Diff for /imach/src/imach.c between versions 1.18 and 1.144

version 1.18, 2002/02/20 17:17:09 version 1.144, 2014/02/10 22:17:31
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.144  2014/02/10 22:17:31  brouard
   individuals from different ages are interviewed on their health status    *** empty log message ***
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.143  2014/01/26 09:45:38  brouard
   Health expectancies are computed from the transistions observed between    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   reach the Maximum Likelihood of the parameters involved in the model.    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.142  2014/01/26 03:57:36  brouard
   to be observed in state i at the first wave. Therefore the model is:    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.141  2014/01/26 02:42:01  brouard
   More covariates you add, less is the speed of the convergence.    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.140  2011/09/02 10:37:54  brouard
   delay between waves is not identical for each individual, or if some    Summary: times.h is ok with mingw32 now.
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.139  2010/06/14 07:50:17  brouard
   hPijx is the probability to be    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   observed in state i at age x+h conditional to the observed state i at age    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.138  2010/04/30 18:19:40  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    *** empty log message ***
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
   Also this programme outputs the covariance matrix of the parameters but also    than V1+V2. A lot of change to be done. Unstable.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.136  2010/04/26 20:30:53  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): merging some libgsl code. Fixing computation
            Institut national d'études démographiques, Paris.    of likelione (using inter/intrapolation if mle = 0) in order to
   This software have been partly granted by Euro-REVES, a concerted action    get same likelihood as if mle=1.
   from the European Union.    Some cleaning of code and comments added.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.135  2009/10/29 15:33:14  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   **********************************************************************/  
      Revision 1.134  2009/10/29 13:18:53  brouard
 #include <math.h>    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.133  2009/07/06 10:21:25  brouard
 #include <unistd.h>    just nforces
   
 #define MAXLINE 256    Revision 1.132  2009/07/06 08:22:05  brouard
 #define FILENAMELENGTH 80    Many tings
 /*#define DEBUG*/  
 #define windows    Revision 1.131  2009/06/20 16:22:47  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Some dimensions resccaled
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.130  2009/05/26 06:44:34  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): Max Covariate is now set to 20 instead of 8. A
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.129  2007/08/31 13:49:27  lievre
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.128  2006/06/30 13:02:05  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Clarifications on computing e.j
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int nvar;    loop. Now we define nhstepma in the age loop.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): In order to speed up (in case of numerous covariates) we
 int npar=NPARMAX;    compute health expectancies (without variances) in a first step
 int nlstate=2; /* Number of live states */    and then all the health expectancies with variances or standard
 int ndeath=1; /* Number of dead states */    deviation (needs data from the Hessian matrices) which slows the
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    computation.
 int popbased=0;    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.126  2006/04/28 17:23:28  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Yes the sum of survivors was wrong since
 int mle, weightopt;    imach-114 because nhstepm was no more computed in the age
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    loop. Now we define nhstepma in the age loop.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Version 0.98h
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.125  2006/04/04 15:20:31  lievre
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Errors in calculation of health expectancies. Age was not initialized.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Forecasting file added.
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.124  2006/03/22 17:13:53  lievre
   char filerese[FILENAMELENGTH];    Parameters are printed with %lf instead of %f (more numbers after the comma).
  FILE  *ficresvij;    The log-likelihood is printed in the log file
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.123  2006/03/20 10:52:43  brouard
   char fileresvpl[FILENAMELENGTH];    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 #define NR_END 1  
 #define FREE_ARG char*    * imach.c (Module): Weights can have a decimal point as for
 #define FTOL 1.0e-10    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 #define NRANSI    Modification of warning when the covariates values are not 0 or
 #define ITMAX 200    1.
     Version 0.98g
 #define TOL 2.0e-4  
     Revision 1.122  2006/03/20 09:45:41  brouard
 #define CGOLD 0.3819660    (Module): Weights can have a decimal point as for
 #define ZEPS 1.0e-10    English (a comma might work with a correct LC_NUMERIC environment,
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define GOLD 1.618034    1.
 #define GLIMIT 100.0    Version 0.98g
 #define TINY 1.0e-20  
     Revision 1.121  2006/03/16 17:45:01  lievre
 static double maxarg1,maxarg2;    * imach.c (Module): Comments concerning covariates added
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Module): refinements in the computation of lli if
      status=-2 in order to have more reliable computation if stepm is
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    not 1 month. Version 0.98f
 #define rint(a) floor(a+0.5)  
     Revision 1.120  2006/03/16 15:10:38  lievre
 static double sqrarg;    (Module): refinements in the computation of lli if
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    status=-2 in order to have more reliable computation if stepm is
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    not 1 month. Version 0.98f
   
 int imx;    Revision 1.119  2006/03/15 17:42:26  brouard
 int stepm;    (Module): Bug if status = -2, the loglikelihood was
 /* Stepm, step in month: minimum step interpolation*/    computed as likelihood omitting the logarithm. Version O.98e
   
 int m,nb;    Revision 1.118  2006/03/14 18:20:07  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): varevsij Comments added explaining the second
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    table of variances if popbased=1 .
 double **pmmij, ***probs, ***mobaverage;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 double *weight;    (Module): Version 0.98d
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.117  2006/03/14 17:16:22  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double ftolhess; /* Tolerance for computing hessian */    (Module): Function pstamp added
     (Module): Version 0.98d
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    Revision 1.116  2006/03/06 10:29:27  brouard
 {    (Module): Variance-covariance wrong links and
    char *s;                             /* pointer */    varian-covariance of ej. is needed (Saito).
    int  l1, l2;                         /* length counters */  
     Revision 1.115  2006/02/27 12:17:45  brouard
    l1 = strlen( path );                 /* length of path */    (Module): One freematrix added in mlikeli! 0.98c
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.114  2006/02/26 12:57:58  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Some improvements in processing parameter
 #if     defined(__bsd__)                /* get current working directory */    filename with strsep.
       extern char       *getwd( );  
     Revision 1.113  2006/02/24 14:20:24  brouard
       if ( getwd( dirc ) == NULL ) {    (Module): Memory leaks checks with valgrind and:
 #else    datafile was not closed, some imatrix were not freed and on matrix
       extern char       *getcwd( );    allocation too.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.112  2006/01/30 09:55:26  brouard
 #endif    (Module): Back to gnuplot.exe instead of wgnuplot.exe
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.111  2006/01/25 20:38:18  brouard
       strcpy( name, path );             /* we've got it */    (Module): Lots of cleaning and bugs added (Gompertz)
    } else {                             /* strip direcotry from path */    (Module): Comments can be added in data file. Missing date values
       s++;                              /* after this, the filename */    can be a simple dot '.'.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.110  2006/01/25 00:51:50  brouard
       strcpy( name, s );                /* save file name */    (Module): Lots of cleaning and bugs added (Gompertz)
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.109  2006/01/24 19:37:15  brouard
    }    (Module): Comments (lines starting with a #) are allowed in data.
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.108  2006/01/19 18:05:42  lievre
    return( 0 );                         /* we're done */    Gnuplot problem appeared...
 }    To be fixed
   
     Revision 1.107  2006/01/19 16:20:37  brouard
 /******************************************/    Test existence of gnuplot in imach path
   
 void replace(char *s, char*t)    Revision 1.106  2006/01/19 13:24:36  brouard
 {    Some cleaning and links added in html output
   int i;  
   int lg=20;    Revision 1.105  2006/01/05 20:23:19  lievre
   i=0;    *** empty log message ***
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.104  2005/09/30 16:11:43  lievre
     (s[i] = t[i]);    (Module): sump fixed, loop imx fixed, and simplifications.
     if (t[i]== '\\') s[i]='/';    (Module): If the status is missing at the last wave but we know
   }    that the person is alive, then we can code his/her status as -2
 }    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 int nbocc(char *s, char occ)    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 {    the healthy state at last known wave). Version is 0.98
   int i,j=0;  
   int lg=20;    Revision 1.103  2005/09/30 15:54:49  lievre
   i=0;    (Module): sump fixed, loop imx fixed, and simplifications.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.102  2004/09/15 17:31:30  brouard
   if  (s[i] == occ ) j++;    Add the possibility to read data file including tab characters.
   }  
   return j;    Revision 1.101  2004/09/15 10:38:38  brouard
 }    Fix on curr_time
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.100  2004/07/12 18:29:06  brouard
 {    Add version for Mac OS X. Just define UNIX in Makefile
   int i,lg,j,p=0;  
   i=0;    Revision 1.99  2004/06/05 08:57:40  brouard
   for(j=0; j<=strlen(t)-1; j++) {    *** empty log message ***
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
   lg=strlen(t);    directly from the data i.e. without the need of knowing the health
   for(j=0; j<p; j++) {    state at each age, but using a Gompertz model: log u =a + b*age .
     (u[j] = t[j]);    This is the basic analysis of mortality and should be done before any
   }    other analysis, in order to test if the mortality estimated from the
      u[p]='\0';    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    The same imach parameter file can be used but the option for mle should be -3.
   }  
 }    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.
 /********************** nrerror ********************/  
     The output is very simple: only an estimate of the intercept and of
 void nrerror(char error_text[])    the slope with 95% confident intervals.
 {  
   fprintf(stderr,"ERREUR ...\n");    Current limitations:
   fprintf(stderr,"%s\n",error_text);    A) Even if you enter covariates, i.e. with the
   exit(1);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 }    B) There is no computation of Life Expectancy nor Life Table.
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.97  2004/02/20 13:25:42  lievre
 {    Version 0.96d. Population forecasting command line is (temporarily)
   double *v;    suppressed.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.96  2003/07/15 15:38:55  brouard
   return v-nl+NR_END;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 }    rewritten within the same printf. Workaround: many printfs.
   
 /************************ free vector ******************/    Revision 1.95  2003/07/08 07:54:34  brouard
 void free_vector(double*v, int nl, int nh)    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   free((FREE_ARG)(v+nl-NR_END));    matrix (cov(a12,c31) instead of numbers.
 }  
     Revision 1.94  2003/06/27 13:00:02  brouard
 /************************ivector *******************************/    Just cleaning
 int *ivector(long nl,long nh)  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   int *v;    (Module): On windows (cygwin) function asctime_r doesn't
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    exist so I changed back to asctime which exists.
   if (!v) nrerror("allocation failure in ivector");    (Module): Version 0.96b
   return v-nl+NR_END;  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /******************free ivector **************************/    exist so I changed back to asctime which exists.
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Repository): Duplicated warning errors corrected.
 }    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 /******************* imatrix *******************************/    is stamped in powell.  We created a new html file for the graphs
 int **imatrix(long nrl, long nrh, long ncl, long nch)    concerning matrix of covariance. It has extension -cov.htm.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.90  2003/06/24 12:34:15  brouard
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): Some bugs corrected for windows. Also, when
   int **m;    mle=-1 a template is output in file "or"mypar.txt with the design
      of the covariance matrix to be input.
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.89  2003/06/24 12:30:52  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Some bugs corrected for windows. Also, when
   m += NR_END;    mle=-1 a template is output in file "or"mypar.txt with the design
   m -= nrl;    of the covariance matrix to be input.
    
      Revision 1.88  2003/06/23 17:54:56  brouard
   /* allocate rows and set pointers to them */    * 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.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.87  2003/06/18 12:26:01  brouard
   m[nrl] += NR_END;    Version 0.96
   m[nrl] -= ncl;  
      Revision 1.86  2003/06/17 20:04:08  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Change position of html and gnuplot routines and added
      routine fileappend.
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.85  2003/06/17 13:12:43  brouard
 }    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 /****************** free_imatrix *************************/    prior to the death. In this case, dh was negative and likelihood
 void free_imatrix(m,nrl,nrh,ncl,nch)    was wrong (infinity). We still send an "Error" but patch by
       int **m;    assuming that the date of death was just one stepm after the
       long nch,ncl,nrh,nrl;    interview.
      /* free an int matrix allocated by imatrix() */    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    memory allocation. But we also truncated to 8 characters (left
   free((FREE_ARG) (m+nrl-NR_END));    truncation)
 }    (Repository): No more line truncation errors.
   
