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version 1.16, 2002/02/20 17:12:32 version 1.142, 2014/01/26 03:57:36
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.142  2014/01/26 03:57:36  brouard
   individuals from different ages are interviewed on their health status    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   Health expectancies are computed from the transistions observed between  
   waves and are computed for each degree of severity of disability (number    Revision 1.141  2014/01/26 02:42:01  brouard
   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.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.140  2011/09/02 10:37:54  brouard
   the probabibility to be observed in state j at the second wave conditional    Summary: times.h is ok with mingw32 now.
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.139  2010/06/14 07:50:17  brouard
   is a covariate. If you want to have a more complex model than "constant and    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   age", you should modify the program where the markup    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.137  2010/04/29 18:11:38  brouard
   individual missed an interview, the information is not rounded or lost, but    (Module): Checking covariates for more complex models
   taken into account using an interpolation or extrapolation.    than V1+V2. A lot of change to be done. Unstable.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    Revision 1.136  2010/04/26 20:30:53  brouard
   x. The delay 'h' can be split into an exact number (nh*stepm) of    (Module): merging some libgsl code. Fixing computation
   unobserved intermediate  states. This elementary transition (by month or    of likelione (using inter/intrapolation if mle = 0) in order to
   quarter trimester, semester or year) is model as a multinomial logistic.    get same likelihood as if mle=1.
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Some cleaning of code and comments added.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.135  2009/10/29 15:33:14  brouard
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.134  2009/10/29 13:18:53  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.133  2009/07/06 10:21:25  brouard
   from the European Union.    just nforces
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.132  2009/07/06 08:22:05  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Many tings
   **********************************************************************/  
      Revision 1.131  2009/06/20 16:22:47  brouard
 #include <math.h>    Some dimensions resccaled
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.130  2009/05/26 06:44:34  brouard
 #include <unistd.h>    (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 #define MAXLINE 256    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.129  2007/08/31 13:49:27  lievre
 #define windows    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 GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 #define NINTERVMAX 8    imach-114 because nhstepm was no more computed in the age
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    loop. Now we define nhstepma in the age loop.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): In order to speed up (in case of numerous covariates) we
 #define NCOVMAX 8 /* Maximum number of covariates */    compute health expectancies (without variances) in a first step
 #define MAXN 20000    and then all the health expectancies with variances or standard
 #define YEARM 12. /* Number of months per year */    deviation (needs data from the Hessian matrices) which slows the
 #define AGESUP 130    computation.
 #define AGEBASE 40    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   
 int nvar;    Revision 1.126  2006/04/28 17:23:28  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): Yes the sum of survivors was wrong since
 int npar=NPARMAX;    imach-114 because nhstepm was no more computed in the age
 int nlstate=2; /* Number of live states */    loop. Now we define nhstepma in the age loop.
 int ndeath=1; /* Number of dead states */    Version 0.98h
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 int *wav; /* Number of waves for this individuual 0 is possible */    Forecasting file added.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.124  2006/03/22 17:13:53  lievre
 int mle, weightopt;    Parameters are printed with %lf instead of %f (more numbers after the comma).
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    The log-likelihood is printed in the log file
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.123  2006/03/20 10:52:43  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    * imach.c (Module): <title> changed, corresponds to .htm file
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    name. <head> headers where missing.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    * imach.c (Module): Weights can have a decimal point as for
 FILE *ficreseij;    English (a comma might work with a correct LC_NUMERIC environment,
   char filerese[FILENAMELENGTH];    otherwise the weight is truncated).
  FILE  *ficresvij;    Modification of warning when the covariates values are not 0 or
   char fileresv[FILENAMELENGTH];    1.
  FILE  *ficresvpl;    Version 0.98g
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.122  2006/03/20 09:45:41  brouard
 #define NR_END 1    (Module): Weights can have a decimal point as for
 #define FREE_ARG char*    English (a comma might work with a correct LC_NUMERIC environment,
 #define FTOL 1.0e-10    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define NRANSI    1.
