 0,");              printf("See log file for details...\n");
     }            }
   }            fprintf(ficlog,"Age %d", i);
            }
   /*3eme*/          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   for (k1=1; k1<= m ; k1 ++) {              pp[jk] += freq[jk][m][i]; 
     for (cpt=1; cpt<= nlstate ; cpt ++) {          }
       k=2+nlstate*(2*cpt-2);          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);            for(m=-1, pos=0; m <=0 ; m++)
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);              pos += freq[jk][m][i];
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            if(pp[jk]>=1.e-10){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              if(first==1){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            }else{
               if(first==1)
 */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for (i=1; i< nlstate ; i ++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);            }
           }
       }  
     }          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                pp[jk] += freq[jk][m][i];
   /* CV preval stat */          }       
     for (k1=1; k1<= m ; k1 ++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     for (cpt=1; cpt<nlstate ; cpt ++) {            pos += pp[jk];
       k=3;            posprop += prop[jk][i];
       fprintf(ficgp,"set out \"p%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);          }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
       for (i=1; i< nlstate ; i ++)              if(first==1)
         fprintf(ficgp,"+$%d",k+i+1);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  }else{
       l=3+(nlstate+ndeath)*cpt;              if(first==1)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for (i=1; i< nlstate ; i ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         l=3+(nlstate+ndeath)*cpt;            }
         fprintf(ficgp,"+$%d",l+i+1);            if( i <= iagemax){
       }              if(pos>=1.e-5){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     }                /*probs[i][jk][j1]= pp[jk]/pos;*/
   }                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                }
   /* proba elementaires */              else
    for(i=1,jk=1; i <=nlstate; i++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for(k=1; k <=(nlstate+ndeath); k++){            }
       if (k != i) {          }
         for(j=1; j <=ncovmodel; j++){          
                  for(jk=-1; jk <=nlstate+ndeath; jk++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            for(m=-1; m <=nlstate+ndeath; m++)
           jk++;              if(freq[jk][m][i] !=0 ) {
           fprintf(ficgp,"\n");              if(first==1)
         }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     }              }
    }          if(i <= iagemax)
             fprintf(ficresp,"\n");
    for(jk=1; jk <=m; jk++) {          if(first==1)
      fprintf(ficgp,"\nset out \"pe%s%d.png\" \n\n",strtok(optionfile, "."),jk);            printf("Others in log...\n");
      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          fprintf(ficlog,"\n");
      i=1;        }
      for(k2=1; k2<=nlstate; k2++) {      }
        k3=i;    }
        for(k=1; k<=(nlstate+ndeath); k++) {    dateintmean=dateintsum/k2cpt; 
          if (k != k2){   
            fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    fclose(ficresp);
            ij=1;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
            for(j=3; j <=ncovmodel; j++) {    free_vector(pp,1,nlstate);
              if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
                fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* End of Freq */
                ij++;  }
              }  
              else  /************ Prevalence ********************/
                fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  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)
            }  {  
            fprintf(ficgp,")/(1");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
                   in each health status at the date of interview (if between dateprev1 and dateprev2).
            for(k1=1; k1 <=nlstate; k1++){         We still use firstpass and lastpass as another selection.
              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++){    int i, m, jk, k1, i1, j1, bool, z1,j;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double ***freq; /* Frequencies */
                  fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double *pp, **prop;
                  ij++;    double pos,posprop; 
                }    double  y2; /* in fractional years */
                else    int iagemin, iagemax;
                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
              }    iagemin= (int) agemin;
              fprintf(ficgp,")");    iagemax= (int) agemax;
            }    /*pp=vector(1,nlstate);*/
            fprintf(ficgp,") t \"p%d%d\" ", k2,k);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
            if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
            i=i+ncovmodel;    j1=0;
          }    
        }    j=cptcoveff;
      }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    }    
        for(k1=1; k1<=j;k1++){
    fclose(ficgp);      for(i1=1; i1<=ncodemax[k1];i1++){
 }  /* end gnuplot */        j1++;
         
         for (i=1; i<=nlstate; i++)  
 /*************** Moving average **************/          for(m=iagemin; m <= iagemax+3; m++)
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){            prop[i][m]=0.0;
        
