Diff for /imach/src/imach.c between versions 1.14 and 1.140

version 1.14, 2002/02/20 17:05:44 version 1.140, 2011/09/02 10:37:54
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.140  2011/09/02 10:37:54  brouard
   individuals from different ages are interviewed on their health status    Summary: times.h is ok with mingw32 now.
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.139  2010/06/14 07:50:17  brouard
   Health expectancies are computed from the transistions observed between    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   waves and are computed for each degree of severity of disability (number    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.138  2010/04/30 18:19:40  brouard
   The simplest model is the multinomial logistic model where pij is    *** empty log message ***
   the probabibility to be observed in state j at the second wave conditional  
   to be observed in state i at the first wave. Therefore the model is:    Revision 1.137  2010/04/29 18:11:38  brouard
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    (Module): Checking covariates for more complex models
   is a covariate. If you want to have a more complex model than "constant and    than V1+V2. A lot of change to be done. Unstable.
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.136  2010/04/26 20:30:53  brouard
   More covariates you add, less is the speed of the convergence.    (Module): merging some libgsl code. Fixing computation
     of likelione (using inter/intrapolation if mle = 0) in order to
   The advantage that this computer programme claims, comes from that if the    get same likelihood as if mle=1.
   delay between waves is not identical for each individual, or if some    Some cleaning of code and comments added.
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.135  2009/10/29 15:33:14  brouard
   hPijx is the probability to be    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.134  2009/10/29 13:18:53  brouard
   unobserved intermediate  states. This elementary transition (by month or    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.133  2009/07/06 10:21:25  brouard
   and the contribution of each individual to the likelihood is simply hPijx.    just nforces
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.132  2009/07/06 08:22:05  brouard
   of the life expectancies. It also computes the prevalence limits.    Many tings
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.131  2009/06/20 16:22:47  brouard
            Institut national d'études démographiques, Paris.    Some dimensions resccaled
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.130  2009/05/26 06:44:34  brouard
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Max Covariate is now set to 20 instead of 8. A
   software can be distributed freely for non commercial use. Latest version    lot of cleaning with variables initialized to 0. Trying to make
   can be accessed at http://euroreves.ined.fr/imach .    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   **********************************************************************/  
      Revision 1.129  2007/08/31 13:49:27  lievre
 #include <math.h>    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.128  2006/06/30 13:02:05  brouard
 #include <unistd.h>    (Module): Clarifications on computing e.j
   
 #define MAXLINE 256    Revision 1.127  2006/04/28 18:11:50  brouard
 #define FILENAMELENGTH 80    (Module): Yes the sum of survivors was wrong since
 /*#define DEBUG*/    imach-114 because nhstepm was no more computed in the age
 #define windows    loop. Now we define nhstepma in the age loop.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): In order to speed up (in case of numerous covariates) we
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    deviation (needs data from the Hessian matrices) which slows the
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    computation.
     In the future we should be able to stop the program is only health
 #define NINTERVMAX 8    expectancies and graph are needed without standard deviations.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.126  2006/04/28 17:23:28  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Yes the sum of survivors was wrong since
 #define MAXN 20000    imach-114 because nhstepm was no more computed in the age
 #define YEARM 12. /* Number of months per year */    loop. Now we define nhstepma in the age loop.
 #define AGESUP 130    Version 0.98h
 #define AGEBASE 40  
     Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 int nvar;    Forecasting file added.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.124  2006/03/22 17:13:53  lievre
 int nlstate=2; /* Number of live states */    Parameters are printed with %lf instead of %f (more numbers after the comma).
 int ndeath=1; /* Number of dead states */    The log-likelihood is printed in the log file
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0, fprev,lprev;    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 int *wav; /* Number of waves for this individuual 0 is possible */    name. <head> headers where missing.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    * imach.c (Module): Weights can have a decimal point as for
 int mle, weightopt;    English (a comma might work with a correct LC_NUMERIC environment,
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    otherwise the weight is truncated).
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Modification of warning when the covariates values are not 0 or
 double jmean; /* Mean space between 2 waves */    1.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Version 0.98g
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Revision 1.122  2006/03/20 09:45:41  brouard
 FILE *ficgp, *fichtm,*ficresprob;    (Module): Weights can have a decimal point as for
 FILE *ficreseij;    English (a comma might work with a correct LC_NUMERIC environment,
   char filerese[FILENAMELENGTH];    otherwise the weight is truncated).
  FILE  *ficresvij;    Modification of warning when the covariates values are not 0 or
   char fileresv[FILENAMELENGTH];    1.
  FILE  *ficresvpl;    Version 0.98g
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.121  2006/03/16 17:45:01  lievre
 #define NR_END 1    * imach.c (Module): Comments concerning covariates added
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 #define NRANSI    not 1 month. Version 0.98f
 #define ITMAX 200  
     Revision 1.120  2006/03/16 15:10:38  lievre
 #define TOL 2.0e-4    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 #define CGOLD 0.3819660    not 1 month. Version 0.98f
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
 #define GOLD 1.618034    computed as likelihood omitting the logarithm. Version O.98e
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
 static double maxarg1,maxarg2;    table of variances if popbased=1 .
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Function pstamp added
      (Module): Version 0.98d
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
 static double sqrarg;    table of variances if popbased=1 .
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Function pstamp added
     (Module): Version 0.98d
 int imx;  
 int stepm;    Revision 1.116  2006/03/06 10:29:27  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.115  2006/02/27 12:17:45  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): One freematrix added in mlikeli! 0.98c
 double **pmmij, ***probs, ***mobaverage;  
     Revision 1.114  2006/02/26 12:57:58  brouard
 double *weight;    (Module): Some improvements in processing parameter
 int **s; /* Status */    filename with strsep.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    datafile was not closed, some imatrix were not freed and on matrix
 double ftolhess; /* Tolerance for computing hessian */    allocation too.
   
 /**************** split *************************/    Revision 1.112  2006/01/30 09:55:26  brouard
 static  int split( char *path, char *dirc, char *name )    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 {  
    char *s;                             /* pointer */    Revision 1.111  2006/01/25 20:38:18  brouard
    int  l1, l2;                         /* length counters */    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
    l1 = strlen( path );                 /* length of path */    can be a simple dot '.'.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.110  2006/01/25 00:51:50  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Lots of cleaning and bugs added (Gompertz)
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.108  2006/01/19 18:05:42  lievre
       extern char       *getcwd( );    Gnuplot problem appeared...
     To be fixed
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.107  2006/01/19 16:20:37  brouard
          return( GLOCK_ERROR_GETCWD );    Test existence of gnuplot in imach path
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.106  2006/01/19 13:24:36  brouard
    } else {                             /* strip direcotry from path */    Some cleaning and links added in html output
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.105  2006/01/05 20:23:19  lievre
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.104  2005/09/30 16:11:43  lievre
       dirc[l1-l2] = 0;                  /* add zero */    (Module): sump fixed, loop imx fixed, and simplifications.
    }    (Module): If the status is missing at the last wave but we know
    l1 = strlen( dirc );                 /* length of directory */    that the person is alive, then we can code his/her status as -2
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (instead of missing=-1 in earlier versions) and his/her
    return( 0 );                         /* we're done */    contributions to the likelihood is 1 - Prob of dying from last
 }    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
   
 /******************************************/    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 void replace(char *s, char*t)  
 {    Revision 1.102  2004/09/15 17:31:30  brouard
   int i;    Add the possibility to read data file including tab characters.
   int lg=20;  
   i=0;    Revision 1.101  2004/09/15 10:38:38  brouard
   lg=strlen(t);    Fix on curr_time
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.100  2004/07/12 18:29:06  brouard
     if (t[i]== '\\') s[i]='/';    Add version for Mac OS X. Just define UNIX in Makefile
   }  
 }    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 int nbocc(char *s, char occ)  
 {    Revision 1.98  2004/05/16 15:05:56  brouard
   int i,j=0;    New version 0.97 . First attempt to estimate force of mortality
   int lg=20;    directly from the data i.e. without the need of knowing the health
   i=0;    state at each age, but using a Gompertz model: log u =a + b*age .
   lg=strlen(s);    This is the basic analysis of mortality and should be done before any
   for(i=0; i<= lg; i++) {    other analysis, in order to test if the mortality estimated from the
   if  (s[i] == occ ) j++;    cross-longitudinal survey is different from the mortality estimated
   }    from other sources like vital statistic data.
   return j;  
 }    The same imach parameter file can be used but the option for mle should be -3.
   
 void cutv(char *u,char *v, char*t, char occ)    Agnès, who wrote this part of the code, tried to keep most of the
 {    former routines in order to include the new code within the former code.
   int i,lg,j,p=0;  
   i=0;    The output is very simple: only an estimate of the intercept and of
   for(j=0; j<=strlen(t)-1; j++) {    the slope with 95% confident intervals.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Current limitations:
     A) Even if you enter covariates, i.e. with the
   lg=strlen(t);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   for(j=0; j<p; j++) {    B) There is no computation of Life Expectancy nor Life Table.
     (u[j] = t[j]);  
   }    Revision 1.97  2004/02/20 13:25:42  lievre
      u[p]='\0';    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.96  2003/07/15 15:38:55  brouard
   }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 }    rewritten within the same printf. Workaround: many printfs.
   
 /********************** nrerror ********************/    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 void nrerror(char error_text[])    (Repository): Using imachwizard code to output a more meaningful covariance
 {    matrix (cov(a12,c31) instead of numbers.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.94  2003/06/27 13:00:02  brouard
   exit(1);    Just cleaning
 }  
 /*********************** vector *******************/    Revision 1.93  2003/06/25 16:33:55  brouard
 double *vector(int nl, int nh)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   double *v;    (Module): Version 0.96b
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.92  2003/06/25 16:30:45  brouard
   return v-nl+NR_END;    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
   
 /************************ free vector ******************/    Revision 1.91  2003/06/25 15:30:29  brouard
 void free_vector(double*v, int nl, int nh)    * imach.c (Repository): Duplicated warning errors corrected.
 {    (Repository): Elapsed time after each iteration is now output. It
   free((FREE_ARG)(v+nl-NR_END));    helps to forecast when convergence will be reached. Elapsed time
 }    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int *v;    mle=-1 a template is output in file "or"mypar.txt with the design
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    of the covariance matrix to be input.
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.89  2003/06/24 12:30:52  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /******************free ivector **************************/    of the covariance matrix to be input.
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.88  2003/06/23 17:54:56  brouard
   free((FREE_ARG)(v+nl-NR_END));    * 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.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /******************* imatrix *******************************/    Version 0.96
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.86  2003/06/17 20:04:08  brouard
 {    (Module): Change position of html and gnuplot routines and added
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    routine fileappend.
   int **m;  
      Revision 1.85  2003/06/17 13:12:43  brouard
   /* allocate pointers to rows */    * imach.c (Repository): Check when date of death was earlier that
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    current date of interview. It may happen when the death was just
   if (!m) nrerror("allocation failure 1 in matrix()");    prior to the death. In this case, dh was negative and likelihood
   m += NR_END;    was wrong (infinity). We still send an "Error" but patch by
   m -= nrl;    assuming that the date of death was just one stepm after the
      interview.
      (Repository): Because some people have very long ID (first column)
   /* allocate rows and set pointers to them */    we changed int to long in num[] and we added a new lvector for
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    memory allocation. But we also truncated to 8 characters (left
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    truncation)
   m[nrl] += NR_END;    (Repository): No more line truncation errors.
   m[nrl] -= ncl;  
      Revision 1.84  2003/06/13 21:44:43  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    * imach.c (Repository): Replace "freqsummary" at a correct
      place. It differs from routine "prevalence" which may be called
   /* return pointer to array of pointers to rows */    many times. Probs is memory consuming and must be used with
   return m;    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /****************** free_imatrix *************************/    Revision 1.83  2003/06/10 13:39:11  lievre
 void free_imatrix(m,nrl,nrh,ncl,nch)    *** empty log message ***
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.82  2003/06/05 15:57:20  brouard
      /* free an int matrix allocated by imatrix() */    Add log in  imach.c and  fullversion number is now printed.
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  */
   free((FREE_ARG) (m+nrl-NR_END));  /*
 }     Interpolated Markov Chain
   
 /******************* matrix *******************************/    Short summary of the programme:
 double **matrix(long nrl, long nrh, long ncl, long nch)    
 {    This program computes Healthy Life Expectancies from
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   double **m;    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    case of a health survey which is our main interest) -2- at least a
   if (!m) nrerror("allocation failure 1 in matrix()");    second wave of interviews ("longitudinal") which measure each change
   m += NR_END;    (if any) in individual health status.  Health expectancies are
   m -= nrl;    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
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Maximum Likelihood of the parameters involved in the model.  The
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    simplest model is the multinomial logistic model where pij is the
   m[nrl] += NR_END;    probability to be observed in state j at the second wave
   m[nrl] -= ncl;    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    'age' is age and 'sex' is a covariate. If you want to have a more
   return m;    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /*************************free matrix ************************/    convergence.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    The advantage of this computer programme, compared to a simple
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    multinomial logistic model, is clear when the delay between waves is not
   free((FREE_ARG)(m+nrl-NR_END));    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    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
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    split into an exact number (nh*stepm) of unobserved intermediate
   double ***m;    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    matrix is simply the matrix product of nh*stepm elementary matrices
   if (!m) nrerror("allocation failure 1 in matrix()");    and the contribution of each individual to the likelihood is simply
   m += NR_END;    hPijx.
   m -= nrl;  
     Also this programme outputs the covariance matrix of the parameters but also
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    of the life expectancies. It also computes the period (stable) prevalence. 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m[nrl] -= ncl;             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    software can be distributed freely for non commercial use. Latest version
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   for (j=ncl+1; j<=nch; j++)    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     m[nrl][j]=m[nrl][j-1]+nlay;    
      **********************************************************************/
   for (i=nrl+1; i<=nrh; i++) {  /*
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    main
     for (j=ncl+1; j<=nch; j++)    read parameterfile
       m[i][j]=m[i][j-1]+nlay;    read datafile
   }    concatwav
   return m;    freqsummary
 }    if (mle >= 1)
       mlikeli
 /*************************free ma3x ************************/    print results files
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if mle==1 
 {       computes hessian
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    read end of parameter file: agemin, agemax, bage, fage, estepm
   free((FREE_ARG)(m[nrl]+ncl-NR_END));        begin-prev-date,...
   free((FREE_ARG)(m+nrl-NR_END));    open gnuplot file
 }    open html file
     period (stable) prevalence
 /***************** f1dim *************************/     for age prevalim()
 extern int ncom;    h Pij x
 extern double *pcom,*xicom;    variance of p varprob
 extern double (*nrfunc)(double []);    forecasting if prevfcast==1 prevforecast call prevalence()
      health expectancies
 double f1dim(double x)    Variance-covariance of DFLE
 {    prevalence()
   int j;     movingaverage()
   double f;    varevsij() 
   double *xt;    if popbased==1 varevsij(,popbased)
      total life expectancies
   xt=vector(1,ncom);    Variance of period (stable) prevalence
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];   end
   f=(*nrfunc)(xt);  */
   free_vector(xt,1,ncom);  
   return f;  
 }  
    