 #define ITMAX 200    Version 0.98g
   
 #define TOL 2.0e-4    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    * imach.c (Module): refinements in the computation of lli if
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.120  2006/03/16 15:10:38  lievre
 #define TINY 1.0e-20    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 static double maxarg1,maxarg2;    not 1 month. Version 0.98f
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.119  2006/03/15 17:42:26  brouard
      (Module): Bug if status = -2, the loglikelihood was
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    computed as likelihood omitting the logarithm. Version O.98e
 #define rint(a) floor(a+0.5)  
     Revision 1.118  2006/03/14 18:20:07  brouard
 static double sqrarg;    (Module): varevsij Comments added explaining the second
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    table of variances if popbased=1 .
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 int imx;    (Module): Version 0.98d
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
 int m,nb;    table of variances if popbased=1 .
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): Function pstamp added
 double **pmmij, ***probs, ***mobaverage;    (Module): Version 0.98d
   
 double *weight;    Revision 1.116  2006/03/06 10:29:27  brouard
 int **s; /* Status */    (Module): Variance-covariance wrong links and
 double *agedc, **covar, idx;    varian-covariance of ej. is needed (Saito).
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.115  2006/02/27 12:17:45  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): One freematrix added in mlikeli! 0.98c
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.114  2006/02/26 12:57:58  brouard
 /**************** split *************************/    (Module): Some improvements in processing parameter
 static  int split( char *path, char *dirc, char *name )    filename with strsep.
 {  
    char *s;                             /* pointer */    Revision 1.113  2006/02/24 14:20:24  brouard
    int  l1, l2;                         /* length counters */    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
    l1 = strlen( path );                 /* length of path */    allocation too.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.112  2006/01/30 09:55:26  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
       if ( getwd( dirc ) == NULL ) {    (Module): Comments can be added in data file. Missing date values
 #else    can be a simple dot '.'.
       extern char       *getcwd( );  
     Revision 1.110  2006/01/25 00:51:50  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Module): Lots of cleaning and bugs added (Gompertz)
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.109  2006/01/24 19:37:15  brouard
       }    (Module): Comments (lines starting with a #) are allowed in data.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.108  2006/01/19 18:05:42  lievre
       s++;                              /* after this, the filename */    Gnuplot problem appeared...
       l2 = strlen( s );                 /* length of filename */    To be fixed
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.107  2006/01/19 16:20:37  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Test existence of gnuplot in imach path
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.106  2006/01/19 13:24:36  brouard
    l1 = strlen( dirc );                 /* length of directory */    Some cleaning and links added in html output
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */    Revision 1.105  2006/01/05 20:23:19  lievre
 }    *** empty log message ***
   
     Revision 1.104  2005/09/30 16:11:43  lievre
 /******************************************/    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 void replace(char *s, char*t)    that the person is alive, then we can code his/her status as -2
 {    (instead of missing=-1 in earlier versions) and his/her
   int i;    contributions to the likelihood is 1 - Prob of dying from last
   int lg=20;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   i=0;    the healthy state at last known wave). Version is 0.98
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.103  2005/09/30 15:54:49  lievre
     (s[i] = t[i]);    (Module): sump fixed, loop imx fixed, and simplifications.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.102  2004/09/15 17:31:30  brouard
 }    Add the possibility to read data file including tab characters.
   
 int nbocc(char *s, char occ)    Revision 1.101  2004/09/15 10:38:38  brouard
 {    Fix on curr_time
   int i,j=0;  
   int lg=20;    Revision 1.100  2004/07/12 18:29:06  brouard
   i=0;    Add version for Mac OS X. Just define UNIX in Makefile
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.99  2004/06/05 08:57:40  brouard
   if  (s[i] == occ ) j++;    *** empty log message ***
   }  
   return j;    Revision 1.98  2004/05/16 15:05:56  brouard
 }    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 void cutv(char *u,char *v, char*t, char occ)    state at each age, but using a Gompertz model: log u =a + b*age .
 {    This is the basic analysis of mortality and should be done before any
   int i,lg,j,p=0;    other analysis, in order to test if the mortality estimated from the
   i=0;    cross-longitudinal survey is different from the mortality estimated
   for(j=0; j<=strlen(t)-1; j++) {    from other sources like vital statistic data.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    The same imach parameter file can be used but the option for mle should be -3.
   
   lg=strlen(t);    Agnès, who wrote this part of the code, tried to keep most of the
   for(j=0; j<p; j++) {    former routines in order to include the new code within the former code.