   int i, cpt, cptcod;        for (i=1; i<=imx; i++) { /* Each individual */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          bool=1;
       for (i=1; i<=nlstate;i++)          if  (cptcovn>0) {
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            for (z1=1; z1<=cptcoveff; z1++) 
           mobaverage[(int)agedeb][i][cptcod]=0.;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          } 
       for (i=1; i<=nlstate;i++){          if (bool==1) { 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           for (cpt=0;cpt<=4;cpt++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                      prop[s[m][i]][(int)agev[m][i]] += weight[i];
 }                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
               }
 /************** Forecasting ******************/            } /* end selection of waves */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          }
          }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for(i=iagemin; i <= iagemax+3; i++){  
   int *popage;          
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double *popeffectif,*popcount;            posprop += prop[jk][i]; 
   double ***p3mat;          } 
   char fileresf[FILENAMELENGTH];  
           for(jk=1; jk <=nlstate ; jk++){     
  agelim=AGESUP;            if( i <=  iagemax){ 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              } else
                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
              } 
   strcpy(fileresf,"f");          }/* end jk */ 
   strcat(fileresf,fileres);        }/* end i */ 
   if((ficresf=fopen(fileresf,"w"))==NULL) {      } /* end i1 */
     printf("Problem with forecast resultfile: %s\n", fileresf);    } /* end k1 */
   }    
   printf("Computing forecasting: result on file '%s' \n", fileresf);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************* Waves Concatenation ***************/
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }  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)
   {
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   if (stepm<=12) stepsize=1;       Death is a valid wave (if date is known).
         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   agelim=AGESUP;       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.
   hstepm=1;       */
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);    int i, mi, m;
   anprojmean=yp;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   yp2=modf((yp1*12),&yp);       double sum=0., jmean=0.;*/
   mprojmean=yp;    int first;
   yp1=modf((yp2*30.5),&yp);    int j, k=0,jk, ju, jl;
   jprojmean=yp;    double sum=0.;
   if(jprojmean==0) jprojmean=1;    first=0;
   if(mprojmean==0) jprojmean=1;    jmin=1e+5;
      jmax=-1;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    jmean=0.;
      for(i=1; i<=imx; i++){
   for(cptcov=1;cptcov<=i2;cptcov++){      mi=0;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      m=firstpass;
       k=k+1;      while(s[m][i] <= nlstate){
       fprintf(ficresf,"\n#******");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       for(j=1;j<=cptcoveff;j++) {          mw[++mi][i]=m;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if(m >=lastpass)
       }          break;
       fprintf(ficresf,"******\n");        else
       fprintf(ficresf,"# StartingAge FinalAge");          m++;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      }/* end while */
            if (s[m][i] > nlstate){
              mi++;     /* Death is another wave */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        /* if(mi==0)  never been interviewed correctly before death */
         fprintf(ficresf,"\n");           /* Only death is a correct wave */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          mw[mi][i]=m;
       }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      wav[i]=mi;
           nhstepm = nhstepm/hstepm;      if(mi==0){
                  nbwarn++;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if(first==0){
           oldm=oldms;savm=savms;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            first=1;
                }
           for (h=0; h<=nhstepm; h++){        if(first==1){
             if (h==(int) (calagedate+YEARM*cpt)) {          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        }
             }      } /* end mi==0 */
             for(j=1; j<=nlstate+ndeath;j++) {    } /* End individuals */
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  for(i=1; i<=imx; i++){
                 if (mobilav==1)      for(mi=1; mi<wav[i];mi++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if (stepm <=0)
                 else {          dh[mi][i]=1;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        else{
                 }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                            if (agedc[i] < 2*AGESUP) {
               }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if (h==(int)(calagedate+12*cpt)){              if(j==0) j=1;  /* Survives at least one month after exam */
                 fprintf(ficresf," %.3f", kk1);              else if(j<0){
                                        nberr++;
               }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }                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);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       }              }
     }              k=k+1;
   }              if (j >= jmax){
                        jmax=j;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                ijmax=i;
               }
   fclose(ficresf);              if (j <= jmin){
 }                jmin=j;
 /************** Forecasting ******************/                ijmin=i;
 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){              }
                sum=sum+j;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   int *popage;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }
   double *popeffectif,*popcount;          }
   double ***p3mat,***tabpop,***tabpopprev;          else{
   char filerespop[FILENAMELENGTH];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            k=k+1;
   agelim=AGESUP;            if (j >= jmax) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              jmax=j;
                ijmax=i;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            }
              else if (j <= jmin){
                jmin=j;
   strcpy(filerespop,"pop");              ijmin=i;
   strcat(filerespop,fileres);            }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     printf("Problem with forecast resultfile: %s\n", filerespop);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   }            if(j<0){
   printf("Computing forecasting: result on file '%s' \n", filerespop);              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
   if (mobilav==1) {            sum=sum+j;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
     movingaverage(agedeb, fage, ageminpar, mobaverage);          jk= j/stepm;
   }          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   if (stepm<=12) stepsize=1;            if(jl==0){
                dh[mi][i]=jk;
   agelim=AGESUP;              bh[mi][i]=0;
              }else{ /* We want a negative bias in order to only have interpolation ie
   hstepm=1;                    * to avoid the price of an extra matrix product in likelihood */
   hstepm=hstepm/stepm;              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   if (popforecast==1) {            }
     if((ficpop=fopen(popfile,"r"))==NULL) {          }else{
       printf("Problem with population file : %s\n",popfile);exit(0);            if(jl <= -ju){
     }              dh[mi][i]=jk;
     popage=ivector(0,AGESUP);              bh[mi][i]=jl;       /* bias is positive if real duration
     popeffectif=vector(0,AGESUP);                                   * is higher than the multiple of stepm and negative otherwise.
     popcount=vector(0,AGESUP);                                   */
                }
     i=1;              else{
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              dh[mi][i]=jk+1;
                  bh[mi][i]=ju;
     imx=i;            }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            if(dh[mi][i]==0){
   }              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   for(cptcov=1;cptcov<=i2;cptcov++){              /*  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);*/
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            }
       k=k+1;          } /* end if mle */
       fprintf(ficrespop,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {      } /* end wave */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       }    jmean=sum/k;
       fprintf(ficrespop,"******\n");    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);
       fprintf(ficrespop,"# Age");    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);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);   }
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
        /*********** Tricode ****************************/
       for (cpt=0; cpt<=0;cpt++) {  void tricode(int *Tvar, int **nbcode, int imx)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    {
            /* Uses cptcovn+2*cptcovprod as the number of covariates */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
              int modmaxcovj=0; /* Modality max of covariates j */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    cptcoveff=0; 
           oldm=oldms;savm=savms;   
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      for (k=0; k<maxncov; k++) Ndum[k]=0;
            for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
             }                                 modality of this covariate Vj*/ 
             for(j=1; j<=nlstate+ndeath;j++) {        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
               kk1=0.;kk2=0;                                        modality of the nth covariate of individual i. */
               for(i=1; i<=nlstate;i++) {                      Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
                 if (mobilav==1)        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if (ij > modmaxcovj) modmaxcovj=ij; 
                 else {        /* getting the maximum value of the modality of the covariate
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                 }           female is 1, then modmaxcovj=1.*/
               }      }
               if (h==(int)(calagedate+12*cpt)){      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
                   /*fprintf(ficrespop," %.3f", kk1);        if( Ndum[i] != 0 )
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          ncodemax[j]++; 
               }        /* Number of modalities of the j th covariate. In fact
             }           ncodemax[j]=2 (dichotom. variables only) but it could be more for
             for(i=1; i<=nlstate;i++){           historical reasons */
               kk1=0.;      } /* Ndum[-1] number of undefined modalities */
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
                 }      ij=1; 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
             }        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                                       k is a modality. If we have model=V1+V1*sex 
           }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            ij++;
         }          }
       }          if (ij > ncodemax[j]) break; 
          }  /* end of loop on */
   /******/      } /* end of loop on modality */ 
     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for (k=0; k< maxncov; k++) Ndum[k]=0;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
           nhstepm = nhstepm/hstepm;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
               ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     Ndum[ij]++;
           oldm=oldms;savm=savms;   }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           for (h=0; h<=nhstepm; h++){   ij=1;
             if (h==(int) (calagedate+YEARM*cpt)) {   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);     if((Ndum[i]!=0) && (i<=ncovcol)){
             }       Tvaraff[ij]=i; /*For printing */
             for(j=1; j<=nlstate+ndeath;j++) {       ij++;
               kk1=0.;kk2=0;     }
               for(i=1; i<=nlstate;i++) {                 }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];       ij--;
               }   cptcoveff=ij; /*Number of simple covariates*/
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  }
             }  
           }  /*********** Health Expectancies ****************/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       }  
    }  {
   }    /* Health expectancies, no variances */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   if (popforecast==1) {    double ***p3mat;
     free_ivector(popage,0,AGESUP);    double eip;
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);    pstamp(ficreseij);
   }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficreseij,"# Age");
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(i=1; i<=nlstate;i++){
   fclose(ficrespop);      for(j=1; j<=nlstate;j++){
 }        fprintf(ficreseij," e%1d%1d ",i,j);
       }
 /***********************************************/      fprintf(ficreseij," e%1d. ",i);
 /**************** Main Program *****************/    }
 /***********************************************/    fprintf(ficreseij,"\n");
   