 /*****************brent *************************/  #include <math.h>
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #include <stdio.h>
 {  #include <stdlib.h>
   int iter;  #include <string.h>
   double a,b,d,etemp;  #include <unistd.h>
   double fu,fv,fw,fx;  
   double ftemp;  #include <limits.h>
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #include <sys/types.h>
   double e=0.0;  #include <sys/stat.h>
    #include <errno.h>
   a=(ax < cx ? ax : cx);  extern int errno;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  #include <sys/time.h>
   fw=fv=fx=(*f)(x);  /*
   for (iter=1;iter<=ITMAX;iter++) {  #include <time.h>
     xm=0.5*(a+b);  #include "timeval.h"
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #ifdef GSL
     printf(".");fflush(stdout);  #include <gsl/gsl_errno.h>
 #ifdef DEBUG  #include <gsl/gsl_multimin.h>
     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);  #endif
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  /* #include <libintl.h> */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /* #define _(String) gettext (String) */
       *xmin=x;  
       return fx;  #define MAXLINE 256
     }  
     ftemp=fu;  #define GNUPLOTPROGRAM "gnuplot"
     if (fabs(e) > tol1) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       r=(x-w)*(fx-fv);  #define FILENAMELENGTH 132
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       q=2.0*(q-r);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       if (q > 0.0) p = -p;  
       q=fabs(q);  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
       etemp=e;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define NINTERVMAX 8
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       else {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
         d=p/q;  #define NCOVMAX 20 /* Maximum number of covariates */
         u=x+d;  #define MAXN 20000
         if (u-a < tol2 || b-u < tol2)  #define YEARM 12. /* Number of months per year */
           d=SIGN(tol1,xm-x);  #define AGESUP 130
       }  #define AGEBASE 40
     } else {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #ifdef UNIX
     }  #define DIRSEPARATOR '/'
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define CHARSEPARATOR "/"
     fu=(*f)(u);  #define ODIRSEPARATOR '\\'
     if (fu <= fx) {  #else
       if (u >= x) a=x; else b=x;  #define DIRSEPARATOR '\\'
       SHFT(v,w,x,u)  #define CHARSEPARATOR "\\"
         SHFT(fv,fw,fx,fu)  #define ODIRSEPARATOR '/'
         } else {  #endif
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /* $Id$ */
             v=w;  /* $State$ */
             w=u;  
             fv=fw;  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
             fw=fu;  char fullversion[]="$Revision$ $Date$"; 
           } else if (fu <= fv || v == x || v == w) {  char strstart[80];
             v=u;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
             fv=fu;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
           }  int nvar=0, nforce=0; /* Number of variables, number of forces */
         }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   }  int npar=NPARMAX;
   nrerror("Too many iterations in brent");  int nlstate=2; /* Number of live states */
   *xmin=x;  int ndeath=1; /* Number of dead states */
   return fx;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 }  int popbased=0;
   
 /****************** mnbrak ***********************/  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav=0; /* Maxim number of waves */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
             double (*func)(double))  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   double ulim,u,r,q, dum;                     to the likelihood and the sum of weights (done by funcone)*/
   double fu;  int mle=1, weightopt=0;
    int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   *fa=(*func)(*ax);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   *fb=(*func)(*bx);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   if (*fb > *fa) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     SHFT(dum,*ax,*bx,dum)  double jmean=1; /* Mean space between 2 waves */
       SHFT(dum,*fb,*fa,dum)  double **oldm, **newm, **savm; /* Working pointers to matrices */
       }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   *cx=(*bx)+GOLD*(*bx-*ax);  /*FILE *fic ; */ /* Used in readdata only */
   *fc=(*func)(*cx);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   while (*fb > *fc) {  FILE *ficlog, *ficrespow;
     r=(*bx-*ax)*(*fb-*fc);  int globpr=0; /* Global variable for printing or not */
     q=(*bx-*cx)*(*fb-*fa);  double fretone; /* Only one call to likelihood */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  long ipmx=0; /* Number of contributions */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  double sw; /* Sum of weights */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  char filerespow[FILENAMELENGTH];
     if ((*bx-u)*(u-*cx) > 0.0) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       fu=(*func)(u);  FILE *ficresilk;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       fu=(*func)(u);  FILE *ficresprobmorprev;
       if (fu < *fc) {  FILE *fichtm, *fichtmcov; /* Html File */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  FILE *ficreseij;
           SHFT(*fb,*fc,fu,(*func)(u))  char filerese[FILENAMELENGTH];
           }  FILE *ficresstdeij;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  char fileresstde[FILENAMELENGTH];
       u=ulim;  FILE *ficrescveij;
       fu=(*func)(u);  char filerescve[FILENAMELENGTH];
     } else {  FILE  *ficresvij;
       u=(*cx)+GOLD*(*cx-*bx);  char fileresv[FILENAMELENGTH];
       fu=(*func)(u);  FILE  *ficresvpl;
     }  char fileresvpl[FILENAMELENGTH];
     SHFT(*ax,*bx,*cx,u)  char title[MAXLINE];
       SHFT(*fa,*fb,*fc,fu)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
 /*************** linmin ************************/  int  outcmd=0;
   
 int ncom;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  char filelog[FILENAMELENGTH]; /* Log file */
    char filerest[FILENAMELENGTH];
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char fileregp[FILENAMELENGTH];
 {  char popfile[FILENAMELENGTH];
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
               double *fc, double (*func)(double));  struct timezone tzp;
   int j;  extern int gettimeofday();
   double xx,xmin,bx,ax;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double fx,fb,fa;  long time_value;
    extern long time();
   ncom=n;  char strcurr[80], strfor[80];
   pcom=vector(1,n);  
   xicom=vector(1,n);  char *endptr;
   nrfunc=func;  long lval;
   for (j=1;j<=n;j++) {  double dval;
     pcom[j]=p[j];  
     xicom[j]=xi[j];  #define NR_END 1
   }  #define FREE_ARG char*
   ax=0.0;  #define FTOL 1.0e-10
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define NRANSI 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define ITMAX 200 
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define TOL 2.0e-4 
 #endif  
   for (j=1;j<=n;j++) {  #define CGOLD 0.3819660 
     xi[j] *= xmin;  #define ZEPS 1.0e-10 
     p[j] += xi[j];  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   }  
   free_vector(xicom,1,n);  #define GOLD 1.618034 
   free_vector(pcom,1,n);  #define GLIMIT 100.0 
 }  #define TINY 1.0e-20 
   
 /*************** powell ************************/  static double maxarg1,maxarg2;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
             double (*func)(double []))  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   void linmin(double p[], double xi[], int n, double *fret,  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
               double (*func)(double []));  #define rint(a) floor(a+0.5)
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  static double sqrarg;
   double fp,fptt;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double *xits;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   pt=vector(1,n);  int agegomp= AGEGOMP;
   ptt=vector(1,n);  
   xit=vector(1,n);  int imx; 
   xits=vector(1,n);  int stepm=1;
   *fret=(*func)(p);  /* Stepm, step in month: minimum step interpolation*/
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  int estepm;
     fp=(*fret);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     ibig=0;  
     del=0.0;  int m,nb;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  long *num;
     for (i=1;i<=n;i++)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       printf(" %d %.12f",i, p[i]);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     printf("\n");  double **pmmij, ***probs;
     for (i=1;i<=n;i++) {  double *ageexmed,*agecens;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  double dateintmean=0;
       fptt=(*fret);  
 #ifdef DEBUG  double *weight;
       printf("fret=%lf \n",*fret);  int **s; /* Status */
 #endif  double *agedc, **covar, idx;
       printf("%d",i);fflush(stdout);  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       linmin(p,xit,n,fret,func);  double *lsurv, *lpop, *tpop;
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
         ibig=i;  double ftolhess; /* Tolerance for computing hessian */
       }  
 #ifdef DEBUG  /**************** split *************************/
       printf("%d %.12e",i,(*fret));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       for (j=1;j<=n;j++) {  {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         printf(" x(%d)=%.12e",j,xit[j]);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       }    */ 
       for(j=1;j<=n;j++)    char  *ss;                            /* pointer */
         printf(" p=%.12e",p[j]);    int   l1, l2;                         /* length counters */
       printf("\n");  
 #endif    l1 = strlen(path );                   /* length of path */
     }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 #ifdef DEBUG    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       int k[2],l;      strcpy( name, path );               /* we got the fullname name because no directory */
       k[0]=1;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       k[1]=-1;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       printf("Max: %.12e",(*func)(p));      /* get current working directory */
       for (j=1;j<=n;j++)      /*    extern  char* getcwd ( char *buf , int len);*/
         printf(" %.12e",p[j]);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       printf("\n");        return( GLOCK_ERROR_GETCWD );
       for(l=0;l<=1;l++) {      }
         for (j=1;j<=n;j++) {      /* got dirc from getcwd*/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      printf(" DIRC = %s \n",dirc);
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    } else {                              /* strip direcotry from path */
         }      ss++;                               /* after this, the filename */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      l2 = strlen( ss );                  /* length of filename */
       }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 #endif      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
       free_vector(xit,1,n);      printf(" DIRC2 = %s \n",dirc);
       free_vector(xits,1,n);    }
       free_vector(ptt,1,n);    /* We add a separator at the end of dirc if not exists */
       free_vector(pt,1,n);    l1 = strlen( dirc );                  /* length of directory */
       return;    if( dirc[l1-1] != DIRSEPARATOR ){
     }      dirc[l1] =  DIRSEPARATOR;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      dirc[l1+1] = 0; 
     for (j=1;j<=n;j++) {      printf(" DIRC3 = %s \n",dirc);
       ptt[j]=2.0*p[j]-pt[j];    }
       xit[j]=p[j]-pt[j];    ss = strrchr( name, '.' );            /* find last / */
       pt[j]=p[j];    if (ss >0){
     }      ss++;
     fptt=(*func)(ptt);      strcpy(ext,ss);                     /* save extension */
     if (fptt < fp) {      l1= strlen( name);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      l2= strlen(ss)+1;
       if (t < 0.0) {      strncpy( finame, name, l1-l2);
         linmin(p,xit,n,fret,func);      finame[l1-l2]= 0;
         for (j=1;j<=n;j++) {    }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];    return( 0 );                          /* we're done */
         }  }
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  /******************************************/
           printf(" %.12e",xit[j]);  
         printf("\n");  void replace_back_to_slash(char *s, char*t)
 #endif  {
       }    int i;
     }    int lg=0;
   }    i=0;
 }    lg=strlen(t);
     for(i=0; i<= lg; i++) {
 /**** Prevalence limit ****************/      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 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 */  char *trimbb(char *out, char *in)
   { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   int i, ii,j,k;    char *s;
   double min, max, maxmin, maxmax,sumnew=0.;    s=out;
   double **matprod2();    while (*in != '\0'){
   double **out, cov[NCOVMAX], **pmij();      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   double **newm;        in++;
   double agefin, delaymax=50 ; /* Max number of years to converge */      }
       *out++ = *in++;
   for (ii=1;ii<=nlstate+ndeath;ii++)    }
     for (j=1;j<=nlstate+ndeath;j++){    *out='\0';
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return s;
     }  }
   