     (u[j] = t[j]);  
   }    The output is very simple: only an estimate of the intercept and of
      u[p]='\0';    the slope with 95% confident intervals.
   
    for(j=0; j<= lg; j++) {    Current limitations:
     if (j>=(p+1))(v[j-p-1] = t[j]);    A) Even if you enter covariates, i.e. with the
   }    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.
   
 /********************** nrerror ********************/    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 void nrerror(char error_text[])    suppressed.
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.96  2003/07/15 15:38:55  brouard
   fprintf(stderr,"%s\n",error_text);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   exit(1);    rewritten within the same printf. Workaround: many printfs.
 }  
 /*********************** vector *******************/    Revision 1.95  2003/07/08 07:54:34  brouard
 double *vector(int nl, int nh)    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   double *v;    matrix (cov(a12,c31) instead of numbers.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.94  2003/06/27 13:00:02  brouard
   return v-nl+NR_END;    Just cleaning
 }  
     Revision 1.93  2003/06/25 16:33:55  brouard
 /************************ free vector ******************/    (Module): On windows (cygwin) function asctime_r doesn't
 void free_vector(double*v, int nl, int nh)    exist so I changed back to asctime which exists.
 {    (Module): Version 0.96b
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /************************ivector *******************************/    exist so I changed back to asctime which exists.
 int *ivector(long nl,long nh)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   int *v;    * imach.c (Repository): Duplicated warning errors corrected.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Repository): Elapsed time after each iteration is now output. It
   if (!v) nrerror("allocation failure in ivector");    helps to forecast when convergence will be reached. Elapsed time
   return v-nl+NR_END;    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 /******************free ivector **************************/    Revision 1.90  2003/06/24 12:34:15  brouard
 void free_ivector(int *v, long nl, long nh)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   free((FREE_ARG)(v+nl-NR_END));    of the covariance matrix to be input.
 }  
     Revision 1.89  2003/06/24 12:30:52  brouard
 /******************* imatrix *******************************/    (Module): Some bugs corrected for windows. Also, when
 int **imatrix(long nrl, long nrh, long ncl, long nch)    mle=-1 a template is output in file "or"mypar.txt with the design
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    of the covariance matrix to be input.
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.88  2003/06/23 17:54:56  brouard
   int **m;    * 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.
    
   /* allocate pointers to rows */    Revision 1.87  2003/06/18 12:26:01  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Version 0.96
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.86  2003/06/17 20:04:08  brouard
   m -= nrl;    (Module): Change position of html and gnuplot routines and added
      routine fileappend.
    
   /* allocate rows and set pointers to them */    Revision 1.85  2003/06/17 13:12:43  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    * imach.c (Repository): Check when date of death was earlier that
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    current date of interview. It may happen when the death was just
   m[nrl] += NR_END;    prior to the death. In this case, dh was negative and likelihood
   m[nrl] -= ncl;    was wrong (infinity). We still send an "Error" but patch by
      assuming that the date of death was just one stepm after the
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    interview.
      (Repository): Because some people have very long ID (first column)
   /* return pointer to array of pointers to rows */    we changed int to long in num[] and we added a new lvector for
   return m;    memory allocation. But we also truncated to 8 characters (left
 }    truncation)
     (Repository): No more line truncation errors.
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.84  2003/06/13 21:44:43  brouard
       int **m;    * imach.c (Repository): Replace "freqsummary" at a correct
       long nch,ncl,nrh,nrl;    place. It differs from routine "prevalence" which may be called
      /* free an int matrix allocated by imatrix() */    many times. Probs is memory consuming and must be used with
 {    parcimony.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  */
   /*
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));     Interpolated Markov Chain
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Short summary of the programme:
   m -= nrl;    
     This program computes Healthy Life Expectancies from
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    first survey ("cross") where individuals from different ages are
   m[nrl] += NR_END;    interviewed on their health status or degree of disability (in the
   m[nrl] -= ncl;    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (if any) in individual health status.  Health expectancies are
   return m;    computed from the time spent in each health state according to a
 }    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 /*************************free matrix ************************/    simplest model is the multinomial logistic model where pij is the
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    probability to be observed in state j at the second wave
 {    conditional to be observed in state i at the first wave. Therefore
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   free((FREE_ARG)(m+nrl-NR_END));    'age' is age and 'sex' is a covariate. If you want to have a more
 }    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 /******************* ma3x *******************************/    you to do it.  More covariates you add, slower the
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    convergence.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    The advantage of this computer programme, compared to a simple
   double ***m;    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    intermediate interview, the information is lost, but taken into
   if (!m) nrerror("allocation failure 1 in matrix()");    account using an interpolation or extrapolation.  