 int main(int argc, char *argv[])    
 {    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    }
   double agedeb, agefin,hf;    else  hstepm=estepm;   
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   double fret;     * if stepm=24 months pijx are given only every 2 years and by summing them
   double **xi,tmp,delta;     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   double dum; /* Dummy variable */     * to the curvature of the survival function. If, for the same date, we 
   double ***p3mat;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   int *indx;     * to compare the new estimate of Life expectancy with the same linear 
   char line[MAXLINE], linepar[MAXLINE];     * hypothesis. A more precise result, taking into account a more precise
   char title[MAXLINE];     * curvature will be obtained if estepm is as small as stepm. */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    /* 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. 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   char filerest[FILENAMELENGTH];       Look at hpijx to understand the reason of that which relies in memory size
   char fileregp[FILENAMELENGTH];       and note for a fixed period like estepm months */
   char popfile[FILENAMELENGTH];    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];       survival function given by stepm (the optimization length). Unfortunately it
   int firstobs=1, lastobs=10;       means that if the survival funtion is printed only each two years of age and if
   int sdeb, sfin; /* Status at beginning and end */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   int c,  h , cpt,l;       results. So we changed our mind and took the option of the best precision.
   int ju,jl, mi;    */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;    agelim=AGESUP;
   int hstepm, nhstepm;    /* If stepm=6 months */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   double bage, fage, age, agelim, agebase;      
   double ftolpl=FTOL;  /* nhstepm age range expressed in number of stepm */
   double **prlim;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   double *severity;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   double ***param; /* Matrix of parameters */    /* if (stepm >= YEARM) hstepm=1;*/
   double  *p;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double **matcov; /* Matrix of covariance */    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double ***delti3; /* Scale */  
   double *delti; /* Scale */    for (age=bage; age<=fage; age ++){ 
   double ***eij, ***vareij;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   double **varpl; /* Variances of prevalence limits by age */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   double *epj, vepp;      /* if (stepm >= YEARM) hstepm=1;*/
   double kk1, kk2;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
        /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
   char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   char *alph[]={"a","a","b","c","d","e"}, str[4];      
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
   char z[1]="c", occ;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 #include <sys/time.h>      
 #include <time.h>      printf("%d|",(int)age);fflush(stdout);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        
   /* long total_usecs;      /* Computing expectancies */
   struct timeval start_time, end_time;      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   getcwd(pathcd, size);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
   printf("\n%s",version);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");          }
     scanf("%s",pathtot);  
   }      fprintf(ficreseij,"%3.0f",age );
   else{      for(i=1; i<=nlstate;i++){
     strcpy(pathtot,argv[1]);        eip=0;
   }        for(j=1; j<=nlstate;j++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          eip +=eij[i][j][(int)age];
   /*cygwin_split_path(pathtot,path,optionfile);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        }
   /* cutv(path,optionfile,pathtot,'\\');*/        fprintf(ficreseij,"%9.4f", eip );
       }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      fprintf(ficreseij,"\n");
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      
   chdir(path);    }
   replace(pathc,path);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
 /*-------- arguments in the command line --------*/    fprintf(ficlog,"\n");
     
   strcpy(fileres,"r");  }
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */  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[] )
   