    cov[1]=1.;  char *cutv(char *blocc, char *alocc, char *in, char occ)
    {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     newm=savm;       gives blocc="abcdef2ghi" and alocc="j".
     /* Covariates have to be included here again */       If occ is not found blocc is null and alocc is equal to in. Returns alocc
      cov[2]=agefin;    */
      char *s, *t;
       for (k=1; k<=cptcovn;k++) {    t=in;s=in;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    while (*in != '\0'){
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      while( *in == occ){
       }        *blocc++ = *in++;
       for (k=1; k<=cptcovage;k++)        s=in;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      }
       for (k=1; k<=cptcovprod;k++)      *blocc++ = *in++;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    }
     if (s == t) /* occ not found */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      *(blocc-(in-s))='\0';
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    else
       *(blocc-(in-s)-1)='\0';
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    in=s;
     while ( *in != '\0'){
     savm=oldm;      *alocc++ = *in++;
     oldm=newm;    }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){    *alocc='\0';
       min=1.;    return s;
       max=0.;  }
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  int nbocc(char *s, char occ)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  {
         prlim[i][j]= newm[i][j]/(1-sumnew);    int i,j=0;
         max=FMAX(max,prlim[i][j]);    int lg=20;
         min=FMIN(min,prlim[i][j]);    i=0;
       }    lg=strlen(s);
       maxmin=max-min;    for(i=0; i<= lg; i++) {
       maxmax=FMAX(maxmax,maxmin);    if  (s[i] == occ ) j++;
     }    }
     if(maxmax < ftolpl){    return j;
       return prlim;  }
     }  
   }  /* void cutv(char *u,char *v, char*t, char occ) */
 }  /* { */
   /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 /*************** transition probabilities ***************/  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /*   int i,lg,j,p=0; */
 {  /*   i=0; */
   double s1, s2;  /*   lg=strlen(t); */
   /*double t34;*/  /*   for(j=0; j<=lg-1; j++) { */
   int i,j,j1, nc, ii, jj;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  /*   for(j=0; j<p; j++) { */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*     (u[j] = t[j]); */
         /*s2 += param[i][j][nc]*cov[nc];*/  /*   } */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*      u[p]='\0'; */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /*    for(j=0; j<= lg; j++) { */
       ps[i][j]=s2;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*   } */
     }  /* } */
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /********************** nrerror ********************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  void nrerror(char error_text[])
       }  {
       ps[i][j]=(s2);    fprintf(stderr,"ERREUR ...\n");
     }    fprintf(stderr,"%s\n",error_text);
   }    exit(EXIT_FAILURE);
     /*ps[3][2]=1;*/  }
   /*********************** vector *******************/
   for(i=1; i<= nlstate; i++){  double *vector(int nl, int nh)
      s1=0;  {
     for(j=1; j<i; j++)    double *v;
       s1+=exp(ps[i][j]);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     for(j=i+1; j<=nlstate+ndeath; j++)    if (!v) nrerror("allocation failure in vector");
       s1+=exp(ps[i][j]);    return v-nl+NR_END;
     ps[i][i]=1./(s1+1.);  }
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /************************ free vector ******************/
     for(j=i+1; j<=nlstate+ndeath; j++)  void free_vector(double*v, int nl, int nh)
       ps[i][j]= exp(ps[i][j])*ps[i][i];  {
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    free((FREE_ARG)(v+nl-NR_END));
   } /* end i */  }
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  /************************ivector *******************************/
     for(jj=1; jj<= nlstate+ndeath; jj++){  int *ivector(long nl,long nh)
       ps[ii][jj]=0;  {
       ps[ii][ii]=1;    int *v;
     }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /******************free ivector **************************/
      printf("%lf ",ps[ii][jj]);  void free_ivector(int *v, long nl, long nh)
    }  {
     printf("\n ");    free((FREE_ARG)(v+nl-NR_END));
     }  }
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*  /************************lvector *******************************/
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  long *lvector(long nl,long nh)
   goto end;*/  {
     return ps;    long *v;
 }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
 /**************** Product of 2 matrices ******************/    return v-nl+NR_END;
   }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {  /******************free lvector **************************/
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  void free_lvector(long *v, long nl, long nh)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  {
   /* in, b, out are matrice of pointers which should have been initialized    free((FREE_ARG)(v+nl-NR_END));
      before: only the contents of out is modified. The function returns  }
      a pointer to pointers identical to out */  
   long i, j, k;  /******************* imatrix *******************************/
   for(i=nrl; i<= nrh; i++)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     for(k=ncolol; k<=ncoloh; k++)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  { 
         out[i][k] +=in[i][j]*b[j][k];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
   return out;    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /************* Higher Matrix Product ***************/    m += NR_END; 
     m -= nrl; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    
 {    
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    /* allocate rows and set pointers to them */ 
      duration (i.e. until    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    m[nrl] += NR_END; 
      (typically every 2 years instead of every month which is too big).    m[nrl] -= ncl; 
      Model is determined by parameters x and covariates have to be    
      included manually here.    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
      */    /* return pointer to array of pointers to rows */ 
     return m; 
   int i, j, d, h, k;  } 
   double **out, cov[NCOVMAX];  
   double **newm;  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   /* Hstepm could be zero and should return the unit matrix */        int **m;
   for (i=1;i<=nlstate+ndeath;i++)        long nch,ncl,nrh,nrl; 
     for (j=1;j<=nlstate+ndeath;j++){       /* free an int matrix allocated by imatrix() */ 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     }    free((FREE_ARG) (m+nrl-NR_END)); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  } 
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  /******************* matrix *******************************/
       newm=savm;  double **matrix(long nrl, long nrh, long ncl, long nch)
       /* Covariates have to be included here again */  {
       cov[1]=1.;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    double **m;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!m) nrerror("allocation failure 1 in matrix()");
       for (k=1; k<=cptcovprod;k++)    m += NR_END;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m -= nrl;
   
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    m[nrl] += NR_END;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    m[nrl] -= ncl;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       oldm=newm;    return m;
     }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     for(i=1; i<=nlstate+ndeath; i++)     */
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /*************************free matrix ************************/
          */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
   } /* end h */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   return po;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
   /******************* ma3x *******************************/
 /*************** log-likelihood *************/  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 double func( double *x)  {
 {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   int i, ii, j, k, mi, d, kk;    double ***m;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double sw; /* Sum of weights */    if (!m) nrerror("allocation failure 1 in matrix()");
   double lli; /* Individual log likelihood */    m += NR_END;
   long ipmx;    m -= nrl;
   /*extern weight */  
   /* We are differentiating ll according to initial status */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   /*for(i=1;i<imx;i++)    m[nrl] += NR_END;
     printf(" %d\n",s[4][i]);    m[nrl] -= ncl;
   */  
   cov[1]=1.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    m[nrl][ncl] += NR_END;
     for(mi=1; mi<= wav[i]-1; mi++){    m[nrl][ncl] -= nll;
       for (ii=1;ii<=nlstate+ndeath;ii++)    for (j=ncl+1; j<=nch; j++) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      m[nrl][j]=m[nrl][j-1]+nlay;
       for(d=0; d<dh[mi][i]; d++){    
         newm=savm;    for (i=nrl+1; i<=nrh; i++) {
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         for (kk=1; kk<=cptcovage;kk++) {      for (j=ncl+1; j<=nch; j++) 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        m[i][j]=m[i][j-1]+nlay;
         }    }
            return m; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         savm=oldm;    */
         oldm=newm;  }
          
          /*************************free ma3x ************************/
       } /* end mult */  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
        {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       ipmx +=1;    free((FREE_ARG)(m+nrl-NR_END));
       sw += weight[i];  }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  /*************** function subdirf ***********/
   } /* end of individual */  char *subdirf(char fileres[])
   {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /* Caution optionfilefiname is hidden */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    strcpy(tmpout,optionfilefiname);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    strcat(tmpout,"/"); /* Add to the right */
   return -l;    strcat(tmpout,fileres);
 }    return tmpout;
   }
   
 /*********** Maximum Likelihood Estimation ***************/  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    
   int i,j, iter;    /* Caution optionfilefiname is hidden */
   double **xi,*delti;    strcpy(tmpout,optionfilefiname);
   double fret;    strcat(tmpout,"/");
   xi=matrix(1,npar,1,npar);    strcat(tmpout,preop);
   for (i=1;i<=npar;i++)    strcat(tmpout,fileres);
     for (j=1;j<=npar;j++)    return tmpout;
       xi[i][j]=(i==j ? 1.0 : 0.0);  }
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    
     /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 /**** Computes Hessian and covariance matrix ***/    strcat(tmpout,preop);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    strcat(tmpout,preop2);
 {    strcat(tmpout,fileres);
   double  **a,**y,*x,pd;    return tmpout;
   double **hess;  }
   int i, j,jk;  
   int *indx;  /***************** f1dim *************************/
   extern int ncom; 
   double hessii(double p[], double delta, int theta, double delti[]);  extern double *pcom,*xicom;
   double hessij(double p[], double delti[], int i, int j);  extern double (*nrfunc)(double []); 
   void lubksb(double **a, int npar, int *indx, double b[]) ;   
   void ludcmp(double **a, int npar, int *indx, double *d) ;  double f1dim(double x) 
   { 
   hess=matrix(1,npar,1,npar);    int j; 
     double f;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double *xt; 
   for (i=1;i<=npar;i++){   
     printf("%d",i);fflush(stdout);    xt=vector(1,ncom); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     /*printf(" %f ",p[i]);*/    f=(*nrfunc)(xt); 
     /*printf(" %lf ",hess[i][i]);*/    free_vector(xt,1,ncom); 
   }    return f; 
    } 
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  /*****************brent *************************/
       if (j>i) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         printf(".%d%d",i,j);fflush(stdout);  { 
         hess[i][j]=hessij(p,delti,i,j);    int iter; 
         hess[j][i]=hess[i][j];        double a,b,d,etemp;
         /*printf(" %lf ",hess[i][j]);*/    double fu,fv,fw,fx;
       }    double ftemp;
     }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   }    double e=0.0; 
   printf("\n");   
     a=(ax < cx ? ax : cx); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    b=(ax > cx ? ax : cx); 
      x=w=v=bx; 
   a=matrix(1,npar,1,npar);    fw=fv=fx=(*f)(x); 
   y=matrix(1,npar,1,npar);    for (iter=1;iter<=ITMAX;iter++) { 
   x=vector(1,npar);      xm=0.5*(a+b); 
   indx=ivector(1,npar);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for (i=1;i<=npar;i++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      printf(".");fflush(stdout);
   ludcmp(a,npar,indx,&pd);      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
   for (j=1;j<=npar;j++) {      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for (i=1;i<=npar;i++) x[i]=0;      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);
     x[j]=1;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       matcov[i][j]=x[i];        *xmin=x; 
     }        return fx; 
   }      } 
       ftemp=fu;
   printf("\n#Hessian matrix#\n");      if (fabs(e) > tol1) { 
   for (i=1;i<=npar;i++) {        r=(x-w)*(fx-fv); 
     for (j=1;j<=npar;j++) {        q=(x-v)*(fx-fw); 
       printf("%.3e ",hess[i][j]);        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     printf("\n");        if (q > 0.0) p = -p; 
   }        q=fabs(q); 
         etemp=e; 
   /* Recompute Inverse */        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++) a[i][j]=matcov[i][j];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   ludcmp(a,npar,indx,&pd);        else { 
           d=p/q; 
   /*  printf("\n#Hessian matrix recomputed#\n");          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
   for (j=1;j<=npar;j++) {            d=SIGN(tol1,xm-x); 
     for (i=1;i<=npar;i++) x[i]=0;        } 
     x[j]=1;      } else { 
     lubksb(a,npar,indx,x);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (i=1;i<=npar;i++){      } 
       y[i][j]=x[i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       printf("%.3e ",y[i][j]);      fu=(*f)(u); 
     }      if (fu <= fx) { 
     printf("\n");        if (u >= x) a=x; else b=x; 
   }        SHFT(v,w,x,u) 
   */          SHFT(fv,fw,fx,fu) 
           } else { 
   free_matrix(a,1,npar,1,npar);            if (u < x) a=u; else b=u; 
   free_matrix(y,1,npar,1,npar);            if (fu <= fw || w == x) { 
   free_vector(x,1,npar);              v=w; 
   free_ivector(indx,1,npar);              w=u; 
   free_matrix(hess,1,npar,1,npar);              fv=fw; 
               fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 }              v=u; 
               fv=fu; 
 /*************** hessian matrix ****************/            } 
 double hessii( double x[], double delta, int theta, double delti[])          } 
 {    } 
   int i;    nrerror("Too many iterations in brent"); 
   int l=1, lmax=20;    *xmin=x; 
   double k1,k2;    return fx; 
   double p2[NPARMAX+1];  } 
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /****************** mnbrak ***********************/
   double fx;  
   int k=0,kmax=10;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double l1;              double (*func)(double)) 
   { 
   fx=func(x);    double ulim,u,r,q, dum;
   for (i=1;i<=npar;i++) p2[i]=x[i];    double fu; 
   for(l=0 ; l <=lmax; l++){   
     l1=pow(10,l);    *fa=(*func)(*ax); 
     delts=delt;    *fb=(*func)(*bx); 
     for(k=1 ; k <kmax; k=k+1){    if (*fb > *fa) { 
       delt = delta*(l1*k);      SHFT(dum,*ax,*bx,dum) 
       p2[theta]=x[theta] +delt;        SHFT(dum,*fb,*fa,dum) 
       k1=func(p2)-fx;        } 
       p2[theta]=x[theta]-delt;    *cx=(*bx)+GOLD*(*bx-*ax); 
       k2=func(p2)-fx;    *fc=(*func)(*cx); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    while (*fb > *fc) { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      r=(*bx-*ax)*(*fb-*fc); 
            q=(*bx-*cx)*(*fb-*fa); 
 #ifdef DEBUG      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       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);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 #endif      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      if ((*bx-u)*(u-*cx) > 0.0) { 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        fu=(*func)(u); 
         k=kmax;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       }        fu=(*func)(u); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        if (fu < *fc) { 
         k=kmax; l=lmax*10.;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       }            SHFT(*fb,*fc,fu,(*func)(u)) 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            } 
         delts=delt;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       }        u=ulim; 
     }        fu=(*func)(u); 
   }      } else { 
   delti[theta]=delts;        u=(*cx)+GOLD*(*cx-*bx); 
   return res;        fu=(*func)(u); 
        } 
 }      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
 double hessij( double x[], double delti[], int thetai,int thetaj)        } 
 {  } 
   int i;  
   int l=1, l1, lmax=20;  /*************** linmin ************************/
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];  int ncom; 
   int k;  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   fx=func(x);   
   for (k=1; k<=2; k++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for (i=1;i<=npar;i++) p2[i]=x[i];  { 
     p2[thetai]=x[thetai]+delti[thetai]/k;    double brent(double ax, double bx, double cx, 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;                 double (*f)(double), double tol, double *xmin); 
     k1=func(p2)-fx;    double f1dim(double x); 
      void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     p2[thetai]=x[thetai]+delti[thetai]/k;                double *fc, double (*func)(double)); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    int j; 
     k2=func(p2)-fx;    double xx,xmin,bx,ax; 
      double fx,fb,fa;
     p2[thetai]=x[thetai]-delti[thetai]/k;   
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    ncom=n; 
     k3=func(p2)-fx;    pcom=vector(1,n); 
      xicom=vector(1,n); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    nrfunc=func; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for (j=1;j<=n;j++) { 
     k4=func(p2)-fx;      pcom[j]=p[j]; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      xicom[j]=xi[j]; 
 #ifdef DEBUG    } 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    ax=0.0; 
 #endif    xx=1.0; 
   }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   return res;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 }  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 /************** Inverse of matrix **************/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 void ludcmp(double **a, int n, int *indx, double *d)  #endif
 {    for (j=1;j<=n;j++) { 
   int i,imax,j,k;      xi[j] *= xmin; 
   double big,dum,sum,temp;      p[j] += xi[j]; 
   double *vv;    } 
      free_vector(xicom,1,n); 
   vv=vector(1,n);    free_vector(pcom,1,n); 
   *d=1.0;  } 
   for (i=1;i<=n;i++) {  
     big=0.0;  char *asc_diff_time(long time_sec, char ascdiff[])
     for (j=1;j<=n;j++)  {
       if ((temp=fabs(a[i][j])) > big) big=temp;    long sec_left, days, hours, minutes;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    days = (time_sec) / (60*60*24);
     vv[i]=1.0/big;    sec_left = (time_sec) % (60*60*24);
   }    hours = (sec_left) / (60*60) ;
   for (j=1;j<=n;j++) {    sec_left = (sec_left) %(60*60);
     for (i=1;i<j;i++) {    minutes = (sec_left) /60;
       sum=a[i][j];    sec_left = (sec_left) % (60);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       a[i][j]=sum;    return ascdiff;
     }  }
     big=0.0;  
     for (i=j;i<=n;i++) {  /*************** powell ************************/
       sum=a[i][j];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for (k=1;k<j;k++)              double (*func)(double [])) 
         sum -= a[i][k]*a[k][j];  { 
       a[i][j]=sum;    void linmin(double p[], double xi[], int n, double *fret, 
       if ( (dum=vv[i]*fabs(sum)) >= big) {                double (*func)(double [])); 
         big=dum;    int i,ibig,j; 
         imax=i;    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
     }    double *xits;
     if (j != imax) {    int niterf, itmp;
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];    pt=vector(1,n); 
         a[imax][k]=a[j][k];    ptt=vector(1,n); 
         a[j][k]=dum;    xit=vector(1,n); 
       }    xits=vector(1,n); 
       *d = -(*d);    *fret=(*func)(p); 
       vv[imax]=vv[j];    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
     indx[j]=imax;      fp=(*fret); 
     if (a[j][j] == 0.0) a[j][j]=TINY;      ibig=0; 
     if (j != n) {      del=0.0; 
       dum=1.0/(a[j][j]);      last_time=curr_time;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      (void) gettimeofday(&curr_time,&tzp);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   }      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);
   free_vector(vv,1,n);  /* Doesn't work */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
 ;     for (i=1;i<=n;i++) {
 }        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
 void lubksb(double **a, int n, int *indx, double b[])        fprintf(ficrespow," %.12lf", p[i]);
 {      }
   int i,ii=0,ip,j;      printf("\n");
   double sum;      fprintf(ficlog,"\n");
        fprintf(ficrespow,"\n");fflush(ficrespow);
   for (i=1;i<=n;i++) {      if(*iter <=3){
     ip=indx[i];        tm = *localtime(&curr_time.tv_sec);
     sum=b[ip];        strcpy(strcurr,asctime(&tm));
     b[ip]=b[i];  /*       asctime_r(&tm,strcurr); */
     if (ii)        forecast_time=curr_time; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        itmp = strlen(strcurr);
     else if (sum) ii=i;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     b[i]=sum;          strcurr[itmp-1]='\0';
   }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   for (i=n;i>=1;i--) {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     sum=b[i];        for(niterf=10;niterf<=30;niterf+=10){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     b[i]=sum/a[i][i];          tmf = *localtime(&forecast_time.tv_sec);
   }  /*      asctime_r(&tmf,strfor); */
 }          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
 /************ Frequencies ********************/          if(strfor[itmp-1]=='\n')
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          strfor[itmp-1]='\0';
 {  /* Some frequencies */          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);
            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);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        }
   double ***freq; /* Frequencies */      }
   double *pp;      for (i=1;i<=n;i++) { 
   double pos;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   FILE *ficresp;        fptt=(*fret); 
   char fileresp[FILENAMELENGTH];  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
   pp=vector(1,nlstate);        fprintf(ficlog,"fret=%lf \n",*fret);
  probs= ma3x(1,130 ,1,8, 1,8);  #endif
   strcpy(fileresp,"p");        printf("%d",i);fflush(stdout);
   strcat(fileresp,fileres);        fprintf(ficlog,"%d",i);fflush(ficlog);
   if((ficresp=fopen(fileresp,"w"))==NULL) {        linmin(p,xit,n,fret,func); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        if (fabs(fptt-(*fret)) > del) { 
     exit(0);          del=fabs(fptt-(*fret)); 
   }          ibig=i; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        } 
   j1=0;  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   j=cptcoveff;        fprintf(ficlog,"%d %.12e",i,(*fret));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for(k1=1; k1<=j;k1++){          printf(" x(%d)=%.12e",j,xit[j]);
    for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        j1++;        }
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        for(j=1;j<=n;j++) {
          scanf("%d", i);*/          printf(" p=%.12e",p[j]);
         for (i=-1; i<=nlstate+ndeath; i++)            fprintf(ficlog," p=%.12e",p[j]);
          for (jk=-1; jk<=nlstate+ndeath; jk++)          }
            for(m=agemin; m <= agemax+3; m++)        printf("\n");
              freq[i][jk][m]=0;        fprintf(ficlog,"\n");
          #endif
        for (i=1; i<=imx; i++) {      } 
          bool=1;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
          if  (cptcovn>0) {  #ifdef DEBUG
            for (z1=1; z1<=cptcoveff; z1++)        int k[2],l;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        k[0]=1;
                bool=0;        k[1]=-1;
          }        printf("Max: %.12e",(*func)(p));
           if (bool==1) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
            for(m=fprev; m<=lprev; m++){        for (j=1;j<=n;j++) {
              if(agev[m][i]==0) agev[m][i]=agemax+1;          printf(" %.12e",p[j]);
              if(agev[m][i]==1) agev[m][i]=agemax+2;          fprintf(ficlog," %.12e",p[j]);
              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");
            }        fprintf(ficlog,"\n");
          }        for(l=0;l<=1;l++) {
        }          for (j=1;j<=n;j++) {
         if  (cptcovn>0) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
          fprintf(ficresp, "\n#********** Variable ");            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
        fprintf(ficresp, "**********\n#");          }
         }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        for(i=1; i<=nlstate;i++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        }
        fprintf(ficresp, "\n");  #endif
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){  
     if(i==(int)agemax+3)        free_vector(xit,1,n); 
       printf("Total");        free_vector(xits,1,n); 
     else        free_vector(ptt,1,n); 
       printf("Age %d", i);        free_vector(pt,1,n); 
     for(jk=1; jk <=nlstate ; jk++){        return; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      } 
         pp[jk] += freq[jk][m][i];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { 
     for(jk=1; jk <=nlstate ; jk++){        ptt[j]=2.0*p[j]-pt[j]; 
       for(m=-1, pos=0; m <=0 ; m++)        xit[j]=p[j]-pt[j]; 
         pos += freq[jk][m][i];        pt[j]=p[j]; 
       if(pp[jk]>=1.e-10)      } 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      fptt=(*func)(ptt); 
       else      if (fptt < fp) { 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     }        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
      for(jk=1; jk <=nlstate ; jk++){          for (j=1;j<=n;j++) { 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            xi[j][ibig]=xi[j][n]; 
         pp[jk] += freq[jk][m][i];            xi[j][n]=xit[j]; 
      }          }
   #ifdef DEBUG
     for(jk=1,pos=0; jk <=nlstate ; jk++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       pos += pp[jk];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(jk=1; jk <=nlstate ; jk++){          for(j=1;j<=n;j++){
       if(pos>=1.e-5)            printf(" %.12e",xit[j]);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            fprintf(ficlog," %.12e",xit[j]);
       else          }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          printf("\n");
       if( i <= (int) agemax){          fprintf(ficlog,"\n");
         if(pos>=1.e-5){  #endif
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        }
           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]);*/    } 
         }  } 
       else  
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  /**** Prevalence limit (stable or period prevalence)  ****************/
       }  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(jk=-1; jk <=nlstate+ndeath; jk++)  {
       for(m=-1; m <=nlstate+ndeath; m++)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);       matrix by transitions matrix until convergence is reached */
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");    int i, ii,j,k;
     printf("\n");    double min, max, maxmin, maxmax,sumnew=0.;
     }    double **matprod2();
     }    double **out, cov[NCOVMAX+1], **pmij();
  }    double **newm;
      double agefin, delaymax=50 ; /* Max number of years to converge */
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(pp,1,nlstate);      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }  /* End of Freq */      }
   