   m += NR_END;  
   m -= nrl;    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    split into an exact number (nh*stepm) of unobserved intermediate
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    states. This elementary transition (by month, quarter,
   m[nrl] += NR_END;    semester or year) is modelled as a multinomial logistic.  The hPx
   m[nrl] -= ncl;    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++) m[i]=m[i-1]+ncol;    hPijx.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Also this programme outputs the covariance matrix of the parameters but also
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    of the life expectancies. It also computes the period (stable) prevalence. 
   m[nrl][ncl] += NR_END;    
   m[nrl][ncl] -= nll;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for (j=ncl+1; j<=nch; j++)             Institut national d'études démographiques, Paris.
     m[nrl][j]=m[nrl][j-1]+nlay;    This software have been partly granted by Euro-REVES, a concerted action
      from the European Union.
   for (i=nrl+1; i<=nrh; i++) {    It is copyrighted identically to a GNU software product, ie programme and
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    software can be distributed freely for non commercial use. Latest version
     for (j=ncl+1; j<=nch; j++)    can be accessed at http://euroreves.ined.fr/imach .
       m[i][j]=m[i][j-1]+nlay;  
   }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   return m;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 }    
     **********************************************************************/
 /*************************free ma3x ************************/  /*
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    main
 {    read parameterfile
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    read datafile
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    concatwav
   free((FREE_ARG)(m+nrl-NR_END));    freqsummary
 }    if (mle >= 1)
       mlikeli
 /***************** f1dim *************************/    print results files
 extern int ncom;    if mle==1 
 extern double *pcom,*xicom;       computes hessian
 extern double (*nrfunc)(double []);    read end of parameter file: agemin, agemax, bage, fage, estepm
          begin-prev-date,...
 double f1dim(double x)    open gnuplot file
 {    open html file
   int j;    period (stable) prevalence
   double f;     for age prevalim()
   double *xt;    h Pij x
      variance of p varprob
   xt=vector(1,ncom);    forecasting if prevfcast==1 prevforecast call prevalence()
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    health expectancies
   f=(*nrfunc)(xt);    Variance-covariance of DFLE
   free_vector(xt,1,ncom);    prevalence()
   return f;     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 /*****************brent *************************/    total life expectancies
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Variance of period (stable) prevalence
 {   end
   int iter;  */
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;   
   double e=0.0;  #include <math.h>
    #include <stdio.h>
   a=(ax < cx ? ax : cx);  #include <stdlib.h>
   b=(ax > cx ? ax : cx);  #include <string.h>
   x=w=v=bx;  #include <unistd.h>
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  #include <limits.h>
     xm=0.5*(a+b);  #include <sys/types.h>
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #include <sys/stat.h>
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #include <errno.h>
     printf(".");fflush(stdout);  extern int errno;
 #ifdef DEBUG  
     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);  #ifdef LINUX
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #include <time.h>
 #endif  #include "timeval.h"
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #else
       *xmin=x;  #include <sys/time.h>
       return fx;  #endif
     }  
     ftemp=fu;  #ifdef GSL
     if (fabs(e) > tol1) {  #include <gsl/gsl_errno.h>
       r=(x-w)*(fx-fv);  #include <gsl/gsl_multimin.h>
       q=(x-v)*(fx-fw);  #endif
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  /* #include <libintl.h> */
       if (q > 0.0) p = -p;  /* #define _(String) gettext (String) */
       q=fabs(q);  
       etemp=e;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define GNUPLOTPROGRAM "gnuplot"
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       else {  #define FILENAMELENGTH 132
         d=p/q;  
         u=x+d;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
         if (u-a < tol2 || b-u < tol2)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
           d=SIGN(tol1,xm-x);  
       }  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
     } else {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  #define NINTERVMAX 8
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
     fu=(*f)(u);  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
     if (fu <= fx) {  #define NCOVMAX 20 /* Maximum number of covariates */
       if (u >= x) a=x; else b=x;  #define MAXN 20000
       SHFT(v,w,x,u)  #define YEARM 12. /* Number of months per year */
         SHFT(fv,fw,fx,fu)  #define AGESUP 130
         } else {  #define AGEBASE 40
           if (u < x) a=u; else b=u;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