   /*---------arguments file --------*/  {
     /* Covariances of health expectancies eij and of total life expectancies according
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     to initial status i, ei. .
     printf("Problem with optionfile %s\n",optionfile);    */
     goto end;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   }    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   strcpy(filereso,"o");    double ***p3matp, ***p3matm, ***varhe;
   strcat(filereso,fileres);    double **dnewm,**doldm;
   if((ficparo=fopen(filereso,"w"))==NULL) {    double *xp, *xm;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    double **gp, **gm;
   }    double ***gradg, ***trgradg;
     int theta;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    double eip, vip;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     puts(line);    xp=vector(1,npar);
     fputs(line,ficparo);    xm=vector(1,npar);
   }    dnewm=matrix(1,nlstate*nlstate,1,npar);
   ungetc(c,ficpar);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    pstamp(ficresstdeij);
   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(ficresstdeij,"# Health expectancies with standard errors\n");
   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(ficresstdeij,"# Age");
 while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     puts(line);      fprintf(ficresstdeij," e%1d. ",i);
     fputs(line,ficparo);    }
   }    fprintf(ficresstdeij,"\n");
   ungetc(c,ficpar);  
      pstamp(ficrescveij);
        fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficrescveij,"# Age");
   cptcovn=0;    for(i=1; i<=nlstate;i++)
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
   ncovmodel=2+cptcovn;        for(i2=1; i2<=nlstate;i2++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          for(j2=1; j2<=nlstate;j2++){
              cptj2= (j2-1)*nlstate+i2;
   /* Read guess parameters */            if(cptj2 <= cptj)
   /* Reads comments: lines beginning with '#' */              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);    fprintf(ficrescveij,"\n");
     puts(line);    
     fputs(line,ficparo);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   ungetc(c,ficpar);    }
      else  hstepm=estepm;   
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(i=1; i <=nlstate; i++)     * This is mainly to measure the difference between two models: for example
     for(j=1; j <=nlstate+ndeath-1; j++){     * if stepm=24 months pijx are given only every 2 years and by summing them
       fscanf(ficpar,"%1d%1d",&i1,&j1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficparo,"%1d%1d",i1,j1);     * progression in between and thus overestimating or underestimating according
       printf("%1d%1d",i,j);     * to the curvature of the survival function. If, for the same date, we 
       for(k=1; k<=ncovmodel;k++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fscanf(ficpar," %lf",&param[i][j][k]);     * to compare the new estimate of Life expectancy with the same linear 
         printf(" %lf",param[i][j][k]);     * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficparo," %lf",param[i][j][k]);     * curvature will be obtained if estepm is as small as stepm. */
       }  
       fscanf(ficpar,"\n");    /* For example we decided to compute the life expectancy with the smallest unit */
       printf("\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficparo,"\n");       nhstepm is the number of hstepm from age to agelim 
     }       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   p=param[1][1];       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
   /* Reads comments: lines beginning with '#' */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   while((c=getc(ficpar))=='#' && c!= EOF){       results. So we changed our mind and took the option of the best precision.
     ungetc(c,ficpar);    */
     fgets(line, MAXLINE, ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     puts(line);  
     fputs(line,ficparo);    /* If stepm=6 months */
   }    /* nhstepm age range expressed in number of stepm */
   ungetc(c,ficpar);    agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    /* if (stepm >= YEARM) hstepm=1;*/
   for(i=1; i <=nlstate; i++){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(j=1; j <=nlstate+ndeath-1; j++){    
       fscanf(ficpar,"%1d%1d",&i1,&j1);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("%1d%1d",i,j);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo,"%1d%1d",i1,j1);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       for(k=1; k<=ncovmodel;k++){    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
         printf(" %le",delti3[i][j][k]);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    for (age=bage; age<=fage; age ++){ 
       fscanf(ficpar,"\n");      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       printf("\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficparo,"\n");      /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   }  
   delti=delti3[1][1];      /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepma matrices, stored
   /* Reads comments: lines beginning with '#' */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      /* Computing  Variances of health expectancies */
     fputs(line,ficparo);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   }         decrease memory allocation */
   ungetc(c,ficpar);      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ 
   matcov=matrix(1,npar,1,npar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   for(i=1; i <=npar; i++){          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     fscanf(ficpar,"%s",&str);        }
     printf("%s",str);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     fprintf(ficparo,"%s",str);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     for(j=1; j <=i; j++){    
       fscanf(ficpar," %le",&matcov[i][j]);        for(j=1; j<= nlstate; j++){
       printf(" %.5le",matcov[i][j]);          for(i=1; i<=nlstate; i++){
       fprintf(ficparo," %.5le",matcov[i][j]);            for(h=0; h<=nhstepm-1; h++){
     }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     fscanf(ficpar,"\n");              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     printf("\n");            }
     fprintf(ficparo,"\n");          }
   }        }
   for(i=1; i <=npar; i++)       
     for(j=i+1;j<=npar;j++)        for(ij=1; ij<= nlstate*nlstate; ij++)
       matcov[i][j]=matcov[j][i];          for(h=0; h<=nhstepm-1; h++){
                gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   printf("\n");          }
       }/* End theta */
       
     /*-------- Rewriting paramater file ----------*/      
      strcpy(rfileres,"r");    /* "Rparameterfile */      for(h=0; h<=nhstepm-1; h++)
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        for(j=1; j<=nlstate*nlstate;j++)
      strcat(rfileres,".");    /* */          for(theta=1; theta <=npar; theta++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            trgradg[h][j][theta]=gradg[h][theta][j];
     if((ficres =fopen(rfileres,"w"))==NULL) {      
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }       for(ij=1;ij<=nlstate*nlstate;ij++)
     fprintf(ficres,"#%s\n",version);        for(ji=1;ji<=nlstate*nlstate;ji++)
              varhe[ij][ji][(int)age] =0.;
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {       printf("%d|",(int)age);fflush(stdout);
       printf("Problem with datafile: %s\n", datafile);goto end;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     }       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
     n= lastobs;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     severity = vector(1,maxwav);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     outcome=imatrix(1,maxwav+1,1,n);          for(ij=1;ij<=nlstate*nlstate;ij++)
     num=ivector(1,n);            for(ji=1;ji<=nlstate*nlstate;ji++)
     moisnais=vector(1,n);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     annais=vector(1,n);        }
     moisdc=vector(1,n);      }
     andc=vector(1,n);  
     agedc=vector(1,n);      /* Computing expectancies */
     cod=ivector(1,n);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     weight=vector(1,n);      for(i=1; i<=nlstate;i++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(j=1; j<=nlstate;j++)
     mint=matrix(1,maxwav,1,n);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     anint=matrix(1,maxwav,1,n);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     s=imatrix(1,maxwav+1,1,n);            
     adl=imatrix(1,maxwav+1,1,n);                /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);          }
   