 /************* Waves Concatenation ***************/     cov[1]=1.;
    
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      newm=savm;
      Death is a valid wave (if date is known).      /* Covariates have to be included here again */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      cov[2]=agefin;
      dh[m][i] of 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.      for (k=1; k<=cptcovn;k++) {
      */        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*        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]]);*/
   int i, mi, m;      }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      double sum=0., jmean=0.;*/      for (k=1; k<=cptcovprod;k++)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   int j, k=0,jk, ju, jl;      
   double sum=0.;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   jmin=1e+5;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   jmax=-1;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   jmean=0.;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for(i=1; i<=imx; i++){      
     mi=0;      savm=oldm;
     m=firstpass;      oldm=newm;
     while(s[m][i] <= nlstate){      maxmax=0.;
       if(s[m][i]>=1)      for(j=1;j<=nlstate;j++){
         mw[++mi][i]=m;        min=1.;
       if(m >=lastpass)        max=0.;
         break;        for(i=1; i<=nlstate; i++) {
       else          sumnew=0;
         m++;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     }/* end while */          prlim[i][j]= newm[i][j]/(1-sumnew);
     if (s[m][i] > nlstate){          max=FMAX(max,prlim[i][j]);
       mi++;     /* Death is another wave */          min=FMIN(min,prlim[i][j]);
       /* if(mi==0)  never been interviewed correctly before death */        }
          /* Only death is a correct wave */        maxmin=max-min;
       mw[mi][i]=m;        maxmax=FMAX(maxmax,maxmin);
     }      }
       if(maxmax < ftolpl){
     wav[i]=mi;        return prlim;
     if(mi==0)      }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    }
   }  }
   
   for(i=1; i<=imx; i++){  /*************** transition probabilities ***************/ 
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         dh[mi][i]=1;  {
       else{    /* According to parameters values stored in x and the covariate's values stored in cov,
         if (s[mw[mi+1][i]][i] > nlstate) {       computes the probability to be observed in state j being in state i by appying the
           if (agedc[i] < 2*AGESUP) {       model to the ncovmodel covariates (including constant and age).
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
           if(j==0) j=1;  /* Survives at least one month after exam */       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
           k=k+1;       ncth covariate in the global vector x is given by the formula:
           if (j >= jmax) jmax=j;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           if (j <= jmin) jmin=j;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
           sum=sum+j;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
           /* if (j<10) printf("j=%d num=%d ",j,i); */       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
           }       Outputs ps[i][j] the probability to be observed in j being in j according to
         }       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
         else{    */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    double s1, lnpijopii;
           k=k+1;    /*double t34;*/
           if (j >= jmax) jmax=j;    int i,j,j1, nc, ii, jj;
           else if (j <= jmin)jmin=j;  
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      for(i=1; i<= nlstate; i++){
           sum=sum+j;        for(j=1; j<i;j++){
         }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         jk= j/stepm;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         jl= j -jk*stepm;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
         ju= j -(jk+1)*stepm;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         if(jl <= -ju)          }
           dh[mi][i]=jk;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         else  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           dh[mi][i]=jk+1;        }
         if(dh[mi][i]==0)        for(j=i+1; j<=nlstate+ndeath;j++){
           dh[mi][i]=1; /* At least one step */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   }  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   jmean=sum/k;          }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
  }        }
 /*********** Tricode ****************************/      }
 void tricode(int *Tvar, int **nbcode, int imx)      
 {      for(i=1; i<= nlstate; i++){
   int Ndum[20],ij=1, k, j, i;        s1=0;
   int cptcode=0;        for(j=1; j<i; j++){
   cptcoveff=0;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
            /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   for (k=0; k<19; k++) Ndum[k]=0;        }
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(j=i+1; j<=nlstate+ndeath; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   for (j=1; j<=(cptcovn+2*cptcovprod); 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<=imx; i++) {        }
       ij=(int)(covar[Tvar[j]][i]);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       Ndum[ij]++;        ps[i][i]=1./(s1+1.);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /* Computing other pijs */
       if (ij > cptcode) cptcode=ij;        for(j=1; j<i; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
     for (i=0; i<=cptcode; i++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
       if(Ndum[i]!=0) ncodemax[j]++;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     }      } /* end i */
     ij=1;      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jj=1; jj<= nlstate+ndeath; jj++){
     for (i=1; i<=ncodemax[j]; i++) {          ps[ii][jj]=0;
       for (k=0; k<=19; k++) {          ps[ii][ii]=1;
         if (Ndum[k] != 0) {        }
           nbcode[Tvar[j]][ij]=k;      }
           ij++;      
         }  
         if (ij > ncodemax[j]) break;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       }    /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     }  /*         printf("ddd %lf ",ps[ii][jj]); */
   }    /*       } */
   /*       printf("\n "); */
  for (k=0; k<19; k++) Ndum[k]=0;  /*        } */
   /*        printf("\n ");printf("%lf ",cov[2]); */
  for (i=1; i<=ncovmodel-2; i++) {         /*
       ij=Tvar[i];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       Ndum[ij]++;        goto end;*/
     }      return ps;
   }
  ij=1;  
  for (i=1; i<=10; i++) {  /**************** Product of 2 matrices ******************/
    if((Ndum[i]!=0) && (i<=ncov)){  
      Tvaraff[ij]=i;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
      ij++;  {
    }    /* 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(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
     cptcoveff=ij-1;       before: only the contents of out is modified. The function returns
 }       a pointer to pointers identical to out */
     long i, j, k;
 /*********** Health Expectancies ****************/    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 {          out[i][k] +=in[i][j]*b[j][k];
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h;    return out;
   double age, agelim,hf;  }
   double ***p3mat;  
    
   fprintf(ficreseij,"# Health expectancies\n");  /************* Higher Matrix Product ***************/
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficreseij," %1d-%1d",i,j);    /* Computes the transition matrix starting at age 'age' over 
   fprintf(ficreseij,"\n");       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   hstepm=1*YEARM; /*  Every j years of age (in month) */       nhstepm*hstepm matrices. 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       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 
   agelim=AGESUP;       for the memory).
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       Model is determined by parameters x and covariates have to be 
     /* nhstepm age range expressed in number of stepm */       included manually here. 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */       */
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    int i, j, d, h, k;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **out, cov[NCOVMAX+1];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double **newm;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
     for(i=1; i<=nlstate;i++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)        po[i][j][0]=(i==j ? 1.0 : 0.0);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      }
           eij[i][j][(int)age] +=p3mat[i][j][h];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         }    for(h=1; h <=nhstepm; h++){
          for(d=1; d <=hstepm; d++){
     hf=1;        newm=savm;
     if (stepm >= YEARM) hf=stepm/YEARM;        /* Covariates have to be included here again */
     fprintf(ficreseij,"%.0f",age );        cov[1]=1.;
     for(i=1; i<=nlstate;i++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for(j=1; j<=nlstate;j++){        for (k=1; k<=cptcovn;k++) 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       }        for (k=1; k<=cptcovage;k++)
     fprintf(ficreseij,"\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovprod;k++)
   }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 }  
   