 /******************* matrix *******************************/    Revision 1.84  2003/06/13 21:44:43  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    many times. Probs is memory consuming and must be used with
   double **m;    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.83  2003/06/10 13:39:11  lievre
   m += NR_END;    *** empty log message ***
   m -= nrl;  
     Revision 1.82  2003/06/05 15:57:20  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Add log in  imach.c and  fullversion number is now printed.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  */
   m[nrl] -= ncl;  /*
      Interpolated Markov Chain
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Short summary of the programme:
 }    
     This program computes Healthy Life Expectancies from
 /*************************free matrix ************************/    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    case of a health survey which is our main interest) -2- at least a
   free((FREE_ARG)(m+nrl-NR_END));    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 /******************* ma3x *******************************/    model. More health states you consider, more time is necessary to reach the
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Maximum Likelihood of the parameters involved in the model.  The
 {    simplest model is the multinomial logistic model where pij is the
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    probability to be observed in state j at the second wave
   double ***m;    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    'age' is age and 'sex' is a covariate. If you want to have a more
   if (!m) nrerror("allocation failure 1 in matrix()");    complex model than "constant and age", you should modify the program
   m += NR_END;    where the markup *Covariates have to be included here again* invites
   m -= nrl;    you to do it.  More covariates you add, slower the
     convergence.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    The advantage of this computer programme, compared to a simple
   m[nrl] += NR_END;    multinomial logistic model, is clear when the delay between waves is not
   m[nrl] -= ncl;    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    account using an interpolation or extrapolation.  
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    hPijx is the probability to be observed in state i at age x+h
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    conditional to the observed state i at age x. The delay 'h' can be
   m[nrl][ncl] += NR_END;    split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl][ncl] -= nll;    states. This elementary transition (by month, quarter,
   for (j=ncl+1; j<=nch; j++)    semester or year) is modelled as a multinomial logistic.  The hPx
     m[nrl][j]=m[nrl][j-1]+nlay;    matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
   for (i=nrl+1; i<=nrh; i++) {    hPijx.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Also this programme outputs the covariance matrix of the parameters but also
       m[i][j]=m[i][j-1]+nlay;    of the life expectancies. It also computes the period (stable) prevalence. 
   }    
   return m;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 }             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 /*************************free ma3x ************************/    from the European Union.
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    can be accessed at http://euroreves.ined.fr/imach .
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 }    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 /***************** f1dim *************************/    **********************************************************************/
 extern int ncom;  /*
 extern double *pcom,*xicom;    main
 extern double (*nrfunc)(double []);    read parameterfile
      read datafile
 double f1dim(double x)    concatwav
 {    freqsummary
   int j;    if (mle >= 1)
   double f;      mlikeli
   double *xt;    print results files
      if mle==1 
   xt=vector(1,ncom);       computes hessian
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    read end of parameter file: agemin, agemax, bage, fage, estepm
   f=(*nrfunc)(xt);        begin-prev-date,...
   free_vector(xt,1,ncom);    open gnuplot file
   return f;    open html file
 }    period (stable) prevalence
      for age prevalim()
 /*****************brent *************************/    h Pij x
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   int iter;    health expectancies
   double a,b,d,etemp;    Variance-covariance of DFLE
   double fu,fv,fw,fx;    prevalence()
   double ftemp;     movingaverage()
   double p,q,r,tol1,tol2,u,v,w,x,xm;    varevsij() 
   double e=0.0;    if popbased==1 varevsij(,popbased)
      total life expectancies
   a=(ax < cx ? ax : cx);    Variance of period (stable) prevalence
   b=(ax > cx ? ax : cx);   end
   x=w=v=bx;  */
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);   
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #include <math.h>
     printf(".");fflush(stdout);  #include <stdio.h>
 #ifdef DEBUG  #include <stdlib.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);  #include <string.h>
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #include <unistd.h>
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #include <limits.h>
       *xmin=x;  #include <sys/types.h>
       return fx;  #include <sys/stat.h>
     }  #include <errno.h>
     ftemp=fu;  extern int errno;
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  #ifdef LINUX
       q=(x-v)*(fx-fw);  #include <time.h>
       p=(x-v)*q-(x-w)*r;  #include "timeval.h"
       q=2.0*(q-r);  #else
       if (q > 0.0) p = -p;  #include <sys/time.h>
       q=fabs(q);  #endif
       etemp=e;  
       e=d;  #ifdef GSL
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #include <gsl/gsl_errno.h>
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #include <gsl/gsl_multimin.h>
       else {  #endif
         d=p/q;  
         u=x+d;  /* #include <libintl.h> */
         if (u-a < tol2 || b-u < tol2)  /* #define _(String) gettext (String) */
           d=SIGN(tol1,xm-x);  
       }  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define GNUPLOTPROGRAM "gnuplot"
     }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define FILENAMELENGTH 132
     fu=(*f)(u);  
     if (fu <= fx) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       if (u >= x) a=x; else b=x;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         } else {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  #define NINTERVMAX 8
             v=w;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
             w=u;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
             fv=fw;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
             fw=fu;  #define MAXN 20000
           } else if (fu <= fv || v == x || v == w) {  #define YEARM 12. /**< Number of months per year */
             v=u;  #define AGESUP 130
             fv=fu;  #define AGEBASE 40
           }  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
         }  #ifdef UNIX
   }  #define DIRSEPARATOR '/'
   nrerror("Too many iterations in brent");  #define CHARSEPARATOR "/"
   *xmin=x;  #define ODIRSEPARATOR '\\'
   return fx;  #else
 }  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
 /****************** mnbrak ***********************/  #define ODIRSEPARATOR '/'
   #endif
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  /* $Id$ */
 {  /* $State$ */
   double ulim,u,r,q, dum;  
   double fu;  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
    char fullversion[]="$Revision$ $Date$"; 
   *fa=(*func)(*ax);  char strstart[80];
   *fb=(*func)(*bx);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   if (*fb > *fa) {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     SHFT(dum,*ax,*bx,dum)  int nvar=0, nforce=0; /* Number of variables, number of forces */
       SHFT(dum,*fb,*fa,dum)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
       }  int npar=NPARMAX;
   *cx=(*bx)+GOLD*(*bx-*ax);  int nlstate=2; /* Number of live states */
   *fc=(*func)(*cx);  int ndeath=1; /* Number of dead states */
   while (*fb > *fc) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     r=(*bx-*ax)*(*fb-*fc);  int popbased=0;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int *wav; /* Number of waves for this individuual 0 is possible */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int maxwav=0; /* Maxim number of waves */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     if ((*bx-u)*(u-*cx) > 0.0) {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       fu=(*func)(u);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     } else if ((*cx-u)*(u-ulim) > 0.0) {                     to the likelihood and the sum of weights (done by funcone)*/
       fu=(*func)(u);  int mle=1, weightopt=0;
       if (fu < *fc) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
           SHFT(*fb,*fc,fu,(*func)(u))  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
           }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double jmean=1; /* Mean space between 2 waves */
       u=ulim;  double **oldm, **newm, **savm; /* Working pointers to matrices */
       fu=(*func)(u);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     } else {  /*FILE *fic ; */ /* Used in readdata only */
       u=(*cx)+GOLD*(*cx-*bx);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       fu=(*func)(u);  FILE *ficlog, *ficrespow;
     }  int globpr=0; /* Global variable for printing or not */
     SHFT(*ax,*bx,*cx,u)  double fretone; /* Only one call to likelihood */
       SHFT(*fa,*fb,*fc,fu)  long ipmx=0; /* Number of contributions */
       }  double sw; /* Sum of weights */
 }  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 /*************** linmin ************************/  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 int ncom;  FILE *ficresprobmorprev;
 double *pcom,*xicom;  FILE *fichtm, *fichtmcov; /* Html File */
 double (*nrfunc)(double []);  FILE *ficreseij;
    char filerese[FILENAMELENGTH];
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  FILE *ficresstdeij;
 {  char fileresstde[FILENAMELENGTH];
   double brent(double ax, double bx, double cx,  FILE *ficrescveij;
                double (*f)(double), double tol, double *xmin);  char filerescve[FILENAMELENGTH];
   double f1dim(double x);  FILE  *ficresvij;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  char fileresv[FILENAMELENGTH];
               double *fc, double (*func)(double));  FILE  *ficresvpl;
   int j;  char fileresvpl[FILENAMELENGTH];
   double xx,xmin,bx,ax;  char title[MAXLINE];
   double fx,fb,fa;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   ncom=n;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   pcom=vector(1,n);  char command[FILENAMELENGTH];
   xicom=vector(1,n);  int  outcmd=0;
   nrfunc=func;  
   for (j=1;j<=n;j++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     pcom[j]=p[j];  
     xicom[j]=xi[j];  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
   ax=0.0;  char fileregp[FILENAMELENGTH];
   xx=1.0;  char popfile[FILENAMELENGTH];
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 #endif  struct timezone tzp;
   for (j=1;j<=n;j++) {  extern int gettimeofday();
     xi[j] *= xmin;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     p[j] += xi[j];  long time_value;
   }  extern long time();
   free_vector(xicom,1,n);  char strcurr[80], strfor[80];
   free_vector(pcom,1,n);  
 }  char *endptr;
   long lval;
 /*************** powell ************************/  double dval;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  #define NR_END 1
 {  #define FREE_ARG char*
   void linmin(double p[], double xi[], int n, double *fret,  #define FTOL 1.0e-10
               double (*func)(double []));  
   int i,ibig,j;  #define NRANSI 
   double del,t,*pt,*ptt,*xit;  #define ITMAX 200 
   double fp,fptt;  
   double *xits;  #define TOL 2.0e-4 
   pt=vector(1,n);  
   ptt=vector(1,n);  #define CGOLD 0.3819660 
   xit=vector(1,n);  #define ZEPS 1.0e-10 
   xits=vector(1,n);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  #define GOLD 1.618034 
   for (*iter=1;;++(*iter)) {  #define GLIMIT 100.0 
     fp=(*fret);  #define TINY 1.0e-20 
     ibig=0;  
     del=0.0;  static double maxarg1,maxarg2;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     for (i=1;i<=n;i++)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       printf(" %d %.12f",i, p[i]);    
     printf("\n");  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for (i=1;i<=n;i++) {  #define rint(a) floor(a+0.5)
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  static double sqrarg;
 #ifdef DEBUG  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       printf("fret=%lf \n",*fret);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #endif  int agegomp= AGEGOMP;
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  int imx; 
       if (fabs(fptt-(*fret)) > del) {  int stepm=1;
         del=fabs(fptt-(*fret));  /* Stepm, step in month: minimum step interpolation*/
         ibig=i;  
       }  int estepm;
 #ifdef DEBUG  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  int m,nb;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  long *num;
         printf(" x(%d)=%.12e",j,xit[j]);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       for(j=1;j<=n;j++)  double **pmmij, ***probs;
         printf(" p=%.12e",p[j]);  double *ageexmed,*agecens;
       printf("\n");  double dateintmean=0;
 #endif  
     }  double *weight;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  int **s; /* Status */
 #ifdef DEBUG  double *agedc;
       int k[2],l;  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
       k[0]=1;                    * covar=matrix(0,NCOVMAX,1,n); 
       k[1]=-1;                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       printf("Max: %.12e",(*func)(p));  double  idx; 
       for (j=1;j<=n;j++)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         printf(" %.12e",p[j]);  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       printf("\n");  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       for(l=0;l<=1;l++) {  double *lsurv, *lpop, *tpop;
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double ftolhess; /**< Tolerance for computing hessian */
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /**************** split *************************/
       }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 #endif  {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
       free_vector(xit,1,n);    */ 
       free_vector(xits,1,n);    char  *ss;                            /* pointer */
       free_vector(ptt,1,n);    int   l1, l2;                         /* length counters */
       free_vector(pt,1,n);  
       return;    l1 = strlen(path );                   /* length of path */
     }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     for (j=1;j<=n;j++) {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       ptt[j]=2.0*p[j]-pt[j];      strcpy( name, path );               /* we got the fullname name because no directory */
       xit[j]=p[j]-pt[j];      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       pt[j]=p[j];        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     }      /* get current working directory */
     fptt=(*func)(ptt);      /*    extern  char* getcwd ( char *buf , int len);*/
     if (fptt < fp) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        return( GLOCK_ERROR_GETCWD );
       if (t < 0.0) {      }
         linmin(p,xit,n,fret,func);      /* got dirc from getcwd*/
         for (j=1;j<=n;j++) {      printf(" DIRC = %s \n",dirc);
           xi[j][ibig]=xi[j][n];    } else {                              /* strip direcotry from path */
           xi[j][n]=xit[j];      ss++;                               /* after this, the filename */
         }      l2 = strlen( ss );                  /* length of filename */
 #ifdef DEBUG      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      strcpy( name, ss );         /* save file name */
         for(j=1;j<=n;j++)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
           printf(" %.12e",xit[j]);      dirc[l1-l2] = 0;                    /* add zero */
         printf("\n");      printf(" DIRC2 = %s \n",dirc);
 #endif    }
       }    /* We add a separator at the end of dirc if not exists */
     }    l1 = strlen( dirc );                  /* length of directory */
   }    if( dirc[l1-1] != DIRSEPARATOR ){
 }      dirc[l1] =  DIRSEPARATOR;
       dirc[l1+1] = 0; 
 /**** Prevalence limit ****************/      printf(" DIRC3 = %s \n",dirc);
     }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    ss = strrchr( name, '.' );            /* find last / */
 {    if (ss >0){
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      ss++;
      matrix by transitions matrix until convergence is reached */      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
   int i, ii,j,k;      l2= strlen(ss)+1;
   double min, max, maxmin, maxmax,sumnew=0.;      strncpy( finame, name, l1-l2);
   double **matprod2();      finame[l1-l2]= 0;
   double **out, cov[NCOVMAX], **pmij();    }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */    return( 0 );                          /* we're done */
   }
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /******************************************/
     }  
   void replace_back_to_slash(char *s, char*t)
    cov[1]=1.;  {
      int i;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int lg=0;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    i=0;
     newm=savm;    lg=strlen(t);
     /* Covariates have to be included here again */    for(i=0; i<= lg; i++) {
      cov[2]=agefin;      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
       for (k=1; k<=cptcovn;k++) {    }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  
       }  char *trimbb(char *out, char *in)
       for (k=1; k<=cptcovage;k++)  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    char *s;
       for (k=1; k<=cptcovprod;k++)    s=out;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        in++;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      }
       *out++ = *in++;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    }
     *out='\0';
     savm=oldm;    return s;
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  char *cutv(char *blocc, char *alocc, char *in, char occ)
       min=1.;  {
       max=0.;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       for(i=1; i<=nlstate; i++) {       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         sumnew=0;       gives blocc="abcdef2ghi" and alocc="j".
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         prlim[i][j]= newm[i][j]/(1-sumnew);    */
         max=FMAX(max,prlim[i][j]);    char *s, *t;
         min=FMIN(min,prlim[i][j]);    t=in;s=in;
       }    while (*in != '\0'){
       maxmin=max-min;      while( *in == occ){
       maxmax=FMAX(maxmax,maxmin);        *blocc++ = *in++;
     }        s=in;
     if(maxmax < ftolpl){      }
       return prlim;      *blocc++ = *in++;
     }    }
   }    if (s == t) /* occ not found */
 }      *(blocc-(in-s))='\0';
     else
 /*************** transition probabilities ***************/      *(blocc-(in-s)-1)='\0';
     in=s;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    while ( *in != '\0'){
 {      *alocc++ = *in++;
   double s1, s2;    }
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;    *alocc='\0';
     return s;
     for(i=1; i<= nlstate; i++){  }
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int nbocc(char *s, char occ)
         /*s2 += param[i][j][nc]*cov[nc];*/  {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int i,j=0;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    int lg=20;
       }    i=0;
       ps[i][j]=s2;    lg=strlen(s);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    for(i=0; i<= lg; i++) {
     }    if  (s[i] == occ ) j++;
     for(j=i+1; j<=nlstate+ndeath;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return j;
         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 cutv(char *u,char *v, char*t, char occ) */
       ps[i][j]=(s2);  /* { */
     }  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     /*ps[3][2]=1;*/  /*      gives u="abcdef2ghi" and v="j" *\/ */
   /*   int i,lg,j,p=0; */
   for(i=1; i<= nlstate; i++){  /*   i=0; */
      s1=0;  /*   lg=strlen(t); */
     for(j=1; j<i; j++)  /*   for(j=0; j<=lg-1; j++) { */
       s1+=exp(ps[i][j]);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     for(j=i+1; j<=nlstate+ndeath; j++)  /*   } */
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  /*   for(j=0; j<p; j++) { */
     for(j=1; j<i; j++)  /*     (u[j] = t[j]); */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /*   } */
     for(j=i+1; j<=nlstate+ndeath; j++)  /*      u[p]='\0'; */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /*    for(j=0; j<= lg; j++) { */
   } /* end i */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  /* } */
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /********************** nrerror ********************/
       ps[ii][ii]=1;  
     }  void nrerror(char error_text[])
   }  {
     fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    exit(EXIT_FAILURE);
     for(jj=1; jj<= nlstate+ndeath; jj++){  }
      printf("%lf ",ps[ii][jj]);  /*********************** vector *******************/
    }  double *vector(int nl, int nh)
     printf("\n ");  {
     }    double *v;
     printf("\n ");printf("%lf ",cov[2]);*/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 /*    if (!v) nrerror("allocation failure in vector");
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    return v-nl+NR_END;
   goto end;*/  }
     return ps;  
 }  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
 /**************** Product of 2 matrices ******************/  {
     free((FREE_ARG)(v+nl-NR_END));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /************************ivector *******************************/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  int *ivector(long nl,long nh)
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    int *v;
      a pointer to pointers identical to out */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   long i, j, k;    if (!v) nrerror("allocation failure in ivector");
   for(i=nrl; i<= nrh; i++)    return v-nl+NR_END;
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   return out;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
   