     i=1;      fprintf(ficresstdeij,"%3.0f",age );
     while (fgets(line, MAXLINE, fic) != NULL)    {      for(i=1; i<=nlstate;i++){
       if ((i >= firstobs) && (i <=lastobs)) {        eip=0.;
                vip=0.;
         for (j=maxwav;j>=1;j--){        for(j=1; j<=nlstate;j++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          eip += eij[i][j][(int)age];
           strcpy(line,stra);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }        }
                fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficresstdeij,"\n");
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficrescveij,"%3.0f",age );
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          cptj= (j-1)*nlstate+i;
         for (j=ncovcol;j>=1;j--){          for(i2=1; i2<=nlstate;i2++)
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(j2=1; j2<=nlstate;j2++){
         }              cptj2= (j2-1)*nlstate+i2;
         num[i]=atol(stra);              if(cptj2 <= cptj)
                        fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            }
           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;}*/        }
       fprintf(ficrescveij,"\n");
         i=i+1;     
       }    }
     }    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     /* printf("ii=%d", ij);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        scanf("%d",i);*/    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   imx=i-1; /* Number of individuals */    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* for (i=1; i<=imx; i++){    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    printf("\n");
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    fprintf(ficlog,"\n");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }*/    free_vector(xm,1,npar);
    /*  for (i=1; i<=imx; i++){    free_vector(xp,1,npar);
      if (s[4][i]==9)  s[4][i]=-1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      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]));}*/    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);  /************ Variance ******************/
   Tprod=ivector(1,15);  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[])
   Tvaraff=ivector(1,15);  {
   Tvard=imatrix(1,15,1,2);    /* Variance of health expectancies */
   Tage=ivector(1,15);          /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
        /* double **newm;*/
   if (strlen(model) >1){    double **dnewm,**doldm;
     j=0, j1=0, k1=1, k2=1;    double **dnewmp,**doldmp;
     j=nbocc(model,'+');    int i, j, nhstepm, hstepm, h, nstepm ;
     j1=nbocc(model,'*');    int k, cptcode;
     cptcovn=j+1;    double *xp;
     cptcovprod=j1;    double **gp, **gm;  /* for var eij */
        double ***gradg, ***trgradg; /*for var eij */
     strcpy(modelsav,model);    double **gradgp, **trgradgp; /* for var p point j */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double *gpp, *gmp; /* for var p point j */
       printf("Error. Non available option model=%s ",model);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       goto end;    double ***p3mat;
     }    double age,agelim, hf;
        double ***mobaverage;
     for(i=(j+1); i>=1;i--){    int theta;
       cutv(stra,strb,modelsav,'+');    char digit[4];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    char digitp[25];
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/    char fileresprobmorprev[FILENAMELENGTH];
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');    if(popbased==1){
         if (strcmp(strc,"age")==0) {      if(mobilav!=0)
           cptcovprod--;        strcpy(digitp,"-populbased-mobilav-");
           cutv(strb,stre,strd,'V');      else strcpy(digitp,"-populbased-nomobil-");
           Tvar[i]=atoi(stre);    }
           cptcovage++;    else 
             Tage[cptcovage]=i;      strcpy(digitp,"-stablbased-");
             /*printf("stre=%s ", stre);*/  
         }    if (mobilav!=0) {
         else if (strcmp(strd,"age")==0) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cptcovprod--;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           cutv(strb,stre,strc,'V');        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           Tvar[i]=atoi(stre);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           cptcovage++;      }
           Tage[cptcovage]=i;    }
         }  
         else {    strcpy(fileresprobmorprev,"prmorprev"); 
           cutv(strb,stre,strc,'V');    sprintf(digit,"%-d",ij);
           Tvar[i]=ncovcol+k1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           cutv(strb,strc,strd,'V');    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           Tprod[k1]=i;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           Tvard[k1][1]=atoi(strc);    strcat(fileresprobmorprev,fileres);
           Tvard[k1][2]=atoi(stre);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           Tvar[cptcovn+k2]=Tvard[k1][1];      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           for (k=1; k<=lastobs;k++)    }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           k1++;   
           k2=k2+2;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         }    pstamp(ficresprobmorprev);
       }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
       else {    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        /*  scanf("%d",i);*/      fprintf(ficresprobmorprev," p.%-d SE",j);
       cutv(strd,strc,strb,'V');      for(i=1; i<=nlstate;i++)
       Tvar[i]=atoi(strc);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       }    }  
       strcpy(modelsav,stra);      fprintf(ficresprobmorprev,"\n");
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    fprintf(ficgp,"\n# Routine varevsij");
         scanf("%d",i);*/    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     }    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
 }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("cptcovprod=%d ", cptcovprod);    pstamp(ficresvij);
   scanf("%d ",i);*/    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     fclose(fic);    if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     /*  if(mle==1){*/    else
     if (weightopt != 1) { /* Maximisation without weights*/      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficresvij,"# Age");
     }    for(i=1; i<=nlstate;i++)
     /*-calculation of age at interview from date of interview and age at death -*/      for(j=1; j<=nlstate;j++)
     agev=matrix(1,maxwav,1,imx);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {    xp=vector(1,npar);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    dnewm=matrix(1,nlstate,1,npar);
          anint[m][i]=9999;    doldm=matrix(1,nlstate,1,nlstate);
          s[m][i]=-1;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
        }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     }    gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     for (i=1; i<=imx; i++)  {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    
       for(m=1; (m<= maxwav); m++){    if(estepm < stepm){
         if(s[m][i] >0){      printf ("Problem %d lower than %d\n",estepm, stepm);
           if (s[m][i] >= nlstate+1) {    }
             if(agedc[i]>0)    else  hstepm=estepm;   
               if(moisdc[i]!=99 && andc[i]!=9999)    /* For example we decided to compute the life expectancy with the smallest unit */
                 agev[m][i]=agedc[i];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/       nhstepm is the number of hstepm from age to agelim 
            else {       nstepm is the number of stepm from age to agelin. 
               if (andc[i]!=9999){       Look at function hpijx to understand why (it is linked to memory size questions) */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               agev[m][i]=-1;       survival function given by stepm (the optimization length). Unfortunately it
               }       means that if the survival funtion is printed every two years of age and if
             }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           }       results. So we changed our mind and took the option of the best precision.
           else if(s[m][i] !=9){ /* Should no more exist */    */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             if(mint[m][i]==99 || anint[m][i]==9999)    agelim = AGESUP;
               agev[m][i]=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             else if(agev[m][i] <agemin){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
               agemin=agev[m][i];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
             else if(agev[m][i] >agemax){      gp=matrix(0,nhstepm,1,nlstate);
               agemax=agev[m][i];      gm=matrix(0,nhstepm,1,nlstate);
              /* 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];*/      for(theta=1; theta <=npar; theta++){
             /*   agev[m][i] = age[i]+2*m;*/        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           else { /* =9 */        }
             agev[m][i]=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             s[m][i]=-1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }  
         }        if (popbased==1) {
         else /*= 0 Unknown */          if(mobilav ==0){
           agev[m][i]=1;            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     for (i=1; i<=imx; i++)  {              prlim[i][i]=mobaverage[(int)age][i][ij];
       for(m=1; (m<= maxwav); m++){          }
         if (s[m][i] > (nlstate+ndeath)) {        }
           printf("Error: Wrong value in nlstate or ndeath\n");      
           goto end;        for(j=1; j<= nlstate; j++){
         }          for(h=0; h<=nhstepm; h++){
       }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        }
         /* This for computing probability of death (h=1 means
     free_vector(severity,1,maxwav);           computed over hstepm matrices product = hstepm*stepm months) 
     free_imatrix(outcome,1,maxwav+1,1,n);           as a weighted average of prlim.
     free_vector(moisnais,1,n);        */
     free_vector(annais,1,n);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     /* free_matrix(mint,1,maxwav,1,n);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
        free_matrix(anint,1,maxwav,1,n);*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     free_vector(moisdc,1,n);        }    
     free_vector(andc,1,n);        /* end probability of death */
   