 /************ Variance ******************/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 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)        /*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, 
   /* Variance of health expectancies */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        savm=oldm;
   double **newm;        oldm=newm;
   double **dnewm,**doldm;      }
   int i, j, nhstepm, hstepm, h;      for(i=1; i<=nlstate+ndeath; i++)
   int k, cptcode;        for(j=1;j<=nlstate+ndeath;j++) {
   double *xp;          po[i][j][h]=newm[i][j];
   double **gp, **gm;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   double ***gradg, ***trgradg;        }
   double ***p3mat;      /*printf("h=%d ",h);*/
   double age,agelim;    } /* end h */
   int theta;  /*     printf("\n H=%d \n",h); */
     return po;
    fprintf(ficresvij,"# Covariances of life expectancies\n");  }
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  /*************** log-likelihood *************/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  double func( double *x)
   fprintf(ficresvij,"\n");  {
     int i, ii, j, k, mi, d, kk;
   xp=vector(1,npar);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   dnewm=matrix(1,nlstate,1,npar);    double **out;
   doldm=matrix(1,nlstate,1,nlstate);    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   hstepm=1*YEARM; /* Every year of age */    int s1, s2;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double bbh, survp;
   agelim = AGESUP;    long ipmx;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /*extern weight */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* We are differentiating ll according to initial status */
     if (stepm >= YEARM) hstepm=1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /*for(i=1;i<imx;i++) 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf(" %d\n",s[4][i]);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    */
     gp=matrix(0,nhstepm,1,nlstate);    cov[1]=1.;
     gm=matrix(0,nhstepm,1,nlstate);  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    if(mle==1){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        /* Computes the values of the ncovmodel covariates of the model
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
       if (popbased==1) {         */
         for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           prlim[i][i]=probs[(int)age][i][ij];        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       }           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
                 has been calculated etc */
       for(j=1; j<= nlstate; j++){        for(mi=1; mi<= wav[i]-1; mi++){
         for(h=0; h<=nhstepm; h++){          for (ii=1;ii<=nlstate+ndeath;ii++)
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];              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++){
       for(i=1; i<=npar; i++) /* Computes gradient */            newm=savm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for (kk=1; kk<=cptcovage;kk++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
             }
       if (popbased==1) {            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));
           prlim[i][i]=probs[(int)age][i][ij];            savm=oldm;
       }            oldm=newm;
           } /* end mult */
       for(j=1; j<= nlstate; j++){        
         for(h=0; h<=nhstepm; h++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          /* But now since version 0.9 we anticipate for bias at large stepm.
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
       }           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for(j=1; j<= nlstate; j++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         for(h=0; h<=nhstepm; h++){           * probability in order to take into account the bias as a fraction of the way
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
     } /* End theta */           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);           */
           s1=s[mw[mi][i]][i];
     for(h=0; h<=nhstepm; h++)          s2=s[mw[mi+1][i]][i];
       for(j=1; j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
         for(theta=1; theta <=npar; theta++)          /* bias bh is positive if real duration
           trgradg[h][j][theta]=gradg[h][theta][j];           * is higher than the multiple of stepm and negative otherwise.
            */
     for(i=1;i<=nlstate;i++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       for(j=1;j<=nlstate;j++)          if( s2 > nlstate){ 
         vareij[i][j][(int)age] =0.;            /* i.e. if s2 is a death state and if the date of death is known 
     for(h=0;h<=nhstepm;h++){               then the contribution to the likelihood is the probability to 
       for(k=0;k<=nhstepm;k++){               die between last step unit time and current  step unit time, 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);               which is also equal to probability to die before dh 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);               minus probability to die before dh-stepm . 
         for(i=1;i<=nlstate;i++)               In version up to 0.92 likelihood was computed
           for(j=1;j<=nlstate;j++)          as if date of death was unknown. Death was treated as any other
             vareij[i][j][(int)age] += doldm[i][j];          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
     }          to consider that at each interview the state was recorded
     h=1;          (healthy, disable or death) and IMaCh was corrected; but when we
     if (stepm >= YEARM) h=stepm/YEARM;          introduced the exact date of death then we should have modified
     fprintf(ficresvij,"%.0f ",age );          the contribution of an exact death to the likelihood. This new
     for(i=1; i<=nlstate;i++)          contribution is smaller and very dependent of the step unit
       for(j=1; j<=nlstate;j++){          stepm. It is no more the probability to die between last interview
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          and month of death but the probability to survive from last
       }          interview up to one month before death multiplied by the
     fprintf(ficresvij,"\n");          probability to die within a month. Thanks to Chris
     free_matrix(gp,0,nhstepm,1,nlstate);          Jackson for correcting this bug.  Former versions increased
     free_matrix(gm,0,nhstepm,1,nlstate);          mortality artificially. The bad side is that we add another loop
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          which slows down the processing. The difference can be up to 10%
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          lower mortality.
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            */
   } /* End age */            lli=log(out[s1][s2] - savm[s1][s2]);
    
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);          } else if  (s2==-2) {
   free_matrix(dnewm,1,nlstate,1,nlstate);            for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 }            /*survp += out[s1][j]; */
             lli= log(survp);
 /************ Variance of prevlim ******************/          }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          
 {          else if  (s2==-4) { 
   /* Variance of prevalence limit */            for (j=3,survp=0. ; j<=nlstate; j++)  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double **newm;            lli= log(survp); 
   double **dnewm,**doldm;          } 
   int i, j, nhstepm, hstepm;  
   int k, cptcode;          else if  (s2==-5) { 
   double *xp;            for (j=1,survp=0. ; j<=2; j++)  
   double *gp, *gm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double **gradg, **trgradg;            lli= log(survp); 
   double age,agelim;          } 
   int theta;          
              else{
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fprintf(ficresvpl,"# Age");            /*  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(i=1; i<=nlstate;i++)          } 
       fprintf(ficresvpl," %1d-%1d",i,i);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fprintf(ficresvpl,"\n");          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   xp=vector(1,npar);          ipmx +=1;
   dnewm=matrix(1,nlstate,1,npar);          sw += weight[i];
   doldm=matrix(1,nlstate,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   hstepm=1*YEARM; /* Every year of age */      } /* end of individual */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    }  else if(mle==2){
   agelim = AGESUP;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) hstepm=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (j=1;j<=nlstate+ndeath;j++){
     gradg=matrix(1,npar,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     gp=vector(1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gm=vector(1,nlstate);            }
           for(d=0; d<=dh[mi][i]; d++){
     for(theta=1; theta <=npar; theta++){            newm=savm;
       for(i=1; i<=npar; i++){ /* Computes gradient */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
       for(i=1;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         gp[i] = prlim[i][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       for(i=1; i<=npar; i++) /* Computes gradient */            oldm=newm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          } /* end mult */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        
       for(i=1;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
         gm[i] = prlim[i][i];          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
       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 */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          ipmx +=1;
     } /* End theta */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     trgradg =matrix(1,nlstate,1,npar);        } /* end of wave */
       } /* end of individual */
     for(j=1; j<=nlstate;j++)    }  else if(mle==3){  /* exponential inter-extrapolation */
       for(theta=1; theta <=npar; theta++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         trgradg[j][theta]=gradg[theta][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       varpl[i][(int)age] =0.;            for (j=1;j<=nlstate+ndeath;j++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1;i<=nlstate;i++)            }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     fprintf(ficresvpl,"%.0f ",age );            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1; i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficresvpl,"\n");            }
     free_vector(gp,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_vector(gm,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_matrix(gradg,1,npar,1,nlstate);            savm=oldm;
     free_matrix(trgradg,1,nlstate,1,npar);            oldm=newm;
   } /* End age */          } /* end mult */
         
   free_vector(xp,1,npar);          s1=s[mw[mi][i]][i];
   free_matrix(doldm,1,nlstate,1,npar);          s2=s[mw[mi+1][i]][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 }          ipmx +=1;
           sw += weight[i];
 /************ Variance of one-step probabilities  ******************/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        } /* end of wave */
 {      } /* end of individual */
   int i, j;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   int k=0, cptcode;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **dnewm,**doldm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double *xp;        for(mi=1; mi<= wav[i]-1; mi++){
   double *gp, *gm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **gradg, **trgradg;            for (j=1;j<=nlstate+ndeath;j++){
   double age,agelim, cov[NCOVMAX];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int theta;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   char fileresprob[FILENAMELENGTH];            }
           for(d=0; d<dh[mi][i]; d++){
   strcpy(fileresprob,"prob");            newm=savm;
   strcat(fileresprob,fileres);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            for (kk=1; kk<=cptcovage;kk++) {
     printf("Problem with resultfile: %s\n", fileresprob);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   xp=vector(1,npar);            savm=oldm;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            oldm=newm;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          } /* end mult */
          
   cov[1]=1;          s1=s[mw[mi][i]][i];
   for (age=bage; age<=fage; age ++){          s2=s[mw[mi+1][i]][i];
     cov[2]=age;          if( s2 > nlstate){ 
     gradg=matrix(1,npar,1,9);            lli=log(out[s1][s2] - savm[s1][s2]);
     trgradg=matrix(1,9,1,npar);          }else{
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
              ipmx +=1;
     for(theta=1; theta <=npar; theta++){          sw += weight[i];
       for(i=1; i<=npar; i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*      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 */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      } /* end of individual */
        }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       k=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<= (nlstate+ndeath); i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(j=1; j<=(nlstate+ndeath);j++){        for(mi=1; mi<= wav[i]-1; mi++){
            k=k+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
           gp[k]=pmmij[i][j];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
       for(i=1; i<=npar; i++)          for(d=0; d<dh[mi][i]; d++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            newm=savm;
                cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       k=0;            }
       for(i=1; i<=(nlstate+ndeath); i++){          
         for(j=1; j<=(nlstate+ndeath);j++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           k=k+1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           gm[k]=pmmij[i][j];            savm=oldm;
         }            oldm=newm;
       }          } /* end mult */
              
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          s1=s[mw[mi][i]][i];
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            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;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          sw += weight[i];
       for(theta=1; theta <=npar; theta++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       trgradg[j][theta]=gradg[theta][j];          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
          } /* end of wave */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      } /* end of individual */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      pmij(pmmij,cov,ncovmodel,x,nlstate);    /* 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 */
      k=0;    return -l;
      for(i=1; i<=(nlstate+ndeath); i++){  }
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;  /*************** log-likelihood *************/
          gm[k]=pmmij[i][j];  double funcone( double *x)
         }  {
      }    /* Same as likeli but slower because of a lot of printf and if */
          int i, ii, j, k, mi, d, kk;
      /*printf("\n%d ",(int)age);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double **out;
            double lli; /* Individual log likelihood */
     double llt;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    int s1, s2;
      }*/    double bbh, survp;
     /*extern weight */
   fprintf(ficresprob,"\n%d ",(int)age);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    /*for(i=1;i<imx;i++) 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      printf(" %d\n",s[4][i]);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    */
   }    cov[1]=1.;
   
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    for(k=1; k<=nlstate; k++) ll[k]=0.;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }      for(mi=1; mi<= wav[i]-1; mi++){
  free_vector(xp,1,npar);        for (ii=1;ii<=nlstate+ndeath;ii++)
 fclose(ficresprob);          for (j=1;j<=nlstate+ndeath;j++){
  exit(0);            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++){
 /**************** Main Program *****************/          newm=savm;
 /***********************************************/          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
 /*int main(int argc, char *argv[])*/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 int main()          }
 {          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          savm=oldm;
   double agedeb, agefin,hf;          oldm=newm;
   double agemin=1.e20, agemax=-1.e20;        } /* end mult */
         
   double fret;        s1=s[mw[mi][i]][i];
   double **xi,tmp,delta;        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
   double dum; /* Dummy variable */        /* bias is positive if real duration
   double ***p3mat;         * is higher than the multiple of stepm and negative otherwise.
   int *indx;         */
   char line[MAXLINE], linepar[MAXLINE];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   char title[MAXLINE];          lli=log(out[s1][s2] - savm[s1][s2]);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];        } else if  (s2==-2) {
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];          for (j=1,survp=0. ; j<=nlstate; j++) 
   char filerest[FILENAMELENGTH];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   char fileregp[FILENAMELENGTH];          lli= log(survp);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        }else if (mle==1){
   int firstobs=1, lastobs=10;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int sdeb, sfin; /* Status at beginning and end */        } else if(mle==2){
   int c,  h , cpt,l;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   int ju,jl, mi;        } else if(mle==3){  /* exponential inter-extrapolation */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   int mobilav=0, fprevfore=1, lprevfore=1;          lli=log(out[s1][s2]); /* Original formula */
   int hstepm, nhstepm;        } else{  /* mle=0 back to 1 */
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double bage, fage, age, agelim, agebase;          /*lli=log(out[s1][s2]); */ /* Original formula */
   double ftolpl=FTOL;        } /* End of if */
   double **prlim;        ipmx +=1;
   double *severity;        sw += weight[i];
   double ***param; /* Matrix of parameters */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double  *p;        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   double **matcov; /* Matrix of covariance */        if(globpr){
   double ***delti3; /* Scale */          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   double *delti; /* Scale */   %11.6f %11.6f %11.6f ", \
   double ***eij, ***vareij;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double **varpl; /* Variances of prevalence limits by age */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double *epj, vepp;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double kk1;            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";          }
   char *alph[]={"a","a","b","c","d","e"}, str[4];          fprintf(ficresilk," %10.6f\n", -llt);
         }
       } /* end of wave */
   char z[1]="c", occ;    } /* end of individual */
 #include <sys/time.h>    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 #include <time.h>    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /* long total_usecs;    if(globpr==0){ /* First time we count the contributions and weights */
   struct timeval start_time, end_time;      gipmx=ipmx;
        gsw=sw;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    }
     return -l;
   }
   printf("\nIMACH, Version 0.64b");  
   printf("\nEnter the parameter file name: ");  
   /*************** function likelione ***********/
 #ifdef windows  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   scanf("%s",pathtot);  {
   getcwd(pathcd, size);    /* This routine should help understanding what is done with 
   /*cygwin_split_path(pathtot,path,optionfile);       the selection of individuals/waves and
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       to check the exact contribution to the likelihood.
   /* cutv(path,optionfile,pathtot,'\\');*/       Plotting could be done.
      */
 split(pathtot, path,optionfile);    int k;
   chdir(path);  
   replace(pathc,path);    if(*globpri !=0){ /* Just counts and sums, no printings */
 #endif      strcpy(fileresilk,"ilk"); 
 #ifdef unix      strcat(fileresilk,fileres);
   scanf("%s",optionfile);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 #endif        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 /*-------- arguments in the command line --------*/      }
       fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   strcpy(fileres,"r");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   strcat(fileres, optionfile);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
   /*---------arguments file --------*/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    *fretone=(*funcone)(p);
   }    if(*globpri !=0){
       fclose(ficresilk);
   strcpy(filereso,"o");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   strcat(filereso,fileres);      fflush(fichtm); 
   if((ficparo=fopen(filereso,"w"))==NULL) {    } 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    return;
   }  }
   