 /************* Higher Matrix Product ***************/  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  {
 {    long *v;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
      duration (i.e. until    if (!v) nrerror("allocation failure in ivector");
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    return v-nl+NR_END;
      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).  
      Model is determined by parameters x and covariates have to be  /******************free lvector **************************/
      included manually here.  void free_lvector(long *v, long nl, long nh)
   {
      */    free((FREE_ARG)(v+nl-NR_END));
   }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  /******************* imatrix *******************************/
   double **newm;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   /* Hstepm could be zero and should return the unit matrix */  { 
   for (i=1;i<=nlstate+ndeath;i++)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     for (j=1;j<=nlstate+ndeath;j++){    int **m; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    
       po[i][j][0]=(i==j ? 1.0 : 0.0);    /* allocate pointers to rows */ 
     }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if (!m) nrerror("allocation failure 1 in matrix()"); 
   for(h=1; h <=nhstepm; h++){    m += NR_END; 
     for(d=1; d <=hstepm; d++){    m -= nrl; 
       newm=savm;    
       /* Covariates have to be included here again */    
       cov[1]=1.;    /* allocate rows and set pointers to them */ 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for (k=1; k<=cptcovage;k++)    m[nrl] += NR_END; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl] -= ncl; 
       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]]];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
     /* return pointer to array of pointers to rows */ 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    return m; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  } 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /****************** free_imatrix *************************/
       savm=oldm;  void free_imatrix(m,nrl,nrh,ncl,nch)
       oldm=newm;        int **m;
     }        long nch,ncl,nrh,nrl; 
     for(i=1; i<=nlstate+ndeath; i++)       /* free an int matrix allocated by imatrix() */ 
       for(j=1;j<=nlstate+ndeath;j++) {  { 
         po[i][j][h]=newm[i][j];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    free((FREE_ARG) (m+nrl-NR_END)); 
          */  } 
       }  
   } /* end h */  /******************* matrix *******************************/
   return po;  double **matrix(long nrl, long nrh, long ncl, long nch)
 }  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 /*************** log-likelihood *************/  
 double func( double *x)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int i, ii, j, k, mi, d, kk;    m += NR_END;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    m -= nrl;
   double **out;  
   double sw; /* Sum of weights */    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double lli; /* Individual log likelihood */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   long ipmx;    m[nrl] += NR_END;
   /*extern weight */    m[nrl] -= ncl;
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   /*for(i=1;i<imx;i++)    return m;
     printf(" %d\n",s[4][i]);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   */     */
   cov[1]=1.;  }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /*************************free matrix ************************/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
     for(mi=1; mi<= wav[i]-1; mi++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for (ii=1;ii<=nlstate+ndeath;ii++)    free((FREE_ARG)(m+nrl-NR_END));
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /******************* ma3x *******************************/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         for (kk=1; kk<=cptcovage;kk++) {  {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         }    double ***m;
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    if (!m) nrerror("allocation failure 1 in matrix()");
         savm=oldm;    m += NR_END;
         oldm=newm;    m -= nrl;
          
            m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       } /* end mult */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
          m[nrl] += NR_END;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    m[nrl] -= ncl;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     } /* end of wave */    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   } /* end of individual */    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for (j=ncl+1; j<=nch; j++) 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      m[nrl][j]=m[nrl][j-1]+nlay;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    
   return -l;    for (i=nrl+1; i<=nrh; i++) {
 }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
 /*********** Maximum Likelihood Estimation ***************/    }
     return m; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   int i,j, iter;    */
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /*************************free ma3x ************************/
   for (i=1;i<=npar;i++)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   printf("Powell\n");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   powell(p,xi,npar,ftol,&iter,&fret,func);    free((FREE_ARG)(m+nrl-NR_END));
   }
    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));  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
 }  {
     /* Caution optionfilefiname is hidden */
 /**** Computes Hessian and covariance matrix ***/    strcpy(tmpout,optionfilefiname);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    strcat(tmpout,"/"); /* Add to the right */
 {    strcat(tmpout,fileres);
   double  **a,**y,*x,pd;    return tmpout;
   double **hess;  }
   int i, j,jk;  
   int *indx;  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
   double hessii(double p[], double delta, int theta, double delti[]);  {
   double hessij(double p[], double delti[], int i, int j);    
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /* Caution optionfilefiname is hidden */
   void ludcmp(double **a, int npar, int *indx, double *d) ;    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   hess=matrix(1,npar,1,npar);    strcat(tmpout,preop);
     strcat(tmpout,fileres);
   printf("\nCalculation of the hessian matrix. Wait...\n");    return tmpout;
   for (i=1;i<=npar;i++){  }
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*************** function subdirf3 ***********/
     /*printf(" %f ",p[i]);*/  char *subdirf3(char fileres[], char *preop, char *preop2)
     /*printf(" %lf ",hess[i][i]);*/  {
   }    
      /* Caution optionfilefiname is hidden */
   for (i=1;i<=npar;i++) {    strcpy(tmpout,optionfilefiname);
     for (j=1;j<=npar;j++)  {    strcat(tmpout,"/");
       if (j>i) {    strcat(tmpout,preop);
         printf(".%d%d",i,j);fflush(stdout);    strcat(tmpout,preop2);
         hess[i][j]=hessij(p,delti,i,j);    strcat(tmpout,fileres);
         hess[j][i]=hess[i][j];        return tmpout;
         /*printf(" %lf ",hess[i][j]);*/  }
       }  
     }  /***************** f1dim *************************/
   }  extern int ncom; 
   printf("\n");  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");   
    double f1dim(double x) 
   a=matrix(1,npar,1,npar);  { 
   y=matrix(1,npar,1,npar);    int j; 
   x=vector(1,npar);    double f;
   indx=ivector(1,npar);    double *xt; 
   for (i=1;i<=npar;i++)   
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    xt=vector(1,ncom); 
   ludcmp(a,npar,indx,&pd);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
   for (j=1;j<=npar;j++) {    free_vector(xt,1,ncom); 
     for (i=1;i<=npar;i++) x[i]=0;    return f; 
     x[j]=1;  } 
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /*****************brent *************************/
       matcov[i][j]=x[i];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
   }    int iter; 
     double a,b,d,etemp;
   printf("\n#Hessian matrix#\n");    double fu,fv,fw,fx;
   for (i=1;i<=npar;i++) {    double ftemp;
     for (j=1;j<=npar;j++) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       printf("%.3e ",hess[i][j]);    double e=0.0; 
     }   
     printf("\n");    a=(ax < cx ? ax : cx); 
   }    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
   /* Recompute Inverse */    fw=fv=fx=(*f)(x); 
   for (i=1;i<=npar;i++)    for (iter=1;iter<=ITMAX;iter++) { 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      xm=0.5*(a+b); 
   ludcmp(a,npar,indx,&pd);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   /*  printf("\n#Hessian matrix recomputed#\n");      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   for (j=1;j<=npar;j++) {  #ifdef DEBUG
     for (i=1;i<=npar;i++) x[i]=0;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     x[j]=1;      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);
     lubksb(a,npar,indx,x);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for (i=1;i<=npar;i++){  #endif
       y[i][j]=x[i];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       printf("%.3e ",y[i][j]);        *xmin=x; 
     }        return fx; 
     printf("\n");      } 
   }      ftemp=fu;
   */      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
   free_matrix(a,1,npar,1,npar);        q=(x-v)*(fx-fw); 
   free_matrix(y,1,npar,1,npar);        p=(x-v)*q-(x-w)*r; 
   free_vector(x,1,npar);        q=2.0*(q-r); 
   free_ivector(indx,1,npar);        if (q > 0.0) p = -p; 
   free_matrix(hess,1,npar,1,npar);        q=fabs(q); 
         etemp=e; 
         e=d; 
 }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 /*************** hessian matrix ****************/        else { 
 double hessii( double x[], double delta, int theta, double delti[])          d=p/q; 
 {          u=x+d; 
   int i;          if (u-a < tol2 || b-u < tol2) 
   int l=1, lmax=20;            d=SIGN(tol1,xm-x); 
   double k1,k2;        } 
   double p2[NPARMAX+1];      } else { 
   double res;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      } 
   double fx;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   int k=0,kmax=10;      fu=(*f)(u); 
   double l1;      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
   fx=func(x);        SHFT(v,w,x,u) 
   for (i=1;i<=npar;i++) p2[i]=x[i];          SHFT(fv,fw,fx,fu) 
   for(l=0 ; l <=lmax; l++){          } else { 
     l1=pow(10,l);            if (u < x) a=u; else b=u; 
     delts=delt;            if (fu <= fw || w == x) { 
     for(k=1 ; k <kmax; k=k+1){              v=w; 
       delt = delta*(l1*k);              w=u; 
       p2[theta]=x[theta] +delt;              fv=fw; 
       k1=func(p2)-fx;              fw=fu; 
       p2[theta]=x[theta]-delt;            } else if (fu <= fv || v == x || v == w) { 
       k2=func(p2)-fx;              v=u; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */              fv=fu; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            } 
                } 
 #ifdef DEBUG    } 
       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);    nrerror("Too many iterations in brent"); 
 #endif    *xmin=x; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    return fx; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  } 
         k=kmax;  
       }  /****************** mnbrak ***********************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       }              double (*func)(double)) 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  { 
         delts=delt;    double ulim,u,r,q, dum;
       }    double fu; 
     }   
   }    *fa=(*func)(*ax); 
   delti[theta]=delts;    *fb=(*func)(*bx); 
   return res;    if (*fb > *fa) { 
        SHFT(dum,*ax,*bx,dum) 
 }        SHFT(dum,*fb,*fa,dum) 
         } 
 double hessij( double x[], double delti[], int thetai,int thetaj)    *cx=(*bx)+GOLD*(*bx-*ax); 
 {    *fc=(*func)(*cx); 
   int i;    while (*fb > *fc) { 
   int l=1, l1, lmax=20;      r=(*bx-*ax)*(*fb-*fc); 
   double k1,k2,k3,k4,res,fx;      q=(*bx-*cx)*(*fb-*fa); 
   double p2[NPARMAX+1];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   int k;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
   fx=func(x);      if ((*bx-u)*(u-*cx) > 0.0) { 
   for (k=1; k<=2; k++) {        fu=(*func)(u); 
     for (i=1;i<=npar;i++) p2[i]=x[i];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;        fu=(*func)(u); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        if (fu < *fc) { 
     k1=func(p2)-fx;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
              SHFT(*fb,*fc,fu,(*func)(u)) 
     p2[thetai]=x[thetai]+delti[thetai]/k;            } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     k2=func(p2)-fx;        u=ulim; 
          fu=(*func)(u); 
     p2[thetai]=x[thetai]-delti[thetai]/k;      } else { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        u=(*cx)+GOLD*(*cx-*bx); 
     k3=func(p2)-fx;        fu=(*func)(u); 
        } 
     p2[thetai]=x[thetai]-delti[thetai]/k;      SHFT(*ax,*bx,*cx,u) 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        SHFT(*fa,*fb,*fc,fu) 
     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  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  /*************** linmin ************************/
 #endif  
   }  int ncom; 
   return res;  double *pcom,*xicom;
 }  double (*nrfunc)(double []); 
    
 /************** Inverse of matrix **************/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 void ludcmp(double **a, int n, int *indx, double *d)  { 
 {    double brent(double ax, double bx, double cx, 
   int i,imax,j,k;                 double (*f)(double), double tol, double *xmin); 
   double big,dum,sum,temp;    double f1dim(double x); 
   double *vv;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                  double *fc, double (*func)(double)); 
   vv=vector(1,n);    int j; 
   *d=1.0;    double xx,xmin,bx,ax; 
   for (i=1;i<=n;i++) {    double fx,fb,fa;
     big=0.0;   
     for (j=1;j<=n;j++)    ncom=n; 
       if ((temp=fabs(a[i][j])) > big) big=temp;    pcom=vector(1,n); 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    xicom=vector(1,n); 
     vv[i]=1.0/big;    nrfunc=func; 
   }    for (j=1;j<=n;j++) { 
   for (j=1;j<=n;j++) {      pcom[j]=p[j]; 
     for (i=1;i<j;i++) {      xicom[j]=xi[j]; 
       sum=a[i][j];    } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    ax=0.0; 
       a[i][j]=sum;    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     big=0.0;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for (i=j;i<=n;i++) {  #ifdef DEBUG
       sum=a[i][j];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=1;k<j;k++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         sum -= a[i][k]*a[k][j];  #endif
       a[i][j]=sum;    for (j=1;j<=n;j++) { 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      xi[j] *= xmin; 
         big=dum;      p[j] += xi[j]; 
         imax=i;    } 
       }    free_vector(xicom,1,n); 
     }    free_vector(pcom,1,n); 
     if (j != imax) {  } 
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  char *asc_diff_time(long time_sec, char ascdiff[])
         a[imax][k]=a[j][k];  {
         a[j][k]=dum;    long sec_left, days, hours, minutes;
       }    days = (time_sec) / (60*60*24);
       *d = -(*d);    sec_left = (time_sec) % (60*60*24);
       vv[imax]=vv[j];    hours = (sec_left) / (60*60) ;
     }    sec_left = (sec_left) %(60*60);
     indx[j]=imax;    minutes = (sec_left) /60;
     if (a[j][j] == 0.0) a[j][j]=TINY;    sec_left = (sec_left) % (60);
     if (j != n) {    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       dum=1.0/(a[j][j]);    return ascdiff;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  }
     }  
   }  /*************** powell ************************/
   free_vector(vv,1,n);  /* Doesn't work */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 ;              double (*func)(double [])) 
 }  { 
     void linmin(double p[], double xi[], int n, double *fret, 
 void lubksb(double **a, int n, int *indx, double b[])                double (*func)(double [])); 
 {    int i,ibig,j; 
   int i,ii=0,ip,j;    double del,t,*pt,*ptt,*xit;
   double sum;    double fp,fptt;
      double *xits;
   for (i=1;i<=n;i++) {    int niterf, itmp;
     ip=indx[i];  
     sum=b[ip];    pt=vector(1,n); 
     b[ip]=b[i];    ptt=vector(1,n); 
     if (ii)    xit=vector(1,n); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    xits=vector(1,n); 
     else if (sum) ii=i;    *fret=(*func)(p); 
     b[i]=sum;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   }    for (*iter=1;;++(*iter)) { 
   for (i=n;i>=1;i--) {      fp=(*fret); 
     sum=b[i];      ibig=0; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      del=0.0; 
     b[i]=sum/a[i][i];      last_time=curr_time;
   }      (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);
 /************ Frequencies ********************/  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint, int boolprev, double dateprev1,double dateprev2)     for (i=1;i<=n;i++) {
 {  /* Some frequencies */        printf(" %d %.12f",i, p[i]);
          fprintf(ficlog," %d %.12lf",i, p[i]);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        fprintf(ficrespow," %.12lf", p[i]);
   double ***freq; /* Frequencies */      }
   double *pp;      printf("\n");
   double pos, k2;      fprintf(ficlog,"\n");
   FILE *ficresp;      fprintf(ficrespow,"\n");fflush(ficrespow);
   char fileresp[FILENAMELENGTH];      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
   pp=vector(1,nlstate);        strcpy(strcurr,asctime(&tm));
   probs= ma3x(1,130 ,1,8, 1,8);  /*       asctime_r(&tm,strcurr); */
   strcpy(fileresp,"p");        forecast_time=curr_time; 
   strcat(fileresp,fileres);        itmp = strlen(strcurr);
   if((ficresp=fopen(fileresp,"w"))==NULL) {        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     printf("Problem with prevalence resultfile: %s\n", fileresp);          strcurr[itmp-1]='\0';
     exit(0);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for(niterf=10;niterf<=30;niterf+=10){
   j1=0;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   j=cptcoveff;  /*      asctime_r(&tmf,strfor); */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
   for(k1=1; k1<=j;k1++){          if(strfor[itmp-1]=='\n')
    for(i1=1; i1<=ncodemax[k1];i1++){          strfor[itmp-1]='\0';
        j1++;          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);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          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);
          scanf("%d", i);*/        }
         for (i=-1; i<=nlstate+ndeath; i++)        }
          for (jk=-1; jk<=nlstate+ndeath; jk++)        for (i=1;i<=n;i++) { 
            for(m=agemin; m <= agemax+3; m++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
              freq[i][jk][m]=0;        fptt=(*fret); 
          #ifdef DEBUG
        for (i=1; i<=imx; i++) {        printf("fret=%lf \n",*fret);
          bool=1;        fprintf(ficlog,"fret=%lf \n",*fret);
          if  (cptcovn>0) {  #endif
            for (z1=1; z1<=cptcoveff; z1++)        printf("%d",i);fflush(stdout);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        fprintf(ficlog,"%d",i);fflush(ficlog);
                bool=0;        linmin(p,xit,n,fret,func); 
          }        if (fabs(fptt-(*fret)) > del) { 
          if (bool==1) {          del=fabs(fptt-(*fret)); 
            if (boolprev==1){          ibig=i; 
              for(m=fprev1; m<=lprev1; m++){        } 
                if(agev[m][i]==0) agev[m][i]=agemax+1;  #ifdef DEBUG
                if(agev[m][i]==1) agev[m][i]=agemax+2;        printf("%d %.12e",i,(*fret));
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        fprintf(ficlog,"%d %.12e",i,(*fret));
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for (j=1;j<=n;j++) {
              }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            }          printf(" x(%d)=%.12e",j,xit[j]);
            else {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
             for(m=firstpass; m<=lastpass; m++){        }
              k2=anint[m][i]+(mint[m][i]/12.);        for(j=1;j<=n;j++) {
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          printf(" p=%.12e",p[j]);
              if(agev[m][i]==0) agev[m][i]=agemax+1;          fprintf(ficlog," p=%.12e",p[j]);
              if(agev[m][i]==1) agev[m][i]=agemax+2;        }
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        printf("\n");
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        fprintf(ficlog,"\n");
              }  #endif
             }      } 
            }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           }  #ifdef DEBUG
        }        int k[2],l;
         if  (cptcovn>0) {        k[0]=1;
          fprintf(ficresp, "\n#********** Variable ");        k[1]=-1;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        printf("Max: %.12e",(*func)(p));
        fprintf(ficresp, "**********\n#");        fprintf(ficlog,"Max: %.12e",(*func)(p));
         }        for (j=1;j<=n;j++) {
        for(i=1; i<=nlstate;i++)          printf(" %.12e",p[j]);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          fprintf(ficlog," %.12e",p[j]);
        fprintf(ficresp, "\n");        }
                printf("\n");
   for(i=(int)agemin; i <= (int)agemax+3; i++){        fprintf(ficlog,"\n");
     if(i==(int)agemax+3)        for(l=0;l<=1;l++) {
       printf("Total");          for (j=1;j<=n;j++) {
     else            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       printf("Age %d", i);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for(jk=1; jk <=nlstate ; jk++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          }
         pp[jk] += freq[jk][m][i];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(jk=1; jk <=nlstate ; jk++){        }
       for(m=-1, pos=0; m <=0 ; m++)  #endif
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)  
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        free_vector(xit,1,n); 
       else        free_vector(xits,1,n); 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
         return; 
      for(jk=1; jk <=nlstate ; jk++){      } 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         pp[jk] += freq[jk][m][i];      for (j=1;j<=n;j++) { 
      }        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)        pt[j]=p[j]; 
       pos += pp[jk];      } 
     for(jk=1; jk <=nlstate ; jk++){      fptt=(*func)(ptt); 
       if(pos>=1.e-5)      if (fptt < fp) { 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       else        if (t < 0.0) { 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          linmin(p,xit,n,fret,func); 
       if( i <= (int) agemax){          for (j=1;j<=n;j++) { 
         if(pos>=1.e-5){            xi[j][ibig]=xi[j][n]; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            xi[j][n]=xit[j]; 
           probs[i][jk][j1]= pp[jk]/pos;          }
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  #ifdef DEBUG
         }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       else          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          for(j=1;j<=n;j++){
       }            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
     for(jk=-1; jk <=nlstate+ndeath; jk++)          }
       for(m=-1; m <=nlstate+ndeath; m++)          printf("\n");
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          fprintf(ficlog,"\n");
     if(i <= (int) agemax)  #endif
       fprintf(ficresp,"\n");        }
     printf("\n");      } 
     }    } 
     }  } 
  }  
    /**** Prevalence limit (stable or period prevalence)  ****************/
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   free_vector(pp,1,nlstate);  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 }  /* End of Freq */       matrix by transitions matrix until convergence is reached */
   