            for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     wav=ivector(1,imx);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       
     /* Concatenates waves */        if (popbased==1) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
       Tcode=ivector(1,100);          }else{ /* mobilav */ 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            for(i=1; i<=nlstate;i++)
       ncodemax[1]=1;              prlim[i][i]=mobaverage[(int)age][i][ij];
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          }
              }
    codtab=imatrix(1,100,1,10);  
    h=0;        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
    m=pow(2,cptcoveff);          for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
    for(k=1;k<=cptcoveff; k++){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
      for(i=1; i <=(m/pow(2,k));i++){          }
        for(j=1; j <= ncodemax[k]; j++){        }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        /* This for computing probability of death (h=1 means
            h++;           computed over hstepm matrices product = hstepm*stepm months) 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;           as a weighted average of prlim.
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        */
          }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
        }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
      }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
    }        }    
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        /* end probability of death */
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){        for(j=1; j<= nlstate; j++) /* vareij */
       for(k=1; k <=cptcovn; k++){          for(h=0; h<=nhstepm; h++){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       }          }
       printf("\n");  
       }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       scanf("%d",i);*/          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
            }
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */      } /* End theta */
   
          trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(h=0; h<=nhstepm; h++) /* veij */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate;j++)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(theta=1; theta <=npar; theta++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            trgradg[h][j][theta]=gradg[h][theta][j];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
            for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     /* For Powell, parameters are in a vector p[] starting at p[1]        for(theta=1; theta <=npar; theta++)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          trgradgp[j][theta]=gradgp[theta][j];
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    
   