           if (fu <= fw || w == x) {  #ifdef UNIX
             v=w;  #define DIRSEPARATOR '/'
             w=u;  #define CHARSEPARATOR "/"
             fv=fw;  #define ODIRSEPARATOR '\\'
             fw=fu;  #else
           } else if (fu <= fv || v == x || v == w) {  #define DIRSEPARATOR '\\'
             v=u;  #define CHARSEPARATOR "\\"
             fv=fu;  #define ODIRSEPARATOR '/'
           }  #endif
         }  
   }  /* $Id$ */
   nrerror("Too many iterations in brent");  /* $State$ */
   *xmin=x;  
   return fx;  char version[]="Imach version 0.98nR, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 }  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
 /****************** mnbrak ***********************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  int nvar=0, nforce=0; /* Number of variables, number of forces */
             double (*func)(double))  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
 {  int npar=NPARMAX;
   double ulim,u,r,q, dum;  int nlstate=2; /* Number of live states */
   double fu;  int ndeath=1; /* Number of dead states */
    int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   *fa=(*func)(*ax);  int popbased=0;
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  int *wav; /* Number of waves for this individuual 0 is possible */
     SHFT(dum,*ax,*bx,dum)  int maxwav=0; /* Maxim number of waves */
       SHFT(dum,*fb,*fa,dum)  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       }  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   *cx=(*bx)+GOLD*(*bx-*ax);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   *fc=(*func)(*cx);                     to the likelihood and the sum of weights (done by funcone)*/
   while (*fb > *fc) {  int mle=1, weightopt=0;
     r=(*bx-*ax)*(*fb-*fc);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     q=(*bx-*cx)*(*fb-*fa);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  double jmean=1; /* Mean space between 2 waves */
     if ((*bx-u)*(u-*cx) > 0.0) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
       fu=(*func)(u);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  /*FILE *fic ; */ /* Used in readdata only */
       fu=(*func)(u);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       if (fu < *fc) {  FILE *ficlog, *ficrespow;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int globpr=0; /* Global variable for printing or not */
           SHFT(*fb,*fc,fu,(*func)(u))  double fretone; /* Only one call to likelihood */
           }  long ipmx=0; /* Number of contributions */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double sw; /* Sum of weights */
       u=ulim;  char filerespow[FILENAMELENGTH];
       fu=(*func)(u);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     } else {  FILE *ficresilk;
       u=(*cx)+GOLD*(*cx-*bx);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       fu=(*func)(u);  FILE *ficresprobmorprev;
     }  FILE *fichtm, *fichtmcov; /* Html File */
     SHFT(*ax,*bx,*cx,u)  FILE *ficreseij;
       SHFT(*fa,*fb,*fc,fu)  char filerese[FILENAMELENGTH];
       }  FILE *ficresstdeij;
 }  char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
 /*************** linmin ************************/  char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
 int ncom;  char fileresv[FILENAMELENGTH];
 double *pcom,*xicom;  FILE  *ficresvpl;
 double (*nrfunc)(double []);  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double brent(double ax, double bx, double cx,  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
                double (*f)(double), double tol, double *xmin);  char command[FILENAMELENGTH];
   double f1dim(double x);  int  outcmd=0;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int j;  
   double xx,xmin,bx,ax;  char filelog[FILENAMELENGTH]; /* Log file */
   double fx,fb,fa;  char filerest[FILENAMELENGTH];
    char fileregp[FILENAMELENGTH];
   ncom=n;  char popfile[FILENAMELENGTH];
   pcom=vector(1,n);  
   xicom=vector(1,n);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   nrfunc=func;  
   for (j=1;j<=n;j++) {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     pcom[j]=p[j];  struct timezone tzp;
     xicom[j]=xi[j];  extern int gettimeofday();
   }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   ax=0.0;  long time_value;
   xx=1.0;  extern long time();
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  char strcurr[80], strfor[80];
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  char *endptr;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  long lval;
 #endif  double dval;
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  #define NR_END 1
     p[j] += xi[j];  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  #define NRANSI 
 }  #define ITMAX 200 
   
 /*************** powell ************************/  #define TOL 2.0e-4 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   void linmin(double p[], double xi[], int n, double *fret,  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
               double (*func)(double []));  
   int i,ibig,j;  #define GOLD 1.618034 
   double del,t,*pt,*ptt,*xit;  #define GLIMIT 100.0 
   double fp,fptt;  #define TINY 1.0e-20 
   double *xits;  
   pt=vector(1,n);  static double maxarg1,maxarg2;