 /************ Prevalence ********************/    int i, ii,j,k;
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1, double **mint,double **anint,int boolprev, double dateprev1, double dateprev2)    double min, max, maxmin, maxmax,sumnew=0.;
 {  /* Some frequencies */    double **matprod2();
      double **out, cov[NCOVMAX+1], **pmij();
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    double **newm;
   double ***freq; /* Frequencies */    double agefin, delaymax=50 ; /* Max number of years to converge */
   double *pp;  
   double pos, k2;    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   pp=vector(1,nlstate);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   probs= ma3x(1,130 ,1,8, 1,8);      }
    
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);     cov[1]=1.;
   j1=0;   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   j=cptcoveff;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      newm=savm;
        /* Covariates have to be included here again */
  for(k1=1; k1<=j;k1++){      cov[2]=agefin;
     for(i1=1; i1<=ncodemax[k1];i1++){      
       j1++;      for (k=1; k<=cptcovn;k++) {
          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (i=-1; i<=nlstate+ndeath; i++)          /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         for (jk=-1; jk<=nlstate+ndeath; jk++)        }
           for(m=agemin; m <= agemax+3; m++)      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           freq[i][jk][m]=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]]];
       for (i=1; i<=imx; i++) {      
         bool=1;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         if  (cptcovn>0) {      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
           for (z1=1; z1<=cptcoveff; z1++)      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
               bool=0;      
               }      savm=oldm;
         if (bool==1) {      oldm=newm;
           if (boolprev==1){      maxmax=0.;
             for(m=fprev1; m<=lprev1; m++){      for(j=1;j<=nlstate;j++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;        min=1.;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        max=0.;
               freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for(i=1; i<=nlstate; i++) {
               freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          sumnew=0;
             }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           }          prlim[i][j]= newm[i][j]/(1-sumnew);
           else {          max=FMAX(max,prlim[i][j]);
             for(m=firstpass; m<=lastpass; m++){          min=FMIN(min,prlim[i][j]);
               k2=anint[m][i]+(mint[m][i]/12.);        }
               if ((k2>=dateprev1) && (k2<=dateprev2)) {        maxmin=max-min;
                 if(agev[m][i]==0) agev[m][i]=agemax+1;        maxmax=FMAX(maxmax,maxmin);
                 if(agev[m][i]==1) agev[m][i]=agemax+2;      }
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      if(maxmax < ftolpl){
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        return prlim;
               }      }
             }    }
           }  }
         }  
       }  /*************** transition probabilities ***************/ 
         for(i=(int)agemin; i <= (int)agemax+3; i++){  
           for(jk=1; jk <=nlstate ; jk++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  {
               pp[jk] += freq[jk][m][i];    /* According to parameters values stored in x and the covariate's values stored in cov,
           }       computes the probability to be observed in state j being in state i by appying the
           for(jk=1; jk <=nlstate ; jk++){       model to the ncovmodel covariates (including constant and age).
             for(m=-1, pos=0; m <=0 ; m++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
             pos += freq[jk][m][i];       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         }       ncth covariate in the global vector x is given by the formula:
               j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
          for(jk=1; jk <=nlstate ; jk++){       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
              pp[jk] += freq[jk][m][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]
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    */
     double s1, lnpijopii;
          for(jk=1; jk <=nlstate ; jk++){              /*double t34;*/
            if( i <= (int) agemax){    int i,j,j1, nc, ii, jj;
              if(pos>=1.e-5){  
                probs[i][jk][j1]= pp[jk]/pos;      for(i=1; i<= nlstate; i++){
              }        for(j=1; j<i;j++){
            }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
          }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
                      lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
         }  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     }          }
   }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
    /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(j=i+1; j<=nlstate+ndeath;j++){
   free_vector(pp,1,nlstate);          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];*/
 }  /* End of Freq */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 /************* Waves Concatenation ***************/  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 {        }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      }
      Death is a valid wave (if date is known).      
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for(i=1; i<= nlstate; i++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        s1=0;
      and mw[mi+1][i]. dh depends on stepm.        for(j=1; j<i; j++){
      */          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); */
   int i, mi, m;        }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for(j=i+1; j<=nlstate+ndeath; j++){
      double sum=0., jmean=0.;*/          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   int j, k=0,jk, ju, jl;        }
   double sum=0.;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   jmin=1e+5;        ps[i][i]=1./(s1+1.);
   jmax=-1;        /* Computing other pijs */
   jmean=0.;        for(j=1; j<i; j++)
   for(i=1; i<=imx; i++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
     mi=0;        for(j=i+1; j<=nlstate+ndeath; j++)
     m=firstpass;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     while(s[m][i] <= nlstate){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       if(s[m][i]>=1)      } /* end i */
         mw[++mi][i]=m;      
       if(m >=lastpass)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         break;        for(jj=1; jj<= nlstate+ndeath; jj++){
       else          ps[ii][jj]=0;
         m++;          ps[ii][ii]=1;
     }/* end while */        }
     if (s[m][i] > nlstate){      }
       mi++;     /* Death is another wave */      
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       mw[mi][i]=m;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     }  /*         printf("ddd %lf ",ps[ii][jj]); */
   /*       } */
     wav[i]=mi;  /*       printf("\n "); */
     if(mi==0)  /*        } */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  /*        printf("\n ");printf("%lf ",cov[2]); */
   }         /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for(i=1; i<=imx; i++){        goto end;*/
     for(mi=1; mi<wav[i];mi++){      return ps;
       if (stepm <=0)  }
         dh[mi][i]=1;  
       else{  /**************** Product of 2 matrices ******************/
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  {
           if(j==0) j=1;  /* Survives at least one month after exam */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           k=k+1;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
           if (j >= jmax) jmax=j;    /* in, b, out are matrice of pointers which should have been initialized 
           if (j <= jmin) jmin=j;       before: only the contents of out is modified. The function returns
           sum=sum+j;       a pointer to pointers identical to out */
           /* if (j<10) printf("j=%d num=%d ",j,i); */    long i, j, k;
           }    for(i=nrl; i<= nrh; i++)
         }      for(k=ncolol; k<=ncoloh; k++)
         else{        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          out[i][k] +=in[i][j]*b[j][k];
           k=k+1;  
           if (j >= jmax) jmax=j;    return out;
           else if (j <= jmin)jmin=j;  }
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  
           sum=sum+j;  
         }  /************* Higher Matrix Product ***************/
         jk= j/stepm;  
         jl= j -jk*stepm;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         ju= j -(jk+1)*stepm;  {
         if(jl <= -ju)    /* Computes the transition matrix starting at age 'age' over 
           dh[mi][i]=jk;       'nhstepm*hstepm*stepm' months (i.e. until
         else       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           dh[mi][i]=jk+1;       nhstepm*hstepm matrices. 
         if(dh[mi][i]==0)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           dh[mi][i]=1; /* At least one step */       (typically every 2 years instead of every month which is too big 
       }       for the memory).
     }       Model is determined by parameters x and covariates have to be 
   }       included manually here. 
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       */
  }  
 /*********** Tricode ****************************/    int i, j, d, h, k;
 void tricode(int *Tvar, int **nbcode, int imx)    double **out, cov[NCOVMAX+1];
 {    double **newm;
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;    /* Hstepm could be zero and should return the unit matrix */
   cptcoveff=0;    for (i=1;i<=nlstate+ndeath;i++)
        for (j=1;j<=nlstate+ndeath;j++){
   for (k=0; k<19; k++) Ndum[k]=0;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   for (k=1; k<=7; k++) ncodemax[k]=0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (i=1; i<=imx; i++) {    for(h=1; h <=nhstepm; h++){
       ij=(int)(covar[Tvar[j]][i]);      for(d=1; d <=hstepm; d++){
       Ndum[ij]++;        newm=savm;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /* Covariates have to be included here again */
       if (ij > cptcode) cptcode=ij;        cov[1]=1.;
     }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
     for (i=0; i<=cptcode; i++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       if(Ndum[i]!=0) ncodemax[j]++;        for (k=1; k<=cptcovage;k++)
     }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     ij=1;        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]]];
   
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         if (Ndum[k] != 0) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           nbcode[Tvar[j]][ij]=k;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           ij++;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         }        savm=oldm;
         if (ij > ncodemax[j]) break;        oldm=newm;
       }        }
     }      for(i=1; i<=nlstate+ndeath; i++)
   }          for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
  for (k=0; k<19; k++) Ndum[k]=0;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
  for (i=1; i<=ncovmodel-2; i++) {      /*printf("h=%d ",h);*/
       ij=Tvar[i];    } /* end h */
       Ndum[ij]++;  /*     printf("\n H=%d \n",h); */
     }    return po;
   }
  ij=1;  
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncov)){  /*************** log-likelihood *************/
      Tvaraff[ij]=i;  double func( double *x)
      ij++;  {
    }    int i, ii, j, k, mi, d, kk;
  }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      double **out;
     cptcoveff=ij-1;    double sw; /* Sum of weights */
 }    double lli; /* Individual log likelihood */
     int s1, s2;
 /*********** Health Expectancies ****************/    double bbh, survp;
     long ipmx;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    /*extern weight */
 {    /* We are differentiating ll according to initial status */
   /* Health expectancies */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   int i, j, nhstepm, hstepm, h;    /*for(i=1;i<imx;i++) 
   double age, agelim,hf;      printf(" %d\n",s[4][i]);
   double ***p3mat;    */
      cov[1]=1.;
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    if(mle==1){
       fprintf(ficreseij," %1d-%1d",i,j);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficreseij,"\n");        /* Computes the values of the ncovmodel covariates of the model
            depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   hstepm=1*YEARM; /*  Every j years of age (in month) */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */           to be observed in j being in i according to the model.
          */
   agelim=AGESUP;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     /* nhstepm age range expressed in number of stepm */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);           has been calculated etc */
     /* Typically if 20 years = 20*12/6=40 stepm */        for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) hstepm=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            for (j=1;j<=nlstate+ndeath;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              savm[ii][j]=(ii==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1; i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<=nlstate;j++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            }
           eij[i][j][(int)age] +=p3mat[i][j][h];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
     hf=1;            oldm=newm;
     if (stepm >= YEARM) hf=stepm/YEARM;          } /* end mult */
     fprintf(ficreseij,"%.0f",age );        
     for(i=1; i<=nlstate;i++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for(j=1; j<=nlstate;j++){          /* But now since version 0.9 we anticipate for bias at large stepm.
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);           * 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 
     fprintf(ficreseij,"\n");           * the nearest (and in case of equal distance, to the lowest) interval but now
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 }           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 /************ Variance ******************/           * -stepm/2 to stepm/2 .
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)           * For 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. 
   /* Variance of health expectancies */           */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          s1=s[mw[mi][i]][i];
   double **newm;          s2=s[mw[mi+1][i]][i];
   double **dnewm,**doldm;          bbh=(double)bh[mi][i]/(double)stepm; 
   int i, j, nhstepm, hstepm, h;          /* bias bh is positive if real duration
   int k, cptcode;           * is higher than the multiple of stepm and negative otherwise.
   double *xp;           */
   double **gp, **gm;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double ***gradg, ***trgradg;          if( s2 > nlstate){ 
   double ***p3mat;            /* i.e. if s2 is a death state and if the date of death is known 
   double age,agelim;               then the contribution to the likelihood is the probability to 
   int theta;               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
    fprintf(ficresvij,"# Covariances of life expectancies\n");               minus probability to die before dh-stepm . 
   fprintf(ficresvij,"# Age");               In version up to 0.92 likelihood was computed
   for(i=1; i<=nlstate;i++)          as if date of death was unknown. Death was treated as any other
     for(j=1; j<=nlstate;j++)          health state: the date of the interview describes the actual state
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          and not the date of a change in health state. The former idea was
   fprintf(ficresvij,"\n");          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
   xp=vector(1,npar);          introduced the exact date of death then we should have modified
   dnewm=matrix(1,nlstate,1,npar);          the contribution of an exact death to the likelihood. This new
   doldm=matrix(1,nlstate,1,nlstate);          contribution is smaller and very dependent of the step unit
            stepm. It is no more the probability to die between last interview
   hstepm=1*YEARM; /* Every year of age */          and month of death but the probability to survive from last
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          interview up to one month before death multiplied by the
   agelim = AGESUP;          probability to die within a month. Thanks to Chris
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          Jackson for correcting this bug.  Former versions increased
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          mortality artificially. The bad side is that we add another loop
     if (stepm >= YEARM) hstepm=1;          which slows down the processing. The difference can be up to 10%
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          lower mortality.
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  
           } else if  (s2==-2) {
     for(theta=1; theta <=npar; theta++){            for (j=1,survp=0. ; j<=nlstate; j++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            /*survp += out[s1][j]; */
       }            lli= log(survp);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          
           else if  (s2==-4) { 
       if (popbased==1) {            for (j=3,survp=0. ; j<=nlstate; j++)  
         for(i=1; i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           prlim[i][i]=probs[(int)age][i][ij];            lli= log(survp); 
       }          } 
        