     if(mle==1){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      for(i=1;i<=nlstate;i++)
     }        for(j=1;j<=nlstate;j++)
              vareij[i][j][(int)age] =0.;
     /*--------- 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);      for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
    jk=1;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          for(i=1;i<=nlstate;i++)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            for(j=1;j<=nlstate;j++)
    for(i=1,jk=1; i <=nlstate; i++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
      for(k=1; k <=(nlstate+ndeath); k++){        }
        if (k != i)      }
          {    
            printf("%d%d ",i,k);      /* pptj */
            fprintf(ficres,"%1d%1d ",i,k);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            for(j=1; j <=ncovmodel; j++){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
              printf("%f ",p[jk]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
              fprintf(ficres,"%f ",p[jk]);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
              jk++;          varppt[j][i]=doldmp[j][i];
            }      /* end ppptj */
            printf("\n");      /*  x centered again */
            fprintf(ficres,"\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
          }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
      }   
    }      if (popbased==1) {
  if(mle==1){        if(mobilav ==0){
     /* Computing hessian and covariance matrix */          for(i=1; i<=nlstate;i++)
     ftolhess=ftol; /* Usually correct */            prlim[i][i]=probs[(int)age][i][ij];
     hesscov(matcov, p, npar, delti, ftolhess, func);        }else{ /* mobilav */ 
  }          for(i=1; i<=nlstate;i++)
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            prlim[i][i]=mobaverage[(int)age][i][ij];
     printf("# 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) {      /* This for computing probability of death (h=1 means
           fprintf(ficres,"%1d%1d",i,j);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           printf("%1d%1d",i,j);         as a weighted average of prlim.
           for(k=1; k<=ncovmodel;k++){      */
             printf(" %.5e",delti[jk]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
             fprintf(ficres," %.5e",delti[jk]);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
             jk++;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           }      }    
           printf("\n");      /* end probability of death */
           fprintf(ficres,"\n");  
         }      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++){
     k=1;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     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");        }
     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");      } 
     for(i=1;i<=npar;i++){      fprintf(ficresprobmorprev,"\n");
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;      fprintf(ficresvij,"%.0f ",age );
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      for(i=1; i<=nlstate;i++)
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for(j=1; j<=nlstate;j++){
       fprintf(ficres,"%3d",i);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       printf("%3d",i);        }
       for(j=1; j<=i;j++){      fprintf(ficresvij,"\n");
         fprintf(ficres," %.5e",matcov[i][j]);      free_matrix(gp,0,nhstepm,1,nlstate);
         printf(" %.5e",matcov[i][j]);      free_matrix(gm,0,nhstepm,1,nlstate);
       }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficres,"\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       printf("\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k++;    } /* End age */
     }    free_vector(gpp,nlstate+1,nlstate+ndeath);
        free_vector(gmp,nlstate+1,nlstate+ndeath);
     while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       ungetc(c,ficpar);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
       puts(line);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fputs(line,ficparo);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     ungetc(c,ficpar);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     estepm=0;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     if (estepm==0 || estepm < stepm) estepm=stepm;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     if (fage <= 2) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       bage = ageminpar;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       fage = agemaxpar;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
      */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
      free_vector(xp,1,npar);
     while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(doldm,1,nlstate,1,nlstate);
     ungetc(c,ficpar);    free_matrix(dnewm,1,nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     puts(line);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     fputs(line,ficparo);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   ungetc(c,ficpar);    fclose(ficresprobmorprev);
      fflush(ficgp);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    fflush(fichtm); 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  }  /* end varevsij */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
        /************ Variance of prevlim ******************/
   while((c=getc(ficpar))=='#' && c!= EOF){  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[])
     ungetc(c,ficpar);  {
     fgets(line, MAXLINE, ficpar);    /* Variance of prevalence limit */
     puts(line);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     fputs(line,ficparo);    double **newm;
   }    double **dnewm,**doldm;
   ungetc(c,ficpar);    int i, j, nhstepm, hstepm;
      int k, cptcode;
     double *xp;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    double *gp, *gm;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    double **gradg, **trgradg;
     double age,agelim;
   fscanf(ficpar,"pop_based=%d\n",&popbased);    int theta;
   fprintf(ficparo,"pop_based=%d\n",popbased);      
   fprintf(ficres,"pop_based=%d\n",popbased);      pstamp(ficresvpl);
      fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresvpl,"# Age");
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);        fprintf(ficresvpl," %1d-%1d",i,i);
     puts(line);    fprintf(ficresvpl,"\n");
     fputs(line,ficparo);  
   }    xp=vector(1,npar);
   ungetc(c,ficpar);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    hstepm=1*YEARM; /* Every year of age */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 while((c=getc(ficpar))=='#' && c!= EOF){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     ungetc(c,ficpar);      if (stepm >= YEARM) hstepm=1;
     fgets(line, MAXLINE, ficpar);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     puts(line);      gradg=matrix(1,npar,1,nlstate);
     fputs(line,ficparo);      gp=vector(1,nlstate);
   }      gm=vector(1,nlstate);
   ungetc(c,ficpar);  
       for(theta=1; theta <=npar; theta++){
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        for(i=1; i<=npar; i++){ /* Computes gradient */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
 /*------------ gnuplot -------------*/      
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);        for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
 /*------------ free_vector  -------------*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  chdir(path);        for(i=1;i<=nlstate;i++)
            gm[i] = prlim[i][i];
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(i=1;i<=nlstate;i++)
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
  free_ivector(num,1,n);      } /* End theta */
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      trgradg =matrix(1,nlstate,1,npar);
  fclose(ficparo);  
  fclose(ficres);      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
 /*--------- index.htm --------*/          trgradg[j][theta]=gradg[theta][j];
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /*--------------- Prevalence limit --------------*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
        for(i=1;i<=nlstate;i++)
   strcpy(filerespl,"pl");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      fprintf(ficresvpl,"%.0f ",age );
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      fprintf(ficresvpl,"\n");
   fprintf(ficrespl,"#Prevalence limit\n");      free_vector(gp,1,nlstate);
   fprintf(ficrespl,"#Age ");      free_vector(gm,1,nlstate);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      free_matrix(gradg,1,npar,1,nlstate);
   fprintf(ficrespl,"\n");      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_vector(xp,1,npar);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(doldm,1,nlstate,1,npar);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(dnewm,1,nlstate,1,nlstate);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  }
   k=0;  
   agebase=ageminpar;  /************ Variance of one-step probabilities  ******************/
   agelim=agemaxpar;  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[])
   ftolpl=1.e-10;  {
   i1=cptcoveff;    int i, j=0,  i1, k1, l1, t, tj;
   if (cptcovn < 1){i1=1;}    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   for(cptcov=1;cptcov<=i1;cptcov++){    int first=1, first1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         k=k+1;    double **dnewm,**doldm;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double *xp;
         fprintf(ficrespl,"\n#******");    double *gp, *gm;
         for(j=1;j<=cptcoveff;j++)    double **gradg, **trgradg;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **mu;
         fprintf(ficrespl,"******\n");    double age,agelim, cov[NCOVMAX];
            double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         for (age=agebase; age<=agelim; age++){    int theta;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    char fileresprob[FILENAMELENGTH];
           fprintf(ficrespl,"%.0f",age );    char fileresprobcov[FILENAMELENGTH];
           for(i=1; i<=nlstate;i++)    char fileresprobcor[FILENAMELENGTH];
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    double ***varpij;
         }  
       }    strcpy(fileresprob,"prob"); 
     }    strcat(fileresprob,fileres);
   fclose(ficrespl);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
   /*------------- h Pij x at various ages ------------*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    strcpy(fileresprobcov,"probcov"); 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    strcat(fileresprobcov,fileres);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   printf("Computing pij: result on file '%s' \n", filerespij);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   stepsize=(int) (stepm+YEARM-1)/YEARM;    strcpy(fileresprobcor,"probcor"); 
   /*if (stepm<=24) stepsize=2;*/    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   agelim=AGESUP;      printf("Problem with resultfile: %s\n", fileresprobcor);
   hstepm=stepsize*YEARM; /* Every year of age */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   k=0;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   for(cptcov=1;cptcov<=i1;cptcov++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       k=k+1;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         fprintf(ficrespij,"\n#****** ");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         for(j=1;j<=cptcoveff;j++)    pstamp(ficresprob);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficrespij,"******\n");    fprintf(ficresprob,"# Age");
            pstamp(ficresprobcov);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficresprobcov,"# Age");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    pstamp(ficresprobcor);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           oldm=oldms;savm=savms;    fprintf(ficresprobcor,"# Age");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)      for(j=1; j<=(nlstate+ndeath);j++){
               fprintf(ficrespij," %1d-%1d",i,j);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           fprintf(ficrespij,"\n");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
            for (h=0; h<=nhstepm; h++){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      }  
             for(i=1; i<=nlstate;i++)   /* fprintf(ficresprob,"\n");
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficresprobcov,"\n");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(ficresprobcor,"\n");
             fprintf(ficrespij,"\n");   */
              }    xp=vector(1,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           fprintf(ficrespij,"\n");    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");
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   fclose(ficrespij);  
     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\
   /*---------- Forecasting ------------------*/    file %s<br>\n",optionfilehtmcov);
   if((stepm == 1) && (strcmp(model,".")==0)){    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  and drawn. It helps understanding how is the covariance between two incidences.\
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);   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. \
   else{  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     erreur=108;  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     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);  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");
   /*---------- Health expectancies and variances ------------*/  
     cov[1]=1;
   strcpy(filerest,"t");    tj=cptcoveff;
   strcat(filerest,fileres);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   if((ficrest=fopen(filerest,"w"))==NULL) {    j1=0;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    for(t=1; t<=tj;t++){
   }      for(i1=1; i1<=ncodemax[t];i1++){ 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
   strcpy(filerese,"e");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(filerese,fileres);          fprintf(ficresprob, "**********\n#\n");
   if((ficreseij=fopen(filerese,"w"))==NULL) {          fprintf(ficresprobcov, "\n#********** Variable "); 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcov, "**********\n#\n");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          
           fprintf(ficgp, "\n#********** Variable "); 
  strcpy(fileresv,"v");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(fileresv,fileres);          fprintf(ficgp, "**********\n#\n");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          
   }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   calagedate=-1;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   k=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresprobcor, "**********\n#");    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;        
       fprintf(ficrest,"\n#****** ");        for (age=bage; age<=fage; age ++){ 
       for(j=1;j<=cptcoveff;j++)          cov[2]=age;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (k=1; k<=cptcovn;k++) {
       fprintf(ficrest,"******\n");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
       fprintf(ficreseij,"\n#****** ");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for(j=1;j<=cptcoveff;j++)          for (k=1; k<=cptcovprod;k++)
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       fprintf(ficreseij,"******\n");          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       fprintf(ficresvij,"\n#****** ");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for(j=1;j<=cptcoveff;j++)          gp=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficresvij,"******\n");      
           for(theta=1; theta <=npar; theta++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            for(i=1; i<=npar; i++)
       oldm=oldms;savm=savms;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);              
              pmij(pmmij,cov,ncovmodel,xp,nlstate);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            
       oldm=oldms;savm=savms;            k=0;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);            for(i=1; i<= (nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                  gp[k]=pmmij[i][j];
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            }
       fprintf(ficrest,"\n");            
             for(i=1; i<=npar; i++)
       epj=vector(1,nlstate+1);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       for(age=bage; age <=fage ;age++){      
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         if (popbased==1) {            k=0;
           for(i=1; i<=nlstate;i++)            for(i=1; i<=(nlstate); i++){
             prlim[i][i]=probs[(int)age][i][k];              for(j=1; j<=(nlstate+ndeath);j++){
         }                k=k+1;
                        gm[k]=pmmij[i][j];
         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];            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }          }
           epj[nlstate+1] +=epj[j];  
         }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
         for(i=1, vepp=0.;i <=nlstate;i++)              trgradg[j][theta]=gradg[theta][j];
           for(j=1;j <=nlstate;j++)          
             vepp += vareij[i][j][(int)age];          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         for(j=1;j <=nlstate;j++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         fprintf(ficrest,"\n");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       }  
     }          pmij(pmmij,cov,ncovmodel,x,nlstate);
   }          
 free_matrix(mint,1,maxwav,1,n);          k=0;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          for(i=1; i<=(nlstate); i++){
     free_vector(weight,1,n);            for(j=1; j<=(nlstate+ndeath);j++){
   fclose(ficreseij);              k=k+1;
   fclose(ficresvij);              mu[k][(int) age]=pmmij[i][j];
   fclose(ficrest);            }
   fclose(ficpar);          }
   free_vector(epj,1,nlstate+1);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
              for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   /*------- Variance limit prevalence------*/                varpij[i][j][(int)age] = doldm[i][j];
   