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /*********** Maximum Likelihood Estimation ***************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     puts(line);  {
     fputs(line,ficparo);    int i,j, iter;
   }    double **xi;
   ungetc(c,ficpar);    double fret;
     double fretone; /* Only one call to likelihood */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    /*  char filerespow[FILENAMELENGTH];*/
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    xi=matrix(1,npar,1,npar);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    for (i=1;i<=npar;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++)
     ungetc(c,ficpar);        xi[i][j]=(i==j ? 1.0 : 0.0);
     fgets(line, MAXLINE, ficpar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     puts(line);    strcpy(filerespow,"pow"); 
     fputs(line,ficparo);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);    }
  while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     ungetc(c,ficpar);    for (i=1;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1;j<=nlstate+ndeath;j++)
     puts(line);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fputs(line,ficparo);    fprintf(ficrespow,"\n");
   }  
   ungetc(c,ficpar);    powell(p,xi,npar,ftol,&iter,&fret,func);
    
   fscanf(ficpar,"fprevalence=%d lprevalence=%d mob_average=%d\n",&fprevfore,&lprevfore,&mobilav);    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   covar=matrix(0,NCOVMAX,1,n);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   cptcovn=0;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   ncovmodel=2+cptcovn;  }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    /**** Computes Hessian and covariance matrix ***/
   /* Read guess parameters */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    double  **a,**y,*x,pd;
     ungetc(c,ficpar);    double **hess;
     fgets(line, MAXLINE, ficpar);    int i, j,jk;
     puts(line);    int *indx;
     fputs(line,ficparo);  
   }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   ungetc(c,ficpar);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      void lubksb(double **a, int npar, int *indx, double b[]) ;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     for(i=1; i <=nlstate; i++)    double gompertz(double p[]);
     for(j=1; j <=nlstate+ndeath-1; j++){    hess=matrix(1,npar,1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);    printf("\nCalculation of the hessian matrix. Wait...\n");
       printf("%1d%1d",i,j);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       for(k=1; k<=ncovmodel;k++){    for (i=1;i<=npar;i++){
         fscanf(ficpar," %lf",&param[i][j][k]);      printf("%d",i);fflush(stdout);
         printf(" %lf",param[i][j][k]);      fprintf(ficlog,"%d",i);fflush(ficlog);
         fprintf(ficparo," %lf",param[i][j][k]);     
       }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       fscanf(ficpar,"\n");      
       printf("\n");      /*  printf(" %f ",p[i]);
       fprintf(ficparo,"\n");          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }    }
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
   p=param[1][1];        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
   /* Reads comments: lines beginning with '#' */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   while((c=getc(ficpar))=='#' && c!= EOF){          hess[i][j]=hessij(p,delti,i,j,func,npar);
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          hess[j][i]=hess[i][j];    
     puts(line);          /*printf(" %lf ",hess[i][j]);*/
     fputs(line,ficparo);        }
   }      }
   ungetc(c,ficpar);    }
     printf("\n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficlog,"\n");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       printf("%1d%1d",i,j);    a=matrix(1,npar,1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    y=matrix(1,npar,1,npar);
       for(k=1; k<=ncovmodel;k++){    x=vector(1,npar);
         fscanf(ficpar,"%le",&delti3[i][j][k]);    indx=ivector(1,npar);
         printf(" %le",delti3[i][j][k]);    for (i=1;i<=npar;i++)
         fprintf(ficparo," %le",delti3[i][j][k]);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
       fscanf(ficpar,"\n");  
       printf("\n");    for (j=1;j<=npar;j++) {
       fprintf(ficparo,"\n");      for (i=1;i<=npar;i++) x[i]=0;
     }      x[j]=1;
   }      lubksb(a,npar,indx,x);
   delti=delti3[1][1];      for (i=1;i<=npar;i++){ 
          matcov[i][j]=x[i];
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    printf("\n#Hessian matrix#\n");
     puts(line);    fprintf(ficlog,"\n#Hessian matrix#\n");
     fputs(line,ficparo);    for (i=1;i<=npar;i++) { 
   }      for (j=1;j<=npar;j++) { 
   ungetc(c,ficpar);        printf("%.3e ",hess[i][j]);
          fprintf(ficlog,"%.3e ",hess[i][j]);
   matcov=matrix(1,npar,1,npar);      }
   for(i=1; i <=npar; i++){      printf("\n");
     fscanf(ficpar,"%s",&str);      fprintf(ficlog,"\n");
     printf("%s",str);    }
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){    /* Recompute Inverse */
       fscanf(ficpar," %le",&matcov[i][j]);    for (i=1;i<=npar;i++)
       printf(" %.5le",matcov[i][j]);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       fprintf(ficparo," %.5le",matcov[i][j]);    ludcmp(a,npar,indx,&pd);
     }  
     fscanf(ficpar,"\n");    /*  printf("\n#Hessian matrix recomputed#\n");
     printf("\n");  
     fprintf(ficparo,"\n");    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   for(i=1; i <=npar; i++)      x[j]=1;
     for(j=i+1;j<=npar;j++)      lubksb(a,npar,indx,x);
       matcov[i][j]=matcov[j][i];      for (i=1;i<=npar;i++){ 
            y[i][j]=x[i];
   printf("\n");        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
       }
     /*-------- data file ----------*/      printf("\n");
     if((ficres =fopen(fileres,"w"))==NULL) {      fprintf(ficlog,"\n");
       printf("Problem with resultfile: %s\n", fileres);goto end;    }
     }    */
     fprintf(ficres,"#%s\n",version);  
        free_matrix(a,1,npar,1,npar);
     if((fic=fopen(datafile,"r"))==NULL)    {    free_matrix(y,1,npar,1,npar);
       printf("Problem with datafile: %s\n", datafile);goto end;    free_vector(x,1,npar);
     }    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
     n= lastobs;  
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);  }
     num=ivector(1,n);  
     moisnais=vector(1,n);  /*************** hessian matrix ****************/
     annais=vector(1,n);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     moisdc=vector(1,n);  {
     andc=vector(1,n);    int i;
     agedc=vector(1,n);    int l=1, lmax=20;
     cod=ivector(1,n);    double k1,k2;
     weight=vector(1,n);    double p2[MAXPARM+1]; /* identical to x */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double res;
     mint=matrix(1,maxwav,1,n);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     anint=matrix(1,maxwav,1,n);    double fx;
     s=imatrix(1,maxwav+1,1,n);    int k=0,kmax=10;
     adl=imatrix(1,maxwav+1,1,n);        double l1;
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     i=1;    for(l=0 ; l <=lmax; l++){
     while (fgets(line, MAXLINE, fic) != NULL)    {      l1=pow(10,l);
       if ((i >= firstobs) && (i <=lastobs)) {      delts=delt;
              for(k=1 ; k <kmax; k=k+1){
         for (j=maxwav;j>=1;j--){        delt = delta*(l1*k);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        p2[theta]=x[theta] +delt;
           strcpy(line,stra);        k1=func(p2)-fx;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        p2[theta]=x[theta]-delt;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        k2=func(p2)-fx;
         }        /*res= (k1-2.0*fx+k2)/delt/delt; */
                res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  #ifdef DEBUGHESS
         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);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        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);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for (j=ncov;j>=1;j--){          k=kmax;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
         }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         num[i]=atol(stra);          k=kmax; l=lmax*10.;
                }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           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;}*/          delts=delt;
         }
         i=i+1;      }
       }    }
     }    delti[theta]=delts;
     /* printf("ii=%d", ij);    return res; 
        scanf("%d",i);*/    
   imx=i-1; /* Number of individuals */  }
   
   /* for (i=1; i<=imx; i++){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    int i;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    double p2[MAXPARM+1];
     int k;
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);    fx=func(x);
   Tprod=ivector(1,15);    for (k=1; k<=2; k++) {
   Tvaraff=ivector(1,15);      for (i=1;i<=npar;i++) p2[i]=x[i];
   Tvard=imatrix(1,15,1,2);      p2[thetai]=x[thetai]+delti[thetai]/k;
   Tage=ivector(1,15);            p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k1=func(p2)-fx;
   if (strlen(model) >1){    
     j=0, j1=0, k1=1, k2=1;      p2[thetai]=x[thetai]+delti[thetai]/k;
     j=nbocc(model,'+');      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     j1=nbocc(model,'*');      k2=func(p2)-fx;
     cptcovn=j+1;    
     cptcovprod=j1;      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k3=func(p2)-fx;
     strcpy(modelsav,model);    
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      p2[thetai]=x[thetai]-delti[thetai]/k;
       printf("Error. Non available option model=%s ",model);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       goto end;      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
     for(i=(j+1); i>=1;i--){      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);
       cutv(stra,strb,modelsav,'+');      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);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  #endif
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    }
       /*scanf("%d",i);*/    return res;
       if (strchr(strb,'*')) {  }
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  /************** Inverse of matrix **************/
           cptcovprod--;  void ludcmp(double **a, int n, int *indx, double *d) 
           cutv(strb,stre,strd,'V');  { 
           Tvar[i]=atoi(stre);    int i,imax,j,k; 
           cptcovage++;    double big,dum,sum,temp; 
             Tage[cptcovage]=i;    double *vv; 
             /*printf("stre=%s ", stre);*/   
         }    vv=vector(1,n); 
         else if (strcmp(strd,"age")==0) {    *d=1.0; 
           cptcovprod--;    for (i=1;i<=n;i++) { 
           cutv(strb,stre,strc,'V');      big=0.0; 
           Tvar[i]=atoi(stre);      for (j=1;j<=n;j++) 
           cptcovage++;        if ((temp=fabs(a[i][j])) > big) big=temp; 
           Tage[cptcovage]=i;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
         else {    } 
           cutv(strb,stre,strc,'V');    for (j=1;j<=n;j++) { 
           Tvar[i]=ncov+k1;      for (i=1;i<j;i++) { 
           cutv(strb,strc,strd,'V');        sum=a[i][j]; 
           Tprod[k1]=i;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           Tvard[k1][1]=atoi(strc);        a[i][j]=sum; 
           Tvard[k1][2]=atoi(stre);      } 
           Tvar[cptcovn+k2]=Tvard[k1][1];      big=0.0; 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for (i=j;i<=n;i++) { 
           for (k=1; k<=lastobs;k++)        sum=a[i][j]; 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        for (k=1;k<j;k++) 
           k1++;          sum -= a[i][k]*a[k][j]; 
           k2=k2+2;        a[i][j]=sum; 
         }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       }          big=dum; 
       else {          imax=i; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        } 
        /*  scanf("%d",i);*/      } 
       cutv(strd,strc,strb,'V');      if (j != imax) { 
       Tvar[i]=atoi(strc);        for (k=1;k<=n;k++) { 
       }          dum=a[imax][k]; 
       strcpy(modelsav,stra);            a[imax][k]=a[j][k]; 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          a[j][k]=dum; 
         scanf("%d",i);*/        } 
     }        *d = -(*d); 
 }        vv[imax]=vv[j]; 
        } 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      indx[j]=imax; 
   printf("cptcovprod=%d ", cptcovprod);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   scanf("%d ",i);*/      if (j != n) { 
     fclose(fic);        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     /*  if(mle==1){*/      } 
     if (weightopt != 1) { /* Maximisation without weights*/    } 
       for(i=1;i<=n;i++) weight[i]=1.0;    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
     /*-calculation of age at interview from date of interview and age at death -*/  } 
     agev=matrix(1,maxwav,1,imx);  
   void lubksb(double **a, int n, int *indx, double b[]) 
    for (i=1; i<=imx; i++)  { 
      for(m=2; (m<= maxwav); m++)    int i,ii=0,ip,j; 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    double sum; 
          anint[m][i]=9999;   
          s[m][i]=-1;    for (i=1;i<=n;i++) { 
        }      ip=indx[i]; 
          sum=b[ip]; 
     for (i=1; i<=imx; i++)  {      b[ip]=b[i]; 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      if (ii) 
       for(m=1; (m<= maxwav); m++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         if(s[m][i] >0){      else if (sum) ii=i; 
           if (s[m][i] == nlstate+1) {      b[i]=sum; 
             if(agedc[i]>0)    } 
               if(moisdc[i]!=99 && andc[i]!=9999)    for (i=n;i>=1;i--) { 
               agev[m][i]=agedc[i];      sum=b[i]; 
             else {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
               if (andc[i]!=9999){      b[i]=sum/a[i][i]; 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    } 
               agev[m][i]=-1;  } 
               }  
             }  void pstamp(FILE *fichier)
           }  {
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  }
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;  /************ Frequencies ********************/
             else if(agev[m][i] <agemin){  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[])
               agemin=agev[m][i];  {  /* Some frequencies */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    
             }    int i, m, jk, k1,i1, j1, bool, z1,j;
             else if(agev[m][i] >agemax){    int first;
               agemax=agev[m][i];    double ***freq; /* Frequencies */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    double *pp, **prop;
             }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             /*agev[m][i]=anint[m][i]-annais[i];*/    char fileresp[FILENAMELENGTH];
             /*   agev[m][i] = age[i]+2*m;*/    
           }    pp=vector(1,nlstate);
           else { /* =9 */    prop=matrix(1,nlstate,iagemin,iagemax+3);
             agev[m][i]=1;    strcpy(fileresp,"p");
             s[m][i]=-1;    strcat(fileresp,fileres);
           }    if((ficresp=fopen(fileresp,"w"))==NULL) {
         }      printf("Problem with prevalence resultfile: %s\n", fileresp);
         else /*= 0 Unknown */      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           agev[m][i]=1;      exit(0);
       }    }
        freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     }    j1=0;
     for (i=1; i<=imx; i++)  {    
       for(m=1; (m<= maxwav); m++){    j=cptcoveff;
         if (s[m][i] > (nlstate+ndeath)) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;    first=1;
         }  
       }    for(k1=1; k1<=j;k1++){
     }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
     free_vector(severity,1,maxwav);        for (i=-5; i<=nlstate+ndeath; i++)  
     free_imatrix(outcome,1,maxwav+1,1,n);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     free_vector(moisnais,1,n);            for(m=iagemin; m <= iagemax+3; m++)
     free_vector(annais,1,n);              freq[i][jk][m]=0;
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n);      for (i=1; i<=nlstate; i++)  
     free_vector(moisdc,1,n);        for(m=iagemin; m <= iagemax+3; m++)
     free_vector(andc,1,n);          prop[i][m]=0;
         
            dateintsum=0;
     wav=ivector(1,imx);        k2cpt=0;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for (i=1; i<=imx; i++) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          bool=1;
              if  (cptcovn>0) {
     /* Concatenates waves */            for (z1=1; z1<=cptcoveff; z1++) 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
           }
       Tcode=ivector(1,100);          if (bool==1){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            for(m=firstpass; m<=lastpass; m++){
       ncodemax[1]=1;              k2=anint[m][i]+(mint[m][i]/12.);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                      if(agev[m][i]==0) agev[m][i]=iagemax+1;
    codtab=imatrix(1,100,1,10);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
    h=0;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
    m=pow(2,cptcoveff);                if (m<lastpass) {
                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    for(k=1;k<=cptcoveff; k++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
      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++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
            h++;                  dateintsum=dateintsum+k2;
            if (h>m) h=1;codtab[h][k]=j;                  k2cpt++;
          }                }
        }                /*}*/
      }            }
    }          }
         }
          