   ptt=vector(1,n);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   xit=vector(1,n);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   xits=vector(1,n);    
   *fret=(*func)(p);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for (j=1;j<=n;j++) pt[j]=p[j];  #define rint(a) floor(a+0.5)
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  static double sqrarg;
     ibig=0;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     del=0.0;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int agegomp= AGEGOMP;
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  int imx; 
     printf("\n");  int stepm=1;
     for (i=1;i<=n;i++) {  /* Stepm, step in month: minimum step interpolation*/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  int estepm;
 #ifdef DEBUG  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       printf("fret=%lf \n",*fret);  
 #endif  int m,nb;
       printf("%d",i);fflush(stdout);  long *num;
       linmin(p,xit,n,fret,func);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       if (fabs(fptt-(*fret)) > del) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         del=fabs(fptt-(*fret));  double **pmmij, ***probs;
         ibig=i;  double *ageexmed,*agecens;
       }  double dateintmean=0;
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  double *weight;
       for (j=1;j<=n;j++) {  int **s; /* Status */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  double *agedc;
         printf(" x(%d)=%.12e",j,xit[j]);  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
       }                    * covar=matrix(0,NCOVMAX,1,n); 
       for(j=1;j<=n;j++)                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
         printf(" p=%.12e",p[j]);  double  idx; 
       printf("\n");  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 #endif  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     }  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double *lsurv, *lpop, *tpop;
 #ifdef DEBUG  
       int k[2],l;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       k[0]=1;  double ftolhess; /* Tolerance for computing hessian */
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /**************** split *************************/
       for (j=1;j<=n;j++)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         printf(" %.12e",p[j]);  {
       printf("\n");    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       for(l=0;l<=1;l++) {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         for (j=1;j<=n;j++) {    */ 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    char  *ss;                            /* pointer */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    int   l1, l2;                         /* length counters */
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    l1 = strlen(path );                   /* length of path */
       }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 #endif    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
       strcpy( name, path );               /* we got the fullname name because no directory */
       free_vector(xit,1,n);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       free_vector(xits,1,n);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       free_vector(ptt,1,n);      /* get current working directory */
       free_vector(pt,1,n);      /*    extern  char* getcwd ( char *buf , int len);*/
       return;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     }        return( GLOCK_ERROR_GETCWD );
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      }
     for (j=1;j<=n;j++) {      /* got dirc from getcwd*/
       ptt[j]=2.0*p[j]-pt[j];      printf(" DIRC = %s \n",dirc);
       xit[j]=p[j]-pt[j];    } else {                              /* strip direcotry from path */
       pt[j]=p[j];      ss++;                               /* after this, the filename */
     }      l2 = strlen( ss );                  /* length of filename */
     fptt=(*func)(ptt);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (fptt < fp) {      strcpy( name, ss );         /* save file name */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       if (t < 0.0) {      dirc[l1-l2] = 0;                    /* add zero */
         linmin(p,xit,n,fret,func);      printf(" DIRC2 = %s \n",dirc);
         for (j=1;j<=n;j++) {    }
           xi[j][ibig]=xi[j][n];    /* We add a separator at the end of dirc if not exists */
           xi[j][n]=xit[j];    l1 = strlen( dirc );                  /* length of directory */
         }    if( dirc[l1-1] != DIRSEPARATOR ){
 #ifdef DEBUG      dirc[l1] =  DIRSEPARATOR;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      dirc[l1+1] = 0; 
         for(j=1;j<=n;j++)      printf(" DIRC3 = %s \n",dirc);
           printf(" %.12e",xit[j]);    }
         printf("\n");    ss = strrchr( name, '.' );            /* find last / */
 #endif    if (ss >0){
       }      ss++;
     }      strcpy(ext,ss);                     /* save extension */
   }      l1= strlen( name);
 }      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 /**** Prevalence limit ****************/      finame[l1-l2]= 0;
     }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    return( 0 );                          /* we're done */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  }