       for(j=1; j<= nlstate; j++){          else if  (s2==-5) { 
         for(h=0; h<=nhstepm; h++){            for (j=1,survp=0. ; j<=2; j++)  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            lli= log(survp); 
         }          } 
       }          
              else{
       for(i=1; i<=npar; i++) /* Computes gradient */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*  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 */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
       if (popbased==1) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         for(i=1; i<=nlstate;i++)          ipmx +=1;
           prlim[i][i]=probs[(int)age][i][ij];          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       for(j=1; j<= nlstate; j++){      } /* end of individual */
         for(h=0; h<=nhstepm; h++){    }  else if(mle==2){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<= nlstate; j++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(h=0; h<=nhstepm; h++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            }
         }          for(d=0; d<=dh[mi][i]; d++){
     } /* End theta */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(h=0; h<=nhstepm; h++)            }
       for(j=1; j<=nlstate;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(theta=1; theta <=npar; theta++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           trgradg[h][j][theta]=gradg[h][theta][j];            savm=oldm;
             oldm=newm;
     for(i=1;i<=nlstate;i++)          } /* end mult */
       for(j=1;j<=nlstate;j++)        
         vareij[i][j][(int)age] =0.;          s1=s[mw[mi][i]][i];
     for(h=0;h<=nhstepm;h++){          s2=s[mw[mi+1][i]][i];
       for(k=0;k<=nhstepm;k++){          bbh=(double)bh[mi][i]/(double)stepm; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          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 */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          ipmx +=1;
         for(i=1;i<=nlstate;i++)          sw += weight[i];
           for(j=1;j<=nlstate;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             vareij[i][j][(int)age] += doldm[i][j];        } /* end of wave */
       }      } /* end of individual */
     }    }  else if(mle==3){  /* exponential inter-extrapolation */
     h=1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (stepm >= YEARM) h=stepm/YEARM;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficresvij,"%.0f ",age );        for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1; i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<=nlstate;j++){            for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficresvij,"\n");            }
     free_matrix(gp,0,nhstepm,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     free_matrix(gm,0,nhstepm,1,nlstate);            newm=savm;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   } /* End age */            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(xp,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(doldm,1,nlstate,1,npar);            savm=oldm;
   free_matrix(dnewm,1,nlstate,1,nlstate);            oldm=newm;
           } /* end mult */
 }        
           s1=s[mw[mi][i]][i];
 /************ Variance of prevlim ******************/          s2=s[mw[mi+1][i]][i];
 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)          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 */
   /* Variance of prevalence limit */          ipmx +=1;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          sw += weight[i];
   double **newm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **dnewm,**doldm;        } /* end of wave */
   int i, j, nhstepm, hstepm;      } /* end of individual */
   int k, cptcode;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double *xp;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *gp, *gm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **gradg, **trgradg;        for(mi=1; mi<= wav[i]-1; mi++){
   double age,agelim;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int theta;            for (j=1;j<=nlstate+ndeath;j++){
                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"# Age");            }
   for(i=1; i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
       fprintf(ficresvpl," %1d-%1d",i,i);            newm=savm;
   fprintf(ficresvpl,"\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   xp=vector(1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   hstepm=1*YEARM; /* Every year of age */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            savm=oldm;
   agelim = AGESUP;            oldm=newm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          } /* end mult */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        
     if (stepm >= YEARM) hstepm=1;          s1=s[mw[mi][i]][i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          s2=s[mw[mi+1][i]][i];
     gradg=matrix(1,npar,1,nlstate);          if( s2 > nlstate){ 
     gp=vector(1,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
     gm=vector(1,nlstate);          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */          ipmx +=1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(i=1;i<=nlstate;i++)        } /* end of wave */
         gp[i] = prlim[i][i];      } /* end of individual */
        }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(mi=1; mi<= wav[i]-1; mi++){
       for(i=1;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         gm[i] = prlim[i][i];            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            }
     } /* End theta */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     trgradg =matrix(1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(j=1; j<=nlstate;j++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(theta=1; theta <=npar; theta++)            }
         trgradg[j][theta]=gradg[theta][j];          
             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));
       varpl[i][(int)age] =0.;            savm=oldm;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            oldm=newm;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          } /* end mult */
     for(i=1;i<=nlstate;i++)        
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     fprintf(ficresvpl,"%.0f ",age );          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(i=1; i<=nlstate;i++)          ipmx +=1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          sw += weight[i];
     fprintf(ficresvpl,"\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_vector(gp,1,nlstate);          /*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]);*/
     free_vector(gm,1,nlstate);        } /* end of wave */
     free_matrix(gradg,1,npar,1,nlstate);      } /* end of individual */
     free_matrix(trgradg,1,nlstate,1,npar);    } /* End of if */
   } /* End age */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   free_vector(xp,1,npar);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   free_matrix(doldm,1,nlstate,1,npar);    return -l;
   free_matrix(dnewm,1,nlstate,1,nlstate);  }
   
 }  /*************** log-likelihood *************/
   double funcone( double *x)
 /************ Variance of one-step probabilities  ******************/  {
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    /* Same as likeli but slower because of a lot of printf and if */
 {    int i, ii, j, k, mi, d, kk;
   int i, j;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   int k=0, cptcode;    double **out;
   double **dnewm,**doldm;    double lli; /* Individual log likelihood */
   double *xp;    double llt;
   double *gp, *gm;    int s1, s2;
   double **gradg, **trgradg;    double bbh, survp;
   double age,agelim, cov[NCOVMAX];    /*extern weight */
   int theta;    /* We are differentiating ll according to initial status */
   char fileresprob[FILENAMELENGTH];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   strcpy(fileresprob,"prob");      printf(" %d\n",s[4][i]);
   strcat(fileresprob,fileres);    */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    cov[1]=1.;
     printf("Problem with resultfile: %s\n", fileresprob);  
   }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   xp=vector(1,npar);      for(mi=1; mi<= wav[i]-1; mi++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for (ii=1;ii<=nlstate+ndeath;ii++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   cov[1]=1;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){          }
     cov[2]=age;        for(d=0; d<dh[mi][i]; d++){
     gradg=matrix(1,npar,1,9);          newm=savm;
     trgradg=matrix(1,9,1,npar);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          for (kk=1; kk<=cptcovage;kk++) {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
     for(theta=1; theta <=npar; theta++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=npar; i++)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          savm=oldm;
                oldm=newm;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        } /* end mult */
            
       k=0;        s1=s[mw[mi][i]][i];
       for(i=1; i<= (nlstate+ndeath); i++){        s2=s[mw[mi+1][i]][i];
         for(j=1; j<=(nlstate+ndeath);j++){        bbh=(double)bh[mi][i]/(double)stepm; 
            k=k+1;        /* bias is positive if real duration
           gp[k]=pmmij[i][j];         * is higher than the multiple of stepm and negative otherwise.
         }         */
       }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=npar; i++)        } else if  (s2==-2) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        }else if (mle==1){
       k=0;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(i=1; i<=(nlstate+ndeath); i++){        } else if(mle==2){
         for(j=1; j<=(nlstate+ndeath);j++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           k=k+1;        } else if(mle==3){  /* exponential inter-extrapolation */
           gm[k]=pmmij[i][j];          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 */
         }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       }          lli=log(out[s1][s2]); /* Original formula */
              } else{  /* mle=0 back to 1 */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            /*lli=log(out[s1][s2]); */ /* Original formula */
     }        } /* End of if */
         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]); */
          if(globpr){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      pmij(pmmij,cov,ncovmodel,x,nlstate);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
      k=0;            llt +=ll[k]*gipmx/gsw;
      for(i=1; i<=(nlstate+ndeath); i++){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
        for(j=1; j<=(nlstate+ndeath);j++){          }
          k=k+1;          fprintf(ficresilk," %10.6f\n", -llt);
          gm[k]=pmmij[i][j];        }
         }      } /* end of wave */
      }    } /* end of individual */
          for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      /*printf("\n%d ",(int)age);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      gsw=sw;
      }*/    }
     return -l;
   fprintf(ficresprob,"\n%d ",(int)age);  }
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  /*************** function likelione ***********/
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   }  {
     /* This routine should help understanding what is done with 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       the selection of individuals/waves and
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));       to check the exact contribution to the likelihood.
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       Plotting could be done.
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);     */
 }    int k;
  free_vector(xp,1,npar);  
 fclose(ficresprob);    if(*globpri !=0){ /* Just counts and sums, no printings */
  exit(0);      strcpy(fileresilk,"ilk"); 
 }      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 /***********************************************/        printf("Problem with resultfile: %s\n", fileresilk);
 /**************** Main Program *****************/        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 /***********************************************/      }
       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");
 /*int main(int argc, char *argv[])*/      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
 int main()      /*  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++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   double agedeb, agefin,hf;    }
   double agemin=1.e20, agemax=-1.e20;  
     *fretone=(*funcone)(p);
   double fret;    if(*globpri !=0){
   double **xi,tmp,delta;      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double dum; /* Dummy variable */      fflush(fichtm); 
   double ***p3mat;    } 
   int *indx;    return;
   char line[MAXLINE], linepar[MAXLINE];  }
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];  /*********** Maximum Likelihood Estimation ***************/
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   char popfile[FILENAMELENGTH];  {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    int i,j, iter;
   int firstobs=1, lastobs=10;    double **xi;
   int sdeb, sfin; /* Status at beginning and end */    double fret;
   int c,  h , cpt,l;    double fretone; /* Only one call to likelihood */
   int ju,jl, mi;    /*  char filerespow[FILENAMELENGTH];*/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    xi=matrix(1,npar,1,npar);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    for (i=1;i<=npar;i++)
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;      for (j=1;j<=npar;j++)
   int hstepm, nhstepm;        xi[i][j]=(i==j ? 1.0 : 0.0);
   int *popage,boolprev=0;/*boolprev=0 if date and zero if wave*/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   double bage, fage, age, agelim, agebase;    strcat(filerespow,fileres);
   double ftolpl=FTOL;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double **prlim;      printf("Problem with resultfile: %s\n", filerespow);
   double *severity;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double ***param; /* Matrix of parameters */    }
   double  *p;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double **matcov; /* Matrix of covariance */    for (i=1;i<=nlstate;i++)
   double ***delti3; /* Scale */      for(j=1;j<=nlstate+ndeath;j++)
   double *delti; /* Scale */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double ***eij, ***vareij;    fprintf(ficrespow,"\n");
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double kk1, kk2;  
   double *popeffectif,*popcount;    free_matrix(xi,1,npar,1,npar);
   double dateprev1, dateprev2;    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   char *alph[]={"a","a","b","c","d","e"}, str[4];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   }
   char z[1]="c", occ;  
 #include <sys/time.h>  /**** Computes Hessian and covariance matrix ***/
 #include <time.h>  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  {
   char strfprev[10], strlprev[10];    double  **a,**y,*x,pd;
   char strfprevfore[10], strlprevfore[10];    double **hess;
   /* long total_usecs;    int i, j,jk;
   struct timeval start_time, end_time;    int *indx;
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
   printf("\nIMACH, Version 0.7");    void ludcmp(double **a, int npar, int *indx, double *d) ;
   printf("\nEnter the parameter file name: ");    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
 #ifdef windows  
   scanf("%s",pathtot);    printf("\nCalculation of the hessian matrix. Wait...\n");
   getcwd(pathcd, size);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   /*cygwin_split_path(pathtot,path,optionfile);    for (i=1;i<=npar;i++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      printf("%d",i);fflush(stdout);
   /* cutv(path,optionfile,pathtot,'\\');*/      fprintf(ficlog,"%d",i);fflush(ficlog);
      
 split(pathtot, path,optionfile);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   chdir(path);      
   replace(pathc,path);      /*  printf(" %f ",p[i]);
 #endif          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
 #ifdef unix    }
   scanf("%s",optionfile);    
 #endif    for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
 /*-------- arguments in the command line --------*/        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
   strcpy(fileres,"r");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   strcat(fileres, optionfile);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
   /*---------arguments file --------*/          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        }
     printf("Problem with optionfile %s\n",optionfile);      }
     goto end;    }
   }    printf("\n");
     fprintf(ficlog,"\n");
   strcpy(filereso,"o");  
   strcat(filereso,fileres);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   if((ficparo=fopen(filereso,"w"))==NULL) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    
   }    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
   /* Reads comments: lines beginning with '#' */    x=vector(1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    indx=ivector(1,npar);
     ungetc(c,ficpar);    for (i=1;i<=npar;i++)
     fgets(line, MAXLINE, ficpar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     puts(line);    ludcmp(a,npar,indx,&pd);
     fputs(line,ficparo);  
   }    for (j=1;j<=npar;j++) {
   ungetc(c,ficpar);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   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);      lubksb(a,npar,indx,x);
   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);      for (i=1;i<=npar;i++){ 
   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);        matcov[i][j]=x[i];
 while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    printf("\n#Hessian matrix#\n");
     fputs(line,ficparo);    fprintf(ficlog,"\n#Hessian matrix#\n");
   }    for (i=1;i<=npar;i++) { 
   ungetc(c,ficpar);      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   fscanf(ficpar,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,&popbased);        fprintf(ficlog,"%.3e ",hess[i][j]);
   fprintf(ficparo,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);      }
        printf("\n");
   /* printf("%s %s",strfprev,strlprev);      fprintf(ficlog,"\n");
      exit(0);*/    }
  while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /* Recompute Inverse */
     fgets(line, MAXLINE, ficpar);    for (i=1;i<=npar;i++)
     puts(line);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fputs(line,ficparo);    ludcmp(a,npar,indx,&pd);
   }  
   ungetc(c,ficpar);    /*  printf("\n#Hessian matrix recomputed#\n");
    