    /*for(i=1; i <=m ;i++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      for(k=1; k <=cptcovn; k++){        pstamp(ficresp);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        if  (cptcovn>0) {
      }          fprintf(ficresp, "\n#********** Variable "); 
      printf("\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    }          fprintf(ficresp, "**********\n#");
    scanf("%d",i);*/        }
            for(i=1; i<=nlstate;i++) 
    /* Calculates basic frequencies. Computes observed prevalence at single age          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        and prints on file fileres'p'. */        fprintf(ficresp, "\n");
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);        
         for(i=iagemin; i <= iagemax+3; i++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(i==iagemax+3){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficlog,"Total");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          }else{
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(first==1){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              first=0;
                    printf("See log file for details...\n");
     /* 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] */            fprintf(ficlog,"Age %d", i);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          }
           for(jk=1; jk <=nlstate ; jk++){
     if(mle==1){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              pp[jk] += freq[jk][m][i]; 
     }          }
              for(jk=1; jk <=nlstate ; jk++){
     /*--------- results files --------------*/            for(m=-1, pos=0; m <=0 ; m++)
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);              pos += freq[jk][m][i];
                if(pp[jk]>=1.e-10){
    jk=1;              if(first==1){
    fprintf(ficres,"# Parameters\n");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    printf("# Parameters\n");              }
    for(i=1,jk=1; i <=nlstate; i++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      for(k=1; k <=(nlstate+ndeath); k++){            }else{
        if (k != i)              if(first==1)
          {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
            printf("%d%d ",i,k);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
            fprintf(ficres,"%1d%1d ",i,k);            }
            for(j=1; j <=ncovmodel; j++){          }
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);          for(jk=1; jk <=nlstate ; jk++){
              jk++;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
            }              pp[jk] += freq[jk][m][i];
            printf("\n");          }       
            fprintf(ficres,"\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
          }            pos += pp[jk];
      }            posprop += prop[jk][i];
    }          }
  if(mle==1){          for(jk=1; jk <=nlstate ; jk++){
     /* Computing hessian and covariance matrix */            if(pos>=1.e-5){
     ftolhess=ftol; /* Usually correct */              if(first==1)
     hesscov(matcov, p, npar, delti, ftolhess, func);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     fprintf(ficres,"# Scales\n");            }else{
     printf("# Scales\n");              if(first==1)
      for(i=1,jk=1; i <=nlstate; i++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j <=nlstate+ndeath; j++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         if (j!=i) {            }
           fprintf(ficres,"%1d%1d",i,j);            if( i <= iagemax){
           printf("%1d%1d",i,j);              if(pos>=1.e-5){
           for(k=1; k<=ncovmodel;k++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
             printf(" %.5e",delti[jk]);                /*probs[i][jk][j1]= pp[jk]/pos;*/
             fprintf(ficres," %.5e",delti[jk]);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             jk++;              }
           }              else
           printf("\n");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           fprintf(ficres,"\n");            }
         }          }
       }          
       }          for(jk=-1; jk <=nlstate+ndeath; jk++)
                for(m=-1; m <=nlstate+ndeath; m++)
     k=1;              if(freq[jk][m][i] !=0 ) {
     fprintf(ficres,"# Covariance\n");              if(first==1)
     printf("# Covariance\n");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(i=1;i<=npar;i++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       /*  if (k>nlstate) k=1;              }
       i1=(i-1)/(ncovmodel*nlstate)+1;          if(i <= iagemax)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            fprintf(ficresp,"\n");
       printf("%s%d%d",alph[k],i1,tab[i]);*/          if(first==1)
       fprintf(ficres,"%3d",i);            printf("Others in log...\n");
       printf("%3d",i);          fprintf(ficlog,"\n");
       for(j=1; j<=i;j++){        }
         fprintf(ficres," %.5e",matcov[i][j]);      }
         printf(" %.5e",matcov[i][j]);    }
       }    dateintmean=dateintsum/k2cpt; 
       fprintf(ficres,"\n");   
       printf("\n");    fclose(ficresp);
       k++;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     }    free_vector(pp,1,nlstate);
        free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     while((c=getc(ficpar))=='#' && c!= EOF){    /* End of Freq */
       ungetc(c,ficpar);  }
       fgets(line, MAXLINE, ficpar);  
       puts(line);  /************ Prevalence ********************/
       fputs(line,ficparo);  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)
     }  {  
     ungetc(c,ficpar);    /* 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).
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       We still use firstpass and lastpass as another selection.
        */
     if (fage <= 2) {   
       bage = agemin;    int i, m, jk, k1, i1, j1, bool, z1,j;
       fage = agemax;    double ***freq; /* Frequencies */
     }    double *pp, **prop;
     double pos,posprop; 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    double  y2; /* in fractional years */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int iagemin, iagemax;
   
        iagemin= (int) agemin;
 /*------------ gnuplot -------------*/    iagemax= (int) agemax;
 chdir(pathcd);    /*pp=vector(1,nlstate);*/
   if((ficgp=fopen("graph.plt","w"))==NULL) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     printf("Problem with file graph.gp");goto end;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   }    j1=0;
 #ifdef windows    
   fprintf(ficgp,"cd \"%s\" \n",pathc);    j=cptcoveff;
 #endif    if (cptcovn<1) {j=1;ncodemax[1]=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 ++) {        
         for (i=1; i<=nlstate; i++)  
 #ifdef windows          for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);            prop[i][m]=0.0;
 #endif       
 #ifdef unix        for (i=1; i<=imx; i++) { /* Each individual */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          bool=1;
 #endif          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 for (i=1; i<= nlstate ; i ++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                bool=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          } 
 }          if (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);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for (i=1; i<= nlstate ; i ++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
      for (i=1; i<= nlstate ; i ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 }                    prop[s[m][i]][iagemax+3] += weight[i]; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                } 
 #ifdef unix              }
 fprintf(ficgp,"\nset ter gif small size 400,300");            } /* end selection of waves */
 #endif          }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
    }        for(i=iagemin; i <= iagemax+3; i++){  
   }          
   /*2 eme*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
   for (k1=1; k1<= m ; k1 ++) {          } 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
              for(jk=1; jk <=nlstate ; jk++){     
     for (i=1; i<= nlstate+1 ; i ++) {            if( i <=  iagemax){ 
       k=2*i;              if(posprop>=1.e-5){ 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                probs[i][jk][j1]= prop[jk][i]/posprop;
       for (j=1; j<= nlstate+1 ; j ++) {              } else
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            } 
 }            }/* end jk */ 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        }/* end i */ 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      } /* end i1 */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    } /* end k1 */
       for (j=1; j<= nlstate+1 ; j ++) {    
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");    /*free_vector(pp,1,nlstate);*/
 }      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fprintf(ficgp,"\" t\"\" w l 0,");  }  /* End of prevalence */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  /************* Waves Concatenation ***************/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  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)
 }    {
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       else fprintf(ficgp,"\" t\"\" w l 0,");       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
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);       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.
         */
   /*3eme*/  
     int i, mi, m;
   for (k1=1; k1<= m ; k1 ++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for (cpt=1; cpt<= nlstate ; cpt ++) {       double sum=0., jmean=0.;*/
       k=2+nlstate*(cpt-1);    int first;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    int j, k=0,jk, ju, jl;
       for (i=1; i< nlstate ; i ++) {    double sum=0.;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    first=0;
       }    jmin=1e+5;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    jmax=-1;
     }    jmean=0.;
   }    for(i=1; i<=imx; i++){
        mi=0;
   /* CV preval stat */      m=firstpass;
   for (k1=1; k1<= m ; k1 ++) {      while(s[m][i] <= nlstate){
     for (cpt=1; cpt<nlstate ; cpt ++) {        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       k=3;          mw[++mi][i]=m;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        if(m >=lastpass)
       for (i=1; i< nlstate ; i ++)          break;
         fprintf(ficgp,"+$%d",k+i+1);        else
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          m++;
            }/* end while */
       l=3+(nlstate+ndeath)*cpt;      if (s[m][i] > nlstate){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        mi++;     /* Death is another wave */
       for (i=1; i< nlstate ; i ++) {        /* if(mi==0)  never been interviewed correctly before death */
         l=3+(nlstate+ndeath)*cpt;           /* Only death is a correct wave */
         fprintf(ficgp,"+$%d",l+i+1);        mw[mi][i]=m;
       }      }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      wav[i]=mi;
     }      if(mi==0){
   }          nbwarn++;
         if(first==0){
   /* proba elementaires */          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
    for(i=1,jk=1; i <=nlstate; i++){          first=1;
     for(k=1; k <=(nlstate+ndeath); k++){        }
       if (k != i) {        if(first==1){
         for(j=1; j <=ncovmodel; j++){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        }
           /*fprintf(ficgp,"%s",alph[1]);*/      } /* end mi==0 */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    } /* End individuals */
           jk++;  
           fprintf(ficgp,"\n");    for(i=1; i<=imx; i++){
         }      for(mi=1; mi<wav[i];mi++){
       }        if (stepm <=0)
     }          dh[mi][i]=1;
     }        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   for(jk=1; jk <=m; jk++) {            if (agedc[i] < 2*AGESUP) {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
    i=1;              if(j==0) j=1;  /* Survives at least one month after exam */
    for(k2=1; k2<=nlstate; k2++) {              else if(j<0){
      k3=i;                nberr++;
      for(k=1; k<=(nlstate+ndeath); k++) {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
        if (k != k2){                j=1; /* Temporary Dangerous patch */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
 ij=1;                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]);
         for(j=3; j <=ncovmodel; j++) {                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);
           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]]]);              k=k+1;
             ij++;              if (j >= jmax){
           }                jmax=j;
           else                ijmax=i;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              }
         }              if (j <= jmin){
           fprintf(ficgp,")/(1");                jmin=j;
                        ijmin=i;
         for(k1=1; k1 <=nlstate; k1++){                }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              sum=sum+j;
 ij=1;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           for(j=3; j <=ncovmodel; j++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           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{
           }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           else  /*        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]); */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
           }            k=k+1;
           fprintf(ficgp,")");            if (j >= jmax) {
         }              jmax=j;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              ijmax=i;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            }
         i=i+ncovmodel;            else if (j <= jmin){
        }              jmin=j;
      }              ijmin=i;
    }            }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                if(j<0){
   fclose(ficgp);              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]);
 chdir(path);              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]);
     free_matrix(agev,1,maxwav,1,imx);            }
     free_ivector(wav,1,imx);            sum=sum+j;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          jk= j/stepm;
              jl= j -jk*stepm;
     free_imatrix(s,1,maxwav+1,1,n);          ju= j -(jk+1)*stepm;
              if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                if(jl==0){
     free_ivector(num,1,n);              dh[mi][i]=jk;
     free_vector(agedc,1,n);              bh[mi][i]=0;
     free_vector(weight,1,n);            }else{ /* We want a negative bias in order to only have interpolation ie
     /*free_matrix(covar,1,NCOVMAX,1,n);*/                    * to avoid the price of an extra matrix product in likelihood */
     fclose(ficparo);              dh[mi][i]=jk+1;
     fclose(ficres);              bh[mi][i]=ju;
     /*  }*/            }
              }else{
    /*________fin mle=1_________*/            if(jl <= -ju){
                  dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                     * is higher than the multiple of stepm and negative otherwise.
     /* No more information from the sample is required now */                                   */
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){            else{
     ungetc(c,ficpar);              dh[mi][i]=jk+1;
     fgets(line, MAXLINE, ficpar);              bh[mi][i]=ju;
     puts(line);            }
     fputs(line,ficparo);            if(dh[mi][i]==0){
   }              dh[mi][i]=1; /* At least one step */
   ungetc(c,ficpar);              bh[mi][i]=ju; /* At least one step */
                /*  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);*/
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          } /* end if mle */
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        }
 /*--------- index.htm --------*/      } /* end wave */
     }
   strcpy(optionfilehtm,optionfile);    jmean=sum/k;
   strcat(optionfilehtm,".htm");    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);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    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);
     printf("Problem with %s \n",optionfilehtm);goto end;   }
   }  
   /*********** Tricode ****************************/
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">  void tricode(int *Tvar, int **nbcode, int imx)
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  {
 Total number of observations=%d <br>    /* Uses cptcovn+2*cptcovprod as the number of covariates */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
 <hr  size=\"2\" color=\"#EC5E5E\">  
 <li>Outputs files<br><br>\n    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    int modmaxcovj=0; /* Modality max of covariates j */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    cptcoveff=0; 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>   
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    for (k=0; k<maxncov; k++) Ndum[k]=0;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                                 modality of this covariate Vj*/ 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                                        modality of the nth covariate of individual i. */
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
  fprintf(fichtm," <li>Graphs</li><p>");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > modmaxcovj) modmaxcovj=ij; 
  m=cptcoveff;        /* getting the maximum value of the modality of the covariate
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            female is 1, then modmaxcovj=1.*/
  j1=0;      }
  for(k1=1; k1<=m;k1++){      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
    for(i1=1; i1<=ncodemax[k1];i1++){      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
        j1++;        if( Ndum[i] != 0 )
        if (cptcovn > 0) {          ncodemax[j]++; 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        /* Number of modalities of the j th covariate. In fact
          for (cpt=1; cpt<=cptcoveff;cpt++)           ncodemax[j]=2 (dichotom. variables only) but it could be more for
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);           historical reasons */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      } /* Ndum[-1] number of undefined modalities */
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          ij=1; 
        for(cpt=1; cpt<nlstate;cpt++){      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
        }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     for(cpt=1; cpt<=nlstate;cpt++) {                                       k is a modality. If we have model=V1+V1*sex 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
 interval) in state (%d): v%s%d%d.gif <br>            ij++;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            }
      }          if (ij > ncodemax[j]) break; 
      for(cpt=1; cpt<=nlstate;cpt++) {        }  /* end of loop on */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      } /* end of loop on modality */ 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
      }    
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    for (k=0; k< maxncov; k++) Ndum[k]=0;
 health expectancies in states (1) and (2): e%s%d.gif<br>    
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
 fprintf(fichtm,"\n</body>");     /* 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 */
  }     Ndum[ij]++;
 fclose(fichtm);   }
   