      matrix by transitions matrix until convergence is reached */  
   
   int i, ii,j,k;  /******************************************/
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  void replace_back_to_slash(char *s, char*t)
   double **out, cov[NCOVMAX], **pmij();  {
   double **newm;    int i;
   double agefin, delaymax=50 ; /* Max number of years to converge */    int lg=0;
     i=0;
   for (ii=1;ii<=nlstate+ndeath;ii++)    lg=strlen(t);
     for (j=1;j<=nlstate+ndeath;j++){    for(i=0; i<= lg; i++) {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      (s[i] = t[i]);
     }      if (t[i]== '\\') s[i]='/';
     }
    cov[1]=1.;  }
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char *trimbb(char *out, char *in)
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     newm=savm;    char *s;
     /* Covariates have to be included here again */    s=out;
      cov[2]=agefin;    while (*in != '\0'){
        while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       for (k=1; k<=cptcovn;k++) {        in++;
         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]);*/      *out++ = *in++;
       }    }
       for (k=1; k<=cptcovage;k++)    *out='\0';
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return s;
       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]]];  
   char *cutv(char *blocc, char *alocc, char *in, char occ)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
        and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
     savm=oldm;    */
     oldm=newm;    char *s, *t;
     maxmax=0.;    t=in;s=in;
     for(j=1;j<=nlstate;j++){    while (*in != '\0'){
       min=1.;      while( *in == occ){
       max=0.;        *blocc++ = *in++;
       for(i=1; i<=nlstate; i++) {        s=in;
         sumnew=0;      }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      *blocc++ = *in++;
         prlim[i][j]= newm[i][j]/(1-sumnew);    }
         max=FMAX(max,prlim[i][j]);    if (s == t) /* occ not found */
         min=FMIN(min,prlim[i][j]);      *(blocc-(in-s))='\0';
       }    else
       maxmin=max-min;      *(blocc-(in-s)-1)='\0';
       maxmax=FMAX(maxmax,maxmin);    in=s;
     }    while ( *in != '\0'){
     if(maxmax < ftolpl){      *alocc++ = *in++;
       return prlim;    }
     }  
   }    *alocc='\0';
 }    return s;
   }
 /*************** transition probabilities ***************/  
   int nbocc(char *s, char occ)
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  {
 {    int i,j=0;
   double s1, s2;    int lg=20;
   /*double t34;*/    i=0;
   int i,j,j1, nc, ii, jj;    lg=strlen(s);
     for(i=0; i<= lg; i++) {
     for(i=1; i<= nlstate; i++){    if  (s[i] == occ ) j++;
     for(j=1; j<i;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return j;
         /*s2 += param[i][j][nc]*cov[nc];*/  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",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'  */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     }  /*      gives u="abcdef2ghi" and v="j" *\/ */
     for(j=i+1; j<=nlstate+ndeath;j++){  /*   int i,lg,j,p=0; */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*   i=0; */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*   lg=strlen(t); */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /*   for(j=0; j<=lg-1; j++) { */
       }  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       ps[i][j]=(s2);  /*   } */
     }  
   }  /*   for(j=0; j<p; j++) { */
     /*ps[3][2]=1;*/  /*     (u[j] = t[j]); */
   /*   } */
   for(i=1; i<= nlstate; i++){  /*      u[p]='\0'; */
      s1=0;  
     for(j=1; j<i; j++)  /*    for(j=0; j<= lg; j++) { */
       s1+=exp(ps[i][j]);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     for(j=i+1; j<=nlstate+ndeath; j++)  /*   } */
       s1+=exp(ps[i][j]);  /* } */
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  /********************** nrerror ********************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  void nrerror(char error_text[])
       ps[i][j]= exp(ps[i][j])*ps[i][i];  {
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    fprintf(stderr,"ERREUR ...\n");
   } /* end i */    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*********************** vector *******************/
       ps[ii][jj]=0;  double *vector(int nl, int nh)
       ps[ii][ii]=1;  {
     }    double *v;
   }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /************************ free vector ******************/
    }  void free_vector(double*v, int nl, int nh)
     printf("\n ");  {
     }    free((FREE_ARG)(v+nl-NR_END));
     printf("\n ");printf("%lf ",cov[2]);*/  }
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /************************ivector *******************************/
   goto end;*/  int *ivector(long nl,long nh)
     return ps;  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /**************** Product of 2 matrices ******************/    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /******************free ivector **************************/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  void free_ivector(int *v, 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    free((FREE_ARG)(v+nl-NR_END));