   fscanf(ficpar,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,&nforecast,&mobilav);    for (j=1;j<=npar;j++) {
   fprintf(ficparo,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);      for (i=1;i<=npar;i++) x[i]=0;
            x[j]=1;
        lubksb(a,npar,indx,x);
 while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1;i<=npar;i++){ 
     ungetc(c,ficpar);        y[i][j]=x[i];
     fgets(line, MAXLINE, ficpar);        printf("%.3e ",y[i][j]);
     puts(line);        fprintf(ficlog,"%.3e ",y[i][j]);
     fputs(line,ficparo);      }
   }      printf("\n");
   ungetc(c,ficpar);      fprintf(ficlog,"\n");
      }
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);    */
    
   covar=matrix(0,NCOVMAX,1,n);    free_matrix(a,1,npar,1,npar);
   cptcovn=0;    free_matrix(y,1,npar,1,npar);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   ncovmodel=2+cptcovn;    free_matrix(hess,1,npar,1,npar);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    
   /* Read guess parameters */  }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /*************** hessian matrix ****************/
     ungetc(c,ficpar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    int i;
     fputs(line,ficparo);    int l=1, lmax=20;
   }    double k1,k2;
   ungetc(c,ficpar);    double p2[MAXPARM+1]; /* identical to x */
      double res;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for(i=1; i <=nlstate; i++)    double fx;
     for(j=1; j <=nlstate+ndeath-1; j++){    int k=0,kmax=10;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double l1;
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);    fx=func(x);
       for(k=1; k<=ncovmodel;k++){    for (i=1;i<=npar;i++) p2[i]=x[i];
         fscanf(ficpar," %lf",&param[i][j][k]);    for(l=0 ; l <=lmax; l++){
         printf(" %lf",param[i][j][k]);      l1=pow(10,l);
         fprintf(ficparo," %lf",param[i][j][k]);      delts=delt;
       }      for(k=1 ; k <kmax; k=k+1){
       fscanf(ficpar,"\n");        delt = delta*(l1*k);
       printf("\n");        p2[theta]=x[theta] +delt;
       fprintf(ficparo,"\n");        k1=func(p2)-fx;
     }        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   p=param[1][1];        
    #ifdef DEBUGHESS
   /* Reads comments: lines beginning with '#' */        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);
   while((c=getc(ficpar))=='#' && c!= EOF){        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);
     ungetc(c,ficpar);  #endif
     fgets(line, MAXLINE, ficpar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     puts(line);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     fputs(line,ficparo);          k=kmax;
   }        }
   ungetc(c,ficpar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   for(i=1; i <=nlstate; i++){          delts=delt;
     for(j=1; j <=nlstate+ndeath-1; j++){        }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      }
       printf("%1d%1d",i,j);    }
       fprintf(ficparo,"%1d%1d",i1,j1);    delti[theta]=delts;
       for(k=1; k<=ncovmodel;k++){    return res; 
         fscanf(ficpar,"%le",&delti3[i][j][k]);    
         printf(" %le",delti3[i][j][k]);  }
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       fscanf(ficpar,"\n");  {
       printf("\n");    int i;
       fprintf(ficparo,"\n");    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
   }    double p2[MAXPARM+1];
   delti=delti3[1][1];    int k;
    
   /* Reads comments: lines beginning with '#' */    fx=func(x);
   while((c=getc(ficpar))=='#' && c!= EOF){    for (k=1; k<=2; k++) {
     ungetc(c,ficpar);      for (i=1;i<=npar;i++) p2[i]=x[i];
     fgets(line, MAXLINE, ficpar);      p2[thetai]=x[thetai]+delti[thetai]/k;
     puts(line);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fputs(line,ficparo);      k1=func(p2)-fx;
   }    
   ungetc(c,ficpar);      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   matcov=matrix(1,npar,1,npar);      k2=func(p2)-fx;
   for(i=1; i <=npar; i++){    
     fscanf(ficpar,"%s",&str);      p2[thetai]=x[thetai]-delti[thetai]/k;
     printf("%s",str);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fprintf(ficparo,"%s",str);      k3=func(p2)-fx;
     for(j=1; j <=i; j++){    
       fscanf(ficpar," %le",&matcov[i][j]);      p2[thetai]=x[thetai]-delti[thetai]/k;
       printf(" %.5le",matcov[i][j]);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       fprintf(ficparo," %.5le",matcov[i][j]);      k4=func(p2)-fx;
     }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     fscanf(ficpar,"\n");  #ifdef DEBUG
     printf("\n");      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     fprintf(ficparo,"\n");      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   }  #endif
   for(i=1; i <=npar; i++)    }
     for(j=i+1;j<=npar;j++)    return res;
       matcov[i][j]=matcov[j][i];  }
      
   printf("\n");  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   { 
     /*-------- data file ----------*/    int i,imax,j,k; 
     if((ficres =fopen(fileres,"w"))==NULL) {    double big,dum,sum,temp; 
       printf("Problem with resultfile: %s\n", fileres);goto end;    double *vv; 
     }   
     fprintf(ficres,"#%s\n",version);    vv=vector(1,n); 
        *d=1.0; 
     if((fic=fopen(datafile,"r"))==NULL)    {    for (i=1;i<=n;i++) { 
       printf("Problem with datafile: %s\n", datafile);goto end;      big=0.0; 
     }      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
     n= lastobs;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     severity = vector(1,maxwav);      vv[i]=1.0/big; 
     outcome=imatrix(1,maxwav+1,1,n);    } 
     num=ivector(1,n);    for (j=1;j<=n;j++) { 
     moisnais=vector(1,n);      for (i=1;i<j;i++) { 
     annais=vector(1,n);        sum=a[i][j]; 
     moisdc=vector(1,n);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     andc=vector(1,n);        a[i][j]=sum; 
     agedc=vector(1,n);      } 
     cod=ivector(1,n);      big=0.0; 
     weight=vector(1,n);      for (i=j;i<=n;i++) { 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        sum=a[i][j]; 
     mint=matrix(1,maxwav,1,n);        for (k=1;k<j;k++) 
     anint=matrix(1,maxwav,1,n);          sum -= a[i][k]*a[k][j]; 
     s=imatrix(1,maxwav+1,1,n);        a[i][j]=sum; 
     adl=imatrix(1,maxwav+1,1,n);            if ( (dum=vv[i]*fabs(sum)) >= big) { 
     tab=ivector(1,NCOVMAX);          big=dum; 
     ncodemax=ivector(1,8);          imax=i; 
         } 
     i=1;      } 
     while (fgets(line, MAXLINE, fic) != NULL)    {      if (j != imax) { 
       if ((i >= firstobs) && (i <=lastobs)) {        for (k=1;k<=n;k++) { 
                  dum=a[imax][k]; 
         for (j=maxwav;j>=1;j--){          a[imax][k]=a[j][k]; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          a[j][k]=dum; 
           strcpy(line,stra);        } 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        *d = -(*d); 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        vv[imax]=vv[j]; 
         }      } 
              indx[j]=imax; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      if (a[j][j] == 0.0) a[j][j]=TINY; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      if (j != n) { 
         dum=1.0/(a[j][j]); 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      } 
     } 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(vv,1,n);  /* Doesn't work */
         for (j=ncov;j>=1;j--){  ;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  } 
         }  
         num[i]=atol(stra);  void lubksb(double **a, int n, int *indx, double b[]) 
          { 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    int i,ii=0,ip,j; 
           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;}*/    double sum; 
    
         i=i+1;    for (i=1;i<=n;i++) { 
       }      ip=indx[i]; 
     }      sum=b[ip]; 
     /* printf("ii=%d", ij);      b[ip]=b[i]; 
        scanf("%d",i);*/      if (ii) 
   imx=i-1; /* Number of individuals */        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
   /* for (i=1; i<=imx; i++){      b[i]=sum; 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    } 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    for (i=n;i>=1;i--) { 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      sum=b[i]; 
     }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     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]));*/      b[i]=sum/a[i][i]; 
     } 
   /* Calculation of the number of parameter from char model*/  } 
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);  void pstamp(FILE *fichier)
   Tvaraff=ivector(1,15);  {
   Tvard=imatrix(1,15,1,2);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   Tage=ivector(1,15);        }
      
   if (strlen(model) >1){  /************ Frequencies ********************/
     j=0, j1=0, k1=1, k2=1;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     j=nbocc(model,'+');  {  /* Some frequencies */
     j1=nbocc(model,'*');    
     cptcovn=j+1;    int i, m, jk, k1,i1, j1, bool, z1,j;
     cptcovprod=j1;    int first;
        double ***freq; /* Frequencies */
        double *pp, **prop;
     strcpy(modelsav,model);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    char fileresp[FILENAMELENGTH];
       printf("Error. Non available option model=%s ",model);    
       goto end;    pp=vector(1,nlstate);
     }    prop=matrix(1,nlstate,iagemin,iagemax+3);
        strcpy(fileresp,"p");
     for(i=(j+1); i>=1;i--){    strcat(fileresp,fileres);
       cutv(stra,strb,modelsav,'+');    if((ficresp=fopen(fileresp,"w"))==NULL) {
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       /*scanf("%d",i);*/      exit(0);
       if (strchr(strb,'*')) {    }
         cutv(strd,strc,strb,'*');    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         if (strcmp(strc,"age")==0) {    j1=0;
           cptcovprod--;    
           cutv(strb,stre,strd,'V');    j=cptcoveff;
           Tvar[i]=atoi(stre);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           cptcovage++;  
             Tage[cptcovage]=i;    first=1;
             /*printf("stre=%s ", stre);*/  
         }    for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
         else if (strcmp(strd,"age")==0) {      for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
           cptcovprod--;        j1++;
           cutv(strb,stre,strc,'V');        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           Tvar[i]=atoi(stre);          scanf("%d", i);*/
           cptcovage++;        for (i=-5; i<=nlstate+ndeath; i++)  
           Tage[cptcovage]=i;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         }            for(m=iagemin; m <= iagemax+3; m++)
         else {              freq[i][jk][m]=0;
           cutv(strb,stre,strc,'V');        
           Tvar[i]=ncov+k1;        for (i=1; i<=nlstate; i++)  
           cutv(strb,strc,strd,'V');          for(m=iagemin; m <= iagemax+3; m++)
           Tprod[k1]=i;            prop[i][m]=0;
           Tvard[k1][1]=atoi(strc);        
           Tvard[k1][2]=atoi(stre);        dateintsum=0;
           Tvar[cptcovn+k2]=Tvard[k1][1];        k2cpt=0;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for (i=1; i<=imx; i++) {
           for (k=1; k<=lastobs;k++)          bool=1;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           k1++;            for (z1=1; z1<=cptcoveff; z1++)       
           k2=k2+2;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
         }                bool=0;
       }                printf("bool=%d i=%d, z1=%d, i1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
       else {                  bool,i,z1, i1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);
        /*  scanf("%d",i);*/                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
       cutv(strd,strc,strb,'V');              } 
       Tvar[i]=atoi(strc);          }
       }   
       strcpy(modelsav,stra);            if (bool==1){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            for(m=firstpass; m<=lastpass; m++){
         scanf("%d",i);*/              k2=anint[m][i]+(mint[m][i]/12.);
     }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   printf("cptcovprod=%d ", cptcovprod);                if (m<lastpass) {
   scanf("%d ",i);*/                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     fclose(fic);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
     /*  if(mle==1){*/                
     if (weightopt != 1) { /* Maximisation without weights*/                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       for(i=1;i<=n;i++) weight[i]=1.0;                  dateintsum=dateintsum+k2;
     }                  k2cpt++;
     /*-calculation of age at interview from date of interview and age at death -*/                }
     agev=matrix(1,maxwav,1,imx);                /*}*/
             }
    for (i=1; i<=imx; i++)          }
      for(m=2; (m<= maxwav); m++)        }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         
          anint[m][i]=9999;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
          s[m][i]=-1;        pstamp(ficresp);
        }        if  (cptcovn>0) {
              fprintf(ficresp, "\n#********** Variable "); 
     for (i=1; i<=imx; i++)  {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          fprintf(ficresp, "**********\n#");
       for(m=1; (m<= maxwav); m++){          fprintf(ficlog, "\n#********** Variable "); 
         if(s[m][i] >0){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           if (s[m][i] == nlstate+1) {          fprintf(ficlog, "**********\n#");
             if(agedc[i]>0)        }
               if(moisdc[i]!=99 && andc[i]!=9999)        for(i=1; i<=nlstate;i++) 
               agev[m][i]=agedc[i];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             else {        fprintf(ficresp, "\n");
               if (andc[i]!=9999){        
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        for(i=iagemin; i <= iagemax+3; i++){
               agev[m][i]=-1;          if(i==iagemax+3){
               }            fprintf(ficlog,"Total");
             }          }else{
           }            if(first==1){
           else if(s[m][i] !=9){ /* Should no more exist */              first=0;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);              printf("See log file for details...\n");
             if(mint[m][i]==99 || anint[m][i]==9999)            }
               agev[m][i]=1;            fprintf(ficlog,"Age %d", i);
             else if(agev[m][i] <agemin){          }
               agemin=agev[m][i];          for(jk=1; jk <=nlstate ; jk++){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             }              pp[jk] += freq[jk][m][i]; 
             else if(agev[m][i] >agemax){          }
               agemax=agev[m][i];          for(jk=1; jk <=nlstate ; jk++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            for(m=-1, pos=0; m <=0 ; m++)
             }              pos += freq[jk][m][i];
             /*agev[m][i]=anint[m][i]-annais[i];*/            if(pp[jk]>=1.e-10){
             /*   agev[m][i] = age[i]+2*m;*/              if(first==1){
           }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           else { /* =9 */              }
             agev[m][i]=1;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             s[m][i]=-1;            }else{
           }              if(first==1)
         }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         else /*= 0 Unknown */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           agev[m][i]=1;            }
       }          }
      
     }          for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<=imx; i++)  {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(m=1; (m<= maxwav); m++){              pp[jk] += freq[jk][m][i];
         if (s[m][i] > (nlstate+ndeath)) {          }       
           printf("Error: Wrong value in nlstate or ndeath\n");            for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           goto end;            pos += pp[jk];
         }            posprop += prop[jk][i];
       }          }
     }          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_vector(severity,1,maxwav);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_imatrix(outcome,1,maxwav+1,1,n);            }else{
     free_vector(moisnais,1,n);              if(first==1)
     free_vector(annais,1,n);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     /* free_matrix(mint,1,maxwav,1,n);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
        free_matrix(anint,1,maxwav,1,n);*/            }
     free_vector(moisdc,1,n);            if( i <= iagemax){
     free_vector(andc,1,n);              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                    /*probs[i][jk][j1]= pp[jk]/pos;*/
     wav=ivector(1,imx);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              else
                    fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     /* Concatenates waves */            }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          }
           
           for(jk=-1; jk <=nlstate+ndeath; jk++)
       Tcode=ivector(1,100);            for(m=-1; m <=nlstate+ndeath; m++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              if(freq[jk][m][i] !=0 ) {
       ncodemax[1]=1;              if(first==1)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                      fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
    codtab=imatrix(1,100,1,10);              }
    h=0;          if(i <= iagemax)
    m=pow(2,cptcoveff);            fprintf(ficresp,"\n");
            if(first==1)
    for(k=1;k<=cptcoveff; k++){            printf("Others in log...\n");
      for(i=1; i <=(m/pow(2,k));i++){          fprintf(ficlog,"\n");
        for(j=1; j <= ncodemax[k]; j++){        }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      }
            h++;    }
            if (h>m) h=1;codtab[h][k]=j;    dateintmean=dateintsum/k2cpt; 
          }   
        }    fclose(ficresp);
      }    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);
    /* Calculates basic frequencies. Computes observed prevalence at single age    /* End of Freq */
        and prints on file fileres'p'. */  }
   
     if ((nbocc(strfprev,'/')==1) && (nbocc(strlprev,'/')==1)){  /************ Prevalence ********************/
      boolprev=0;  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)
      cutv(stra,strb,strfprev,'/');  {  
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      cutv(stra,strb,strlprev,'/');       in each health status at the date of interview (if between dateprev1 and dateprev2).
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);       We still use firstpass and lastpass as another selection.
    }    */
       
    else if ((nbocc(strfprev,'/')==0) &&(nbocc(strlprev,'/')==0)){    int i, m, jk, k1, i1, j1, bool, z1,j;
      boolprev=1;    double ***freq; /* Frequencies */
      fprev=atoi(strfprev); lprev=atoi(strlprev);    double *pp, **prop;
    }    double pos,posprop; 
     else {    double  y2; /* in fractional years */
       printf("Error in statement lprevalence or fprevalence\n");    int iagemin, iagemax;
       goto end;  
     }    iagemin= (int) agemin;
        iagemax= (int) agemax;
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint,boolprev,dateprev1,dateprev2);    /*pp=vector(1,nlstate);*/
      prop=matrix(1,nlstate,iagemin,iagemax+3); 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    j1=0;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    j=cptcoveff;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
          