   strcpy(fileresvpl,"vpl");          /*printf("\n%d ",(int)age);
   strcat(fileresvpl,fileres);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     exit(0);            }*/
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
   k=0;          fprintf(ficresprobcor,"\n%d ",(int)age);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       k=k+1;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       fprintf(ficresvpl,"\n#****** ");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       for(j=1;j<=cptcoveff;j++)            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       fprintf(ficresvpl,"******\n");          }
                i=0;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          for (k=1; k<=(nlstate);k++){
       oldm=oldms;savm=savms;            for (l=1; l<=(nlstate+ndeath);l++){ 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              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++){
   fclose(ficresvpl);                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 : free ----------------*/              }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            }
            }/* end of loop for state */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        } /* end of loop for age */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
          /* Confidence intervalle of pij  */
          /*
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficgp,"\nunset parametric;unset label");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          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);
   free_matrix(matcov,1,npar,1,npar);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   free_vector(delti,1,npar);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   free_matrix(agev,1,maxwav,1,imx);        */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   if(erreur >0)        first1=1;
     printf("End of Imach with error or warning %d\n",erreur);        for (k2=1; k2<=(nlstate);k2++){
   else   printf("End of Imach\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            if(l2==k2) continue;
              j=(k2-1)*(nlstate+ndeath)+l2;
   /* 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);*/            for (k1=1; k1<=(nlstate);k1++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   /*------ End -----------*/                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
  end:                for (age=bage; age<=fage; age ++){ 
 #ifdef windows                  if ((int)age %5==0){
   /* chdir(pathcd);*/                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
 #endif                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
  /*system("wgnuplot graph.plt");*/                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
  /*system("../gp37mgw/wgnuplot graph.plt");*/                    mu1=mu[i][(int) age]/stepm*YEARM ;
  /*system("cd ../gp37mgw");*/                    mu2=mu[j][(int) age]/stepm*YEARM;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                    c12=cv12/sqrt(v1*v2);
  strcpy(plotcmd,GNUPLOTPROGRAM);                    /* Computing eigen value of matrix of covariance */
  strcat(plotcmd," ");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
  strcat(plotcmd,optionfilegnuplot);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
  system(plotcmd);                    if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
 #ifdef windows                      fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
   while (z[0] != 'q') {                      lc1=fabs(lc1);
     /* chdir(path); */                      lc2=fabs(lc2);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                    }
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");                    /* Eigen vectors */
     else if (z[0] == 'e') system(optionfilehtm);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     else if (z[0] == 'g') system(plotcmd);                    /*v21=sqrt(1.-v11*v11); *//* error */
     else if (z[0] == 'q') exit(0);                    v21=(lc1-v1)/cv12*v11;
   }                    v12=-v21;
 #endif                    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;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     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]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+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);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* 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);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     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);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld 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);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld 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);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (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 birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  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 birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         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);
         return 1;
       }
       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);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           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);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     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*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* 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 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=cptcovn; k>=1;k--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 
                                       */ 
         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 V2+V1+V4+V3*age strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=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'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
             Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
             Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
             k1++;
             k2=k2+2;
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutv(strd,strc,strb,'V');
           Tvar[k]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+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);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     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);     
           return 1;
         }
       }
     }
   
     /*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); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     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];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*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 ***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  *strt;*/
     char strtend[80];
   
     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 plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     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 */
   
   
     n= lastobs;
     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); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); 
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     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); 
   /*     ximort=gsl_matrix_alloc(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]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       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);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  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");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       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);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* 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);
     }
   }
   
   
   

Removed from v.1.42  
changed lines
  Added in v.1.137


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