   /*--------------- Prevalence limit --------------*/   ij=1;
     for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   strcpy(filerespl,"pl");     if((Ndum[i]!=0) && (i<=ncovcol)){
   strcat(filerespl,fileres);       Tvaraff[ij]=i; /*For printing */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       ij++;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;     }
   }   }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);   ij--;
   fprintf(ficrespl,"#Prevalence limit\n");   cptcoveff=ij; /*Number of simple covariates*/
   fprintf(ficrespl,"#Age ");  }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");  /*********** Health Expectancies ****************/
    
   prlim=matrix(1,nlstate,1,nlstate);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   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 */    /* Health expectancies, no variances */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int nhstepma, nstepma; /* Decreasing with age */
   k=0;    double age, agelim, hf;
   agebase=agemin;    double ***p3mat;
   agelim=agemax;    double eip;
   ftolpl=1.e-10;  
   i1=cptcoveff;    pstamp(ficreseij);
   if (cptcovn < 1){i1=1;}    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
   for(cptcov=1;cptcov<=i1;cptcov++){    for(i=1; i<=nlstate;i++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(j=1; j<=nlstate;j++){
         k=k+1;        fprintf(ficreseij," e%1d%1d ",i,j);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      }
         fprintf(ficrespl,"\n#******");      fprintf(ficreseij," e%1d. ",i);
         for(j=1;j<=cptcoveff;j++)    }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficreseij,"\n");
         fprintf(ficrespl,"******\n");  
            
         for (age=agebase; age<=agelim; age++){    if(estepm < stepm){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      printf ("Problem %d lower than %d\n",estepm, stepm);
           fprintf(ficrespl,"%.0f",age );    }
           for(i=1; i<=nlstate;i++)    else  hstepm=estepm;   
           fprintf(ficrespl," %.5f", prlim[i][i]);    /* We compute the life expectancy from trapezoids spaced every estepm months
           fprintf(ficrespl,"\n");     * This is mainly to measure the difference between two models: for example
         }     * if stepm=24 months pijx are given only every 2 years and by summing them
       }     * we are calculating an estimate of the Life Expectancy assuming a linear 
     }     * progression in between and thus overestimating or underestimating according
   fclose(ficrespl);     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   /*------------- h Pij x at various ages ------------*/     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);     * curvature will be obtained if estepm is as small as stepm. */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* 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. 
   printf("Computing pij: result on file '%s' \n", filerespij);       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   stepsize=(int) (stepm+YEARM-1)/YEARM;       Look at hpijx to understand the reason of that which relies in memory size
   /*if (stepm<=24) stepsize=2;*/       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   agelim=AGESUP;       survival function given by stepm (the optimization length). Unfortunately it
   hstepm=stepsize*YEARM; /* Every year of age */       means that if the survival funtion is printed only each two years of age and if
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       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.
   k=0;    */
   for(cptcov=1;cptcov<=i1;cptcov++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    agelim=AGESUP;
         fprintf(ficrespij,"\n#****** ");    /* If stepm=6 months */
         for(j=1;j<=cptcoveff;j++)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         fprintf(ficrespij,"******\n");      
          /* nhstepm age range expressed in number of stepm */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /* if (stepm >= YEARM) hstepm=1;*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           oldm=oldms;savm=savms;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");    for (age=bage; age<=fage; age ++){ 
           for(i=1; i<=nlstate;i++)      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             for(j=1; j<=nlstate+ndeath;j++)      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
               fprintf(ficrespij," %1d-%1d",i,j);      /* if (stepm >= YEARM) hstepm=1;*/
           fprintf(ficrespij,"\n");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      /* If stepm=6 months */
             for(i=1; i<=nlstate;i++)      /* Computed by stepm unit matrices, product of hstepma matrices, stored
               for(j=1; j<=nlstate+ndeath;j++)         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      
             fprintf(ficrespij,"\n");      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           }      
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           fprintf(ficrespij,"\n");      
         }      printf("%d|",(int)age);fflush(stdout);
     }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   }      
       /* Computing expectancies */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   fclose(ficrespij);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   /*---------- Forecasting ------------------*/            
             /* 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]);*/
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);          }
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      fprintf(ficreseij,"%3.0f",age );
   }      for(i=1; i<=nlstate;i++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);        eip=0;
         for(j=1; j<=nlstate;j++){
   /* Mobile average */          eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   /* for (agedeb=bage; agedeb<=fage; agedeb++)        }
     for (i=1; i<=nlstate;i++)        fprintf(ficreseij,"%9.4f", eip );
       for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++)      }
       printf("%f %d i=%d j1=%d\n", probs[(int)agedeb][i][cptcod],(int) agedeb,i,cptcod);*/      fprintf(ficreseij,"\n");
       
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (mobilav==1) {    printf("\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficlog,"\n");
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    
       for (i=1; i<=nlstate;i++)  }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
      
     for (agedeb=bage+4; agedeb<=fage; agedeb++){  {
       for (i=1; i<=nlstate;i++){    /* Covariances of health expectancies eij and of total life expectancies according
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){     to initial status i, ei. .
           for (cpt=0;cpt<=4;cpt++){    */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           }    int nhstepma, nstepma; /* Decreasing with age */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    double age, agelim, hf;
         }    double ***p3matp, ***p3matm, ***varhe;
       }    double **dnewm,**doldm;
     }      double *xp, *xm;
   }    double **gp, **gm;
     double ***gradg, ***trgradg;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int theta;
   if (stepm<=24) stepsize=2;  
     double eip, vip;
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    xp=vector(1,npar);
   hstepm=12;    xm=vector(1,npar);
    k=0;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    pstamp(ficresstdeij);
       fprintf(ficresf,"\n#****** ");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
       for(j=1;j<=cptcoveff;j++) {    fprintf(ficresstdeij,"# Age");
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i<=nlstate;i++){
       }      for(j=1; j<=nlstate;j++)
              fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresf,"******\n");      fprintf(ficresstdeij," e%1d. ",i);
     }
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");    fprintf(ficresstdeij,"\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
     pstamp(ficrescveij);
       for (agedeb=fage; agedeb>=bage; agedeb--){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);    fprintf(ficrescveij,"# Age");
        if (mobilav==1) {    for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++){
           fprintf(ficresf,"%.5f ",mobaverage[(int)agedeb][j][cptcod]);        cptj= (j-1)*nlstate+i;
         }        for(i2=1; i2<=nlstate;i2++)
         else {          for(j2=1; j2<=nlstate;j2++){
           for(j=1; j<=nlstate;j++)            cptj2= (j2-1)*nlstate+i2;
           fprintf(ficresf,"%.5f ",probs[(int)agedeb][j][cptcod]);            if(cptj2 <= cptj)
         }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
                  }
       for(j=1; j<=ndeath;j++) fprintf(ficresf,"0.");      }
       }    fprintf(ficrescveij,"\n");
       for (cpt=1; cpt<=NCOVMAX;cpt++)      
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    else  hstepm=estepm;   
         /*printf("stepm=%d hstepm=%d nhstepm=%d \n",stepm,hstepm,nhstepm);*/    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * if stepm=24 months pijx are given only every 2 years and by summing them
         oldm=oldms;savm=savms;     * we are calculating an estimate of the Life Expectancy assuming a linear 
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * progression in between and thus overestimating or underestimating according
                     * to the curvature of the survival function. If, for the same date, we 
         for (h=0; h<=nhstepm; h++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
             * to compare the new estimate of Life expectancy with the same linear 
           if (h*hstepm/YEARM*stepm==cpt)     * hypothesis. A more precise result, taking into account a more precise
  fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);     * curvature will be obtained if estepm is as small as stepm. */
            
           for(j=1; j<=nlstate+ndeath;j++) {    /* For example we decided to compute the life expectancy with the smallest unit */
             kk1=0.;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             for(i=1; i<=nlstate;i++) {               nhstepm is the number of hstepm from age to agelim 
               if (mobilav==1)       nstepm is the number of stepm from age to agelin. 
               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];       Look at hpijx to understand the reason of that which relies in memory size
               else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];       and note for a fixed period like estepm months */
             }        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);       survival function given by stepm (the optimization length). Unfortunately it
           }       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       results. So we changed our mind and took the option of the best precision.
       }    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* If stepm=6 months */
   fclose(ficresf);    /* nhstepm age range expressed in number of stepm */
   /*---------- Health expectancies and variances ------------*/    agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   strcpy(filerest,"t");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   strcat(filerest,fileres);    /* if (stepm >= YEARM) hstepm=1;*/
   if((ficrest=fopen(filerest,"w"))==NULL) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    
   }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   strcpy(filerese,"e");    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   strcat(filerese,fileres);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    for (age=bage; age<=fage; age ++){ 
   }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
  strcpy(fileresv,"v");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      /* If stepm=6 months */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){      /* Computing  Variances of health expectancies */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       k=k+1;         decrease memory allocation */
       fprintf(ficrest,"\n#****** ");      for(theta=1; theta <=npar; theta++){
       for(j=1;j<=cptcoveff;j++)        for(i=1; i<=npar; i++){ 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficrest,"******\n");          xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
       fprintf(ficreseij,"\n#****** ");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       for(j=1;j<=cptcoveff;j++)        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
       fprintf(ficresvij,"\n#****** ");            for(h=0; h<=nhstepm-1; h++){
       for(j=1;j<=cptcoveff;j++)              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       fprintf(ficresvij,"******\n");            }
           }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }
       oldm=oldms;savm=savms;       
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          for(ij=1; ij<= nlstate*nlstate; ij++)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for(h=0; h<=nhstepm-1; h++){
       oldm=oldms;savm=savms;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          }
            }/* End theta */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      
       fprintf(ficrest,"\n");      for(h=0; h<=nhstepm-1; h++)
                for(j=1; j<=nlstate*nlstate;j++)
       hf=1;          for(theta=1; theta <=npar; theta++)
       if (stepm >= YEARM) hf=stepm/YEARM;            trgradg[h][j][theta]=gradg[h][theta][j];
       epj=vector(1,nlstate+1);      
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       for(ij=1;ij<=nlstate*nlstate;ij++)
         if (popbased==1) {        for(ji=1;ji<=nlstate*nlstate;ji++)
           for(i=1; i<=nlstate;i++)          varhe[ij][ji][(int)age] =0.;
             prlim[i][i]=probs[(int)age][i][k];  
         }       printf("%d|",(int)age);fflush(stdout);
               fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         fprintf(ficrest," %.0f",age);       for(h=0;h<=nhstepm-1;h++){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        for(k=0;k<=nhstepm-1;k++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           }          for(ij=1;ij<=nlstate*nlstate;ij++)
           epj[nlstate+1] +=epj[j];            for(ji=1;ji<=nlstate*nlstate;ji++)
         }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         for(i=1, vepp=0.;i <=nlstate;i++)        }
           for(j=1;j <=nlstate;j++)      }
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      /* Computing expectancies */
         for(j=1;j <=nlstate;j++){      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++)
         fprintf(ficrest,"\n");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     }            
   }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
          
                  }
   
       fprintf(ficresstdeij,"%3.0f",age );
  fclose(ficreseij);      for(i=1; i<=nlstate;i++){
  fclose(ficresvij);        eip=0.;
   fclose(ficrest);        vip=0.;
   fclose(ficpar);        for(j=1; j<=nlstate;j++){
   free_vector(epj,1,nlstate+1);          eip += eij[i][j][(int)age];
   /*  scanf("%d ",i); */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   /*------- Variance limit prevalence------*/            fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
 strcpy(fileresvpl,"vpl");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   strcat(fileresvpl,fileres);      }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      fprintf(ficresstdeij,"\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);      fprintf(ficrescveij,"%3.0f",age );
   }      for(i=1; i<=nlstate;i++)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
  k=0;          for(i2=1; i2<=nlstate;i2++)
  for(cptcov=1;cptcov<=i1;cptcov++){            for(j2=1; j2<=nlstate;j2++){
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              cptj2= (j2-1)*nlstate+i2;
      k=k+1;              if(cptj2 <= cptj)
      fprintf(ficresvpl,"\n#****** ");                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
      for(j=1;j<=cptcoveff;j++)            }
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
      fprintf(ficresvpl,"******\n");      fprintf(ficrescveij,"\n");
           
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    }
      oldm=oldms;savm=savms;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
    }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
  }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficresvpl);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
   /*---------- End : free ----------------*/    fprintf(ficlog,"\n");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      free_vector(xm,1,npar);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_vector(xp,1,npar);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   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);  /************ Variance ******************/
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  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[])
    {
   free_matrix(matcov,1,npar,1,npar);    /* Variance of health expectancies */
   free_vector(delti,1,npar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
      /* double **newm;*/
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
   printf("End of Imach\n");    int i, j, nhstepm, hstepm, h, nstepm ;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int k, cptcode;
      double *xp;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    double **gp, **gm;  /* for var eij */
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double ***gradg, ***trgradg; /*for var eij */
   /*------ End -----------*/    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
  end:    double ***p3mat;
 #ifdef windows    double age,agelim, hf;
  chdir(pathcd);    double ***mobaverage;
 #endif    int theta;
      char digit[4];
  system("..\\gp37mgw\\wgnuplot graph.plt");    char digitp[25];
   
 #ifdef windows    char fileresprobmorprev[FILENAMELENGTH];
   while (z[0] != 'q') {  
     chdir(pathcd);    if(popbased==1){
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      if(mobilav!=0)
     scanf("%s",z);        strcpy(digitp,"-populbased-mobilav-");
     if (z[0] == 'c') system("./imach");      else strcpy(digitp,"-populbased-nomobil-");
     else if (z[0] == 'e') {    }
       chdir(path);    else 
       system(optionfilehtm);      strcpy(digitp,"-stablbased-");
     }  
     else if (z[0] == 'q') exit(0);    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #endif      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; 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); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     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);
                       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);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #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(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\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.1.14  
changed lines
  Added in v.1.140


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