     /* For Powell, parameters are in a vector p[] starting at p[1]    for(k1=1; k1<=j;k1++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(i1=1; i1<=ncodemax[k1];i1++){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        j1++;
         
     if(mle==1){        for (i=1; i<=nlstate; i++)  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0.0;
           
     /*--------- results files --------------*/        for (i=1; i<=imx; i++) { /* Each individual */
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);          bool=1;
    fprintf(ficres,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);          if  (cptcovn>0) {
    fprintf(ficres,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    jk=1;                bool=0;
    fprintf(ficres,"# Parameters\n");          } 
    printf("# Parameters\n");          if (bool==1) { 
    for(i=1,jk=1; i <=nlstate; i++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
      for(k=1; k <=(nlstate+ndeath); k++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
        if (k != i)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
          {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
            printf("%d%d ",i,k);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
            fprintf(ficres,"%1d%1d ",i,k);                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(j=1; j <=ncovmodel; j++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
              printf("%f ",p[jk]);                  /*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]]);*/
              fprintf(ficres,"%f ",p[jk]);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
              jk++;                  prop[s[m][i]][iagemax+3] += weight[i]; 
            }                } 
            printf("\n");              }
            fprintf(ficres,"\n");            } /* end selection of waves */
          }          }
      }        }
    }        for(i=iagemin; i <= iagemax+3; i++){  
  if(mle==1){          
     /* Computing hessian and covariance matrix */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     ftolhess=ftol; /* Usually correct */            posprop += prop[jk][i]; 
     hesscov(matcov, p, npar, delti, ftolhess, func);          } 
  }  
     fprintf(ficres,"# Scales\n");          for(jk=1; jk <=nlstate ; jk++){     
     printf("# Scales\n");            if( i <=  iagemax){ 
      for(i=1,jk=1; i <=nlstate; i++){              if(posprop>=1.e-5){ 
       for(j=1; j <=nlstate+ndeath; j++){                probs[i][jk][j1]= prop[jk][i]/posprop;
         if (j!=i) {              } else
           fprintf(ficres,"%1d%1d",i,j);                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
           printf("%1d%1d",i,j);            } 
           for(k=1; k<=ncovmodel;k++){          }/* end jk */ 
             printf(" %.5e",delti[jk]);        }/* end i */ 
             fprintf(ficres," %.5e",delti[jk]);      } /* end i1 */
             jk++;    } /* end k1 */
           }    
           printf("\n");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           fprintf(ficres,"\n");    /*free_vector(pp,1,nlstate);*/
         }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       }  }  /* End of prevalence */
      }  
      /************* Waves Concatenation ***************/
     k=1;  
     fprintf(ficres,"# Covariance\n");  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     printf("# Covariance\n");  {
     for(i=1;i<=npar;i++){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       /*  if (k>nlstate) k=1;       Death is a valid wave (if date is known).
       i1=(i-1)/(ncovmodel*nlstate)+1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       printf("%s%d%d",alph[k],i1,tab[i]);*/       and mw[mi+1][i]. dh depends on stepm.
       fprintf(ficres,"%3d",i);       */
       printf("%3d",i);  
       for(j=1; j<=i;j++){    int i, mi, m;
         fprintf(ficres," %.5e",matcov[i][j]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         printf(" %.5e",matcov[i][j]);       double sum=0., jmean=0.;*/
       }    int first;
       fprintf(ficres,"\n");    int j, k=0,jk, ju, jl;
       printf("\n");    double sum=0.;
       k++;    first=0;
     }    jmin=1e+5;
        jmax=-1;
     while((c=getc(ficpar))=='#' && c!= EOF){    jmean=0.;
       ungetc(c,ficpar);    for(i=1; i<=imx; i++){
       fgets(line, MAXLINE, ficpar);      mi=0;
       puts(line);      m=firstpass;
       fputs(line,ficparo);      while(s[m][i] <= nlstate){
     }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     ungetc(c,ficpar);          mw[++mi][i]=m;
          if(m >=lastpass)
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          break;
            else
     if (fage <= 2) {          m++;
       bage = agemin;      }/* end while */
       fage = agemax;      if (s[m][i] > nlstate){
     }        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");           /* Only death is a correct wave */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        mw[mi][i]=m;
       }
      
 /*------------ gnuplot -------------*/      wav[i]=mi;
 chdir(pathcd);      if(mi==0){
   if((ficgp=fopen("graph.plt","w"))==NULL) {        nbwarn++;
     printf("Problem with file graph.gp");goto end;        if(first==0){
   }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 #ifdef windows          first=1;
   fprintf(ficgp,"cd \"%s\" \n",pathc);        }
 #endif        if(first==1){
 m=pow(2,cptcoveff);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
          }
  /* 1eme*/      } /* end mi==0 */
   for (cpt=1; cpt<= nlstate ; cpt ++) {    } /* End individuals */
    for (k1=1; k1<= m ; k1 ++) {  
     for(i=1; i<=imx; i++){
 #ifdef windows      for(mi=1; mi<wav[i];mi++){
     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);        if (stepm <=0)
 #endif          dh[mi][i]=1;
 #ifdef unix        else{
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 #endif            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 for (i=1; i<= nlstate ; i ++) {              if(j==0) j=1;  /* Survives at least one month after exam */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              else if(j<0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");                nberr++;
 }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                j=1; /* Temporary Dangerous patch */
     for (i=1; i<= nlstate ; i ++) {                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);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                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]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
 }              }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              k=k+1;
      for (i=1; i<= nlstate ; i ++) {              if (j >= jmax){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                jmax=j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                ijmax=i;
 }                }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));              if (j <= jmin){
 #ifdef unix                jmin=j;
 fprintf(ficgp,"\nset ter gif small size 400,300");                ijmin=i;
 #endif              }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              sum=sum+j;
    }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   /*2 eme*/            }
           }
   for (k1=1; k1<= m ; k1 ++) {          else{
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
      /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;            k=k+1;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            if (j >= jmax) {
       for (j=1; j<= nlstate+1 ; j ++) {              jmax=j;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              ijmax=i;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }              else if (j <= jmin){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              jmin=j;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              ijmin=i;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            }
       for (j=1; j<= nlstate+1 ; j ++) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            /*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]);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");            if(j<0){
 }                nberr++;
       fprintf(ficgp,"\" t\"\" w l 0,");              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]);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for (j=1; j<= nlstate+1 ; j ++) {            }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            sum=sum+j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }            jk= j/stepm;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          jl= j -jk*stepm;
       else fprintf(ficgp,"\" t\"\" w l 0,");          ju= j -(jk+1)*stepm;
     }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            if(jl==0){
   }              dh[mi][i]=jk;
                bh[mi][i]=0;
   /*3eme*/            }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
   for (k1=1; k1<= m ; k1 ++) {              dh[mi][i]=jk+1;
     for (cpt=1; cpt<= nlstate ; cpt ++) {              bh[mi][i]=ju;
       k=2+nlstate*(cpt-1);            }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          }else{
       for (i=1; i< nlstate ; i ++) {            if(jl <= -ju){
         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);              dh[mi][i]=jk;
       }              bh[mi][i]=jl;       /* bias is positive if real duration
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                                   * is higher than the multiple of stepm and negative otherwise.
     }                                   */
   }            }
              else{
   /* CV preval stat */              dh[mi][i]=jk+1;
   for (k1=1; k1<= m ; k1 ++) {              bh[mi][i]=ju;
     for (cpt=1; cpt<nlstate ; cpt ++) {            }
       k=3;            if(dh[mi][i]==0){
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              dh[mi][i]=1; /* At least one step */
       for (i=1; i< nlstate ; i ++)              bh[mi][i]=ju; /* At least one step */
         fprintf(ficgp,"+$%d",k+i+1);              /*  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);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            }
                } /* end if mle */
       l=3+(nlstate+ndeath)*cpt;        }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      } /* end wave */
       for (i=1; i< nlstate ; i ++) {    }
         l=3+(nlstate+ndeath)*cpt;    jmean=sum/k;
         fprintf(ficgp,"+$%d",l+i+1);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
       }    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
       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);  
     }  /*********** Tricode ****************************/
   }    void tricode(int *Tvar, int **nbcode, int imx)
   {
   /* proba elementaires */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
    for(i=1,jk=1; i <=nlstate; i++){    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     for(k=1; k <=(nlstate+ndeath); k++){    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
       if (k != i) {    /* nbcode[Tvar[j][1]= 
         for(j=1; j <=ncovmodel; j++){    */
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/  
           /*fprintf(ficgp,"%s",alph[1]);*/    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    int modmaxcovj=0; /* Modality max of covariates j */
           jk++;    cptcoveff=0; 
           fprintf(ficgp,"\n");   
         }    for (k=0; k < maxncov; k++) Ndum[k]=0;
       }    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     }  
     }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
   for(jk=1; jk <=m; jk++) {                                 modality of this covariate Vj*/ 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
    i=1;                                        modality of the nth covariate of individual i. */
    for(k2=1; k2<=nlstate; k2++) {        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
      k3=i;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
      for(k=1; k<=(nlstate+ndeath); k++) {        if (ij > modmaxcovj) modmaxcovj=ij; 
        if (k != k2){        /* getting the maximum value of the modality of the covariate
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
 ij=1;           female is 1, then modmaxcovj=1.*/
         for(j=3; j <=ncovmodel; j++) {      }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
             ij++;        if( Ndum[i] != 0 )
           }          ncodemax[j]++; 
           else        /* Number of modalities of the j th covariate. In fact
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);           ncodemax[j]=2 (dichotom. variables only) but it could be more for
         }           historical reasons */
           fprintf(ficgp,")/(1");      } /* Ndum[-1] number of undefined modalities */
          
         for(k1=1; k1 <=nlstate; k1++){        /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      ij=1; 
 ij=1;      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
           for(j=3; j <=ncovmodel; j++){        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
             ij++;                                       k is a modality. If we have model=V1+V1*sex 
           }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           else            ij++;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
           }          if (ij > ncodemax[j]) break; 
           fprintf(ficgp,")");        }  /* end of loop on */
         }      } /* end of loop on modality */ 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    
         i=i+ncovmodel;    for (k=0; k< maxncov; k++) Ndum[k]=0;
        }    
      }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
    }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
   }     Ndum[ij]++;
       }
   fclose(ficgp);  
       ij=1;
 chdir(path);   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
         if((Ndum[i]!=0) && (i<=ncovcol)){
     free_ivector(wav,1,imx);       Tvaraff[ij]=i; /*For printing */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       ij++;
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       }
     free_ivector(num,1,n);   }
     free_vector(agedc,1,n);   ij--;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/   cptcoveff=ij; /*Number of total covariates*/
     fclose(ficparo);  }
     fclose(ficres);  
     /*  }*/  /*********** Health Expectancies ****************/
      
    /*________fin mle=1_________*/  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
      
   {
      /* Health expectancies, no variances */
     /* No more information from the sample is required now */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   /* Reads comments: lines beginning with '#' */    int nhstepma, nstepma; /* Decreasing with age */
   while((c=getc(ficpar))=='#' && c!= EOF){    double age, agelim, hf;
     ungetc(c,ficpar);    double ***p3mat;
     fgets(line, MAXLINE, ficpar);    double eip;
     puts(line);  
     fputs(line,ficparo);    pstamp(ficreseij);
   }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   ungetc(c,ficpar);    fprintf(ficreseij,"# Age");
      for(i=1; i<=nlstate;i++){
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      for(j=1; j<=nlstate;j++){
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        fprintf(ficreseij," e%1d%1d ",i,j);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      }
 /*--------- index.htm --------*/      fprintf(ficreseij," e%1d. ",i);
     }
   strcpy(optionfilehtm,optionfile);    fprintf(ficreseij,"\n");
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    
     printf("Problem with %s \n",optionfilehtm);goto end;    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    else  hstepm=estepm;   
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    /* We compute the life expectancy from trapezoids spaced every estepm months
 Total number of observations=%d <br>     * This is mainly to measure the difference between two models: for example
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>     * if stepm=24 months pijx are given only every 2 years and by summing them
 <hr  size=\"2\" color=\"#EC5E5E\">     * we are calculating an estimate of the Life Expectancy assuming a linear 
 <li>Outputs files<br><br>\n     * progression in between and thus overestimating or underestimating according
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n     * to the curvature of the survival function. If, for the same date, we 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>     * to compare the new estimate of Life expectancy with the same linear 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>     * hypothesis. A more precise result, taking into account a more precise
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>     * curvature will be obtained if estepm is as small as stepm. */
         - 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 example we decided to compute the life expectancy with the smallest unit */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>       nhstepm is the number of hstepm from age to agelim 
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>       nstepm is the number of stepm from age to agelin. 
 <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);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
  fprintf(fichtm," <li>Graphs</li><p>");    /* 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
  m=cptcoveff;       means that if the survival funtion is printed only each two years of age and if
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       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.
  j1=0;    */
  for(k1=1; k1<=m;k1++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;    agelim=AGESUP;
        if (cptcovn > 0) {    /* If stepm=6 months */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          for (cpt=1; cpt<=cptcoveff;cpt++)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  /* nhstepm age range expressed in number of stepm */
        }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        /* if (stepm >= YEARM) hstepm=1;*/
        for(cpt=1; cpt<nlstate;cpt++){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
        }    for (age=bage; age<=fage; age ++){ 
     for(cpt=1; cpt<=nlstate;cpt++) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 interval) in state (%d): v%s%d%d.gif <br>      /* if (stepm >= YEARM) hstepm=1;*/
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {      /* If stepm=6 months */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      /* Computed by stepm unit matrices, product of hstepma matrices, stored
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      }      
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 health expectancies in states (1) and (2): e%s%d.gif<br>      
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 fprintf(fichtm,"\n</body>");      
    }      printf("%d|",(int)age);fflush(stdout);
  }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 fclose(fichtm);      
       /* Computing expectancies */
   /*--------------- Prevalence limit --------------*/      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   strcpy(filerespl,"pl");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   strcat(filerespl,fileres);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          }
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");      fprintf(ficreseij,"%3.0f",age );
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(i=1; i<=nlstate;i++){
   fprintf(ficrespl,"\n");        eip=0;
          for(j=1; j<=nlstate;j++){
   prlim=matrix(1,nlstate,1,nlstate);          eip +=eij[i][j][(int)age];
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficreseij,"%9.4f", eip );
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fprintf(ficreseij,"\n");
   k=0;      
   agebase=agemin;    }
   agelim=agemax;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ftolpl=1.e-10;    printf("\n");
   i1=cptcoveff;    fprintf(ficlog,"\n");
   if (cptcovn < 1){i1=1;}    
   }
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  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[] )
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  {
         fprintf(ficrespl,"\n#******");    /* Covariances of health expectancies eij and of total life expectancies according
         for(j=1;j<=cptcoveff;j++)     to initial status i, ei. .
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    */
         fprintf(ficrespl,"******\n");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
            int nhstepma, nstepma; /* Decreasing with age */
         for (age=agebase; age<=agelim; age++){    double age, agelim, hf;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double ***p3matp, ***p3matm, ***varhe;
           fprintf(ficrespl,"%.0f",age );    double **dnewm,**doldm;
           for(i=1; i<=nlstate;i++)    double *xp, *xm;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double **gp, **gm;
           fprintf(ficrespl,"\n");    double ***gradg, ***trgradg;
         }    int theta;
       }  
     }    double eip, vip;
   fclose(ficrespl);  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   /*------------- h Pij x at various ages ------------*/    xp=vector(1,npar);
      xm=vector(1,npar);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    
   }    pstamp(ficresstdeij);
   printf("Computing pij: result on file '%s' \n", filerespij);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
      fprintf(ficresstdeij,"# Age");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(i=1; i<=nlstate;i++){
   /*if (stepm<=24) stepsize=2;*/      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   agelim=AGESUP;      fprintf(ficresstdeij," e%1d. ",i);
   hstepm=stepsize*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fprintf(ficresstdeij,"\n");
    
   k=0;    pstamp(ficrescveij);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficrescveij,"# Age");
       k=k+1;    for(i=1; i<=nlstate;i++)
         fprintf(ficrespij,"\n#****** ");      for(j=1; j<=nlstate;j++){
         for(j=1;j<=cptcoveff;j++)        cptj= (j-1)*nlstate+i;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(i2=1; i2<=nlstate;i2++)
         fprintf(ficrespij,"******\n");          for(j2=1; j2<=nlstate;j2++){
                    cptj2= (j2-1)*nlstate+i2;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            if(cptj2 <= cptj)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           oldm=oldms;savm=savms;    fprintf(ficrescveij,"\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           fprintf(ficrespij,"# Age");    if(estepm < stepm){
           for(i=1; i<=nlstate;i++)      printf ("Problem %d lower than %d\n",estepm, stepm);
             for(j=1; j<=nlstate+ndeath;j++)    }
               fprintf(ficrespij," %1d-%1d",i,j);    else  hstepm=estepm;   
           fprintf(ficrespij,"\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
           for (h=0; h<=nhstepm; h++){     * This is mainly to measure the difference between two models: for example
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );     * if stepm=24 months pijx are given only every 2 years and by summing them
             for(i=1; i<=nlstate;i++)     * we are calculating an estimate of the Life Expectancy assuming a linear 
               for(j=1; j<=nlstate+ndeath;j++)     * progression in between and thus overestimating or underestimating according
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);     * to the curvature of the survival function. If, for the same date, we 
             fprintf(ficrespij,"\n");     * 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 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * hypothesis. A more precise result, taking into account a more precise
           fprintf(ficrespij,"\n");     * curvature will be obtained if estepm is as small as stepm. */
         }  
     }    /* 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 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   fclose(ficrespij);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /*---------- Forecasting ------------------*/       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   strcpy(fileresf,"f");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   strcat(fileresf,fileres);       results. So we changed our mind and took the option of the best precision.
   if((ficresf=fopen(fileresf,"w"))==NULL) {    */
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);    /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
  if ((nbocc(strfprevfore,'/')==1) && (nbocc(strlprevfore,'/')==1)){    agelim=AGESUP;
      boolprev=0;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
      cutv(stra,strb,strfprevfore,'/');    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);    /* if (stepm >= YEARM) hstepm=1;*/
      cutv(stra,strb,strlprevfore,'/');    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);    
    }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    else if ((nbocc(strfprevfore,'/')==0) &&(nbocc(strlprevfore,'/')==0)){    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
      boolprev=1;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      fprev=atoi(strfprevfore); lprev=atoi(strlprevfore);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
    }    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     else {  
       printf("Error in statement lprevalence or fprevalence\n");    for (age=bage; age<=fage; age ++){ 
       goto end;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore,mint,anint,boolprev,dateprev1,dateprev2);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    
   free_matrix(mint,1,maxwav,1,n);      /* If stepm=6 months */
   free_matrix(anint,1,maxwav,1,n);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   free_matrix(agev,1,maxwav,1,imx);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   /* Mobile average */      
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       /* Computing  Variances of health expectancies */
   if (mobilav==1) {      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         decrease memory allocation */
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      for(theta=1; theta <=npar; theta++){
       for (i=1; i<=nlstate;i++)        for(i=1; i<=npar; i++){ 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           mobaverage[(int)agedeb][i][cptcod]=0.;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
            }
     for (agedeb=bage+4; agedeb<=fage; agedeb++){        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       for (i=1; i<=nlstate;i++){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
           for (cpt=0;cpt<=4;cpt++){        for(j=1; j<= nlstate; j++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for(i=1; i<=nlstate; i++){
           }            for(h=0; h<=nhstepm-1; h++){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         }              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       }            }
     }            }
   }        }
        
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(ij=1; ij<= nlstate*nlstate; ij++)
   if (stepm<=12) stepsize=1;          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   agelim=AGESUP;          }
   hstepm=stepsize*YEARM; /* Every year of age */      }/* End theta */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */      
        
   if (popforecast==1) {      for(h=0; h<=nhstepm-1; h++)
     if((ficpop=fopen(popfile,"r"))==NULL)    {        for(j=1; j<=nlstate*nlstate;j++)
       printf("Problem with population file : %s\n",popfile);goto end;          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
     popage=ivector(0,AGESUP);      
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
     i=1;            varhe[ij][ji][(int)age] =0.;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)  
       {       printf("%d|",(int)age);fflush(stdout);
         i=i+1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       }       for(h=0;h<=nhstepm-1;h++){
     imx=i;        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   }          for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
   for(cptcov=1;cptcov<=i1;cptcov++){              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
       k=k+1;      }
       fprintf(ficresf,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++) {      /* Computing expectancies */
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       }      for(i=1; i<=nlstate;i++)
       fprintf(ficresf,"******\n");        for(j=1; j<=nlstate;j++)
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
       if (popforecast==1)  fprintf(ficresf," [Population]");            
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       for (agedeb=fage; agedeb>=bage; agedeb--){  
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);          }
        if (mobilav==1) {  
         for(j=1; j<=nlstate;j++)      fprintf(ficresstdeij,"%3.0f",age );
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);      for(i=1; i<=nlstate;i++){
         }        eip=0.;
         else {        vip=0.;
           for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++){
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);          eip += eij[i][j][(int)age];
         }            for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);        }
       }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
            }
       for (cpt=1; cpt<=nforecast;cpt++) {      fprintf(ficresstdeij,"\n");
         fprintf(ficresf,"\n");  
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      fprintf(ficrescveij,"%3.0f",age );
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(i=1; i<=nlstate;i++)
         nhstepm = nhstepm/hstepm;        for(j=1; j<=nlstate;j++){
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/          cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j2=1; j2<=nlstate;j2++){
         oldm=oldms;savm=savms;              cptj2= (j2-1)*nlstate+i2;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                if(cptj2 <= cptj)
                                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         for (h=0; h<=nhstepm; h++){            }
                }
          if (h*hstepm/YEARM*stepm==cpt)      fprintf(ficrescveij,"\n");
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);     
              }
              free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
          for(j=1; j<=nlstate+ndeath;j++) {    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
            kk1=0.;kk2=0;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
            for(i=1; i<=nlstate;i++) {            free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
              if (mobilav==1)    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];    printf("\n");
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    fprintf(ficlog,"\n");
             }  
            if (h*hstepm/YEARM*stepm==cpt) {    free_vector(xm,1,npar);
              fprintf(ficresf," %.3f", kk1);    free_vector(xp,1,npar);
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    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_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
          /************ Variance ******************/
       }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
       }  {
     }    /* Variance of health expectancies */
   }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* double **newm;*/
   if (popforecast==1) {    double **dnewm,**doldm;
     free_ivector(popage,0,AGESUP);    double **dnewmp,**doldmp;
     free_vector(popeffectif,0,AGESUP);    int i, j, nhstepm, hstepm, h, nstepm ;
     free_vector(popcount,0,AGESUP);    int k, cptcode;
   }    double *xp;
   free_imatrix(s,1,maxwav+1,1,n);    double **gp, **gm;  /* for var eij */
   free_vector(weight,1,n);    double ***gradg, ***trgradg; /*for var eij */
   fclose(ficresf);    double **gradgp, **trgradgp; /* for var p point j */
   /*---------- Health expectancies and variances ------------*/    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   strcpy(filerest,"t");    double ***p3mat;
   strcat(filerest,fileres);    double age,agelim, hf;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double ***mobaverage;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    int theta;
   }    char digit[4];
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   strcpy(filerese,"e");  
   strcat(filerese,fileres);    if(popbased==1){
   if((ficreseij=fopen(filerese,"w"))==NULL) {      if(mobilav!=0)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        strcpy(digitp,"-populbased-mobilav-");
   }      else strcpy(digitp,"-populbased-nomobil-");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    }
     else 
  strcpy(fileresv,"v");      strcpy(digitp,"-stablbased-");
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if (mobilav!=0) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   k=0;      }
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    strcpy(fileresprobmorprev,"prmorprev"); 
       fprintf(ficrest,"\n#****** ");    sprintf(digit,"%-d",ij);
       for(j=1;j<=cptcoveff;j++)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       fprintf(ficrest,"******\n");    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
       fprintf(ficreseij,"\n#****** ");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       for(j=1;j<=cptcoveff;j++)      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficreseij,"******\n");    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficresvij,"\n#****** ");   
       for(j=1;j<=cptcoveff;j++)    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    pstamp(ficresprobmorprev);
       fprintf(ficresvij,"******\n");    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);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       oldm=oldms;savm=savms;      fprintf(ficresprobmorprev," p.%-d SE",j);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        for(i=1; i<=nlstate;i++)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       oldm=oldms;savm=savms;    }  
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficresprobmorprev,"\n");
          fprintf(ficgp,"\n# Routine varevsij");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    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(ficrest,"\n");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
          /*   } */
       hf=1;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       if (stepm >= YEARM) hf=stepm/YEARM;    pstamp(ficresvij);
       epj=vector(1,nlstate+1);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
       for(age=bage; age <=fage ;age++){    if(popbased==1)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
         if (popbased==1) {    else
           for(i=1; i<=nlstate;i++)      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
             prlim[i][i]=probs[(int)age][i][k];    fprintf(ficresvij,"# Age");
         }    for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++)
         fprintf(ficrest," %.0f",age);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(ficresvij,"\n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    xp=vector(1,npar);
           }    dnewm=matrix(1,nlstate,1,npar);
           epj[nlstate+1] +=epj[j];    doldm=matrix(1,nlstate,1,nlstate);
         }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         for(i=1, vepp=0.;i <=nlstate;i++)    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    gpp=vector(nlstate+1,nlstate+ndeath);
         for(j=1;j <=nlstate;j++){    gmp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         }    
         fprintf(ficrest,"\n");    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. 
  fclose(ficreseij);       Look at function hpijx to understand why (it is linked to memory size questions) */
  fclose(ficresvij);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fclose(ficrest);       survival function given by stepm (the optimization length). Unfortunately it
   fclose(ficpar);       means that if the survival funtion is printed every two years of age and if
   free_vector(epj,1,nlstate+1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /*  scanf("%d ",i); */       results. So we changed our mind and took the option of the best precision.
     */
   /*------- Variance limit prevalence------*/      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
 strcpy(fileresvpl,"vpl");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   strcat(fileresvpl,fileres);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     exit(0);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   }      gp=matrix(0,nhstepm,1,nlstate);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      gm=matrix(0,nhstepm,1,nlstate);
   
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){      for(theta=1; theta <=npar; theta++){
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
      k=k+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      fprintf(ficresvpl,"\n#****** ");        }
      for(j=1;j<=cptcoveff;j++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      fprintf(ficresvpl,"******\n");  
              if (popbased==1) {
      varpl=matrix(1,nlstate,(int) bage, (int) fage);          if(mobilav ==0){
      oldm=oldms;savm=savms;            for(i=1; i<=nlstate;i++)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              prlim[i][i]=probs[(int)age][i][ij];
    }          }else{ /* mobilav */ 
  }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   fclose(ficresvpl);          }
         }
   /*---------- End : free ----------------*/    
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
          }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        /* This for computing probability of death (h=1 means
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);           computed over hstepm matrices product = hstepm*stepm months) 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);           as a weighted average of prlim.
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_matrix(matcov,1,npar,1,npar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   free_vector(delti,1,npar);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        /* end probability of death */
   
   printf("End of Imach\n");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /* 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);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*printf("Total time was %d uSec.\n", total_usecs);*/   
   /*------ End -----------*/        if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
  end:              prlim[i][i]=probs[(int)age][i][ij];
 #ifdef windows          }else{ /* mobilav */ 
  chdir(pathcd);            for(i=1; i<=nlstate;i++)
 #endif              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
  system("..\\gp37mgw\\wgnuplot graph.plt");        }
   
 #ifdef windows        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   while (z[0] != 'q') {          for(h=0; h<=nhstepm; h++){
     chdir(pathcd);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     printf("\nType e to edit output files, c to start again, and q for exiting: ");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     scanf("%s",z);          }
     if (z[0] == 'c') system("./imach");        }
     else if (z[0] == 'e') {        /* This for computing probability of death (h=1 means
       chdir(path);           computed over hstepm matrices product = hstepm*stepm months) 
       system(optionfilehtm);           as a weighted average of prlim.
     }        */
     else if (z[0] == 'q') exit(0);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
 #endif           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 lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 3 ",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 lt 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\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",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 lt 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)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
         else fprintf(ficgp,"\" t\"\" w l lt 1,");
       }
     }
     
     /*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;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    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 %d 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 %d 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 %d 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 %d 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 %d 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 %d 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 %d 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 %d 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 %d 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 %d 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 %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%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 '%ld' at line number %d 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 '%ld' at line number %d 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 '%ld' at line number %d 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 '%ld' at line number %d 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;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper 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++;
       fputs(line,stdout);
       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++;
       fputs(line, stdout);
       //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++;
         fputs(line,stdout);
         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++;
         fputs(line,stdout);
         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++;
         fputs(line,stdout);
         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,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* 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); /* Gives the position of a product */
     /* 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); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * 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); /**< codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) 
                                  */
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-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 ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); 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)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     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");
       fprintf(ficgp,"set datafile 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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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=pow(2,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\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
       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); /*here or after loop ? */
       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 %ld 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 %ld 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.1.18  
changed lines
  Added in v.1.144


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