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /************************lvector *******************************/
     for(k=ncolol; k<=ncoloh; k++)  long *lvector(long nl,long nh)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   return out;    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
   
 /************* Higher Matrix Product ***************/  /******************free lvector **************************/
   void free_lvector(long *v, 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 )  {
 {    free((FREE_ARG)(v+nl-NR_END));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  }
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /******************* imatrix *******************************/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  int **imatrix(long nrl, long nrh, long ncl, long nch) 
      (typically every 2 years instead of every month which is too big).       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
      Model is determined by parameters x and covariates have to be  { 
      included manually here.    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
      */    
     /* allocate pointers to rows */ 
   int i, j, d, h, k;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double **out, cov[NCOVMAX];    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double **newm;    m += NR_END; 
     m -= nrl; 
   /* Hstepm could be zero and should return the unit matrix */    
   for (i=1;i<=nlstate+ndeath;i++)    
     for (j=1;j<=nlstate+ndeath;j++){    /* allocate rows and set pointers to them */ 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl] -= ncl; 
   for(h=1; h <=nhstepm; h++){    
     for(d=1; d <=hstepm; d++){    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       newm=savm;    
       /* Covariates have to be included here again */    /* return pointer to array of pointers to rows */ 
       cov[1]=1.;    return m; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  /****************** free_imatrix *************************/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (k=1; k<=cptcovprod;k++)        int **m;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    free((FREE_ARG) (m+nrl-NR_END)); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  } 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  /******************* matrix *******************************/
       oldm=newm;  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
     for(i=1; i<=nlstate+ndeath; i++)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       for(j=1;j<=nlstate+ndeath;j++) {    double **m;
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
          */    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
   } /* end h */    m -= nrl;
   return po;  
 }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /*************** log-likelihood *************/    m[nrl] -= ncl;
 double func( double *x)  
 {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int i, ii, j, k, mi, d, kk;    return m;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   double **out;     */
   double sw; /* Sum of weights */  }
   double lli; /* Individual log likelihood */  
   long ipmx;  /*************************free matrix ************************/
   /*extern weight */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   /*for(i=1;i<imx;i++)    free((FREE_ARG)(m+nrl-NR_END));
     printf(" %d\n",s[4][i]);  }
   */  
   cov[1]=1.;  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for(k=1; k<=nlstate; k++) ll[k]=0.;  {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    double ***m;
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    if (!m) nrerror("allocation failure 1 in matrix()");
       for(d=0; d<dh[mi][i]; d++){    m += NR_END;
         newm=savm;    m -= nrl;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         }    m[nrl] += NR_END;
            m[nrl] -= ncl;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         savm=oldm;  
         oldm=newm;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
            if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
            m[nrl][ncl] += NR_END;
       } /* end mult */    m[nrl][ncl] -= nll;
          for (j=ncl+1; j<=nch; j++) 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      m[nrl][j]=m[nrl][j-1]+nlay;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    
       ipmx +=1;    for (i=nrl+1; i<=nrh; i++) {
       sw += weight[i];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for (j=ncl+1; j<=nch; j++) 
     } /* end of wave */        m[i][j]=m[i][j-1]+nlay;
   } /* end of individual */    }
     return m; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    */
   return -l;  }
 }  
   /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /*********** Maximum Likelihood Estimation ***************/  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  /*************** function subdirf ***********/
   xi=matrix(1,npar,1,npar);  char *subdirf(char fileres[])
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++)    /* Caution optionfilefiname is hidden */
       xi[i][j]=(i==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
   printf("Powell\n");    strcat(tmpout,"/"); /* Add to the right */
   powell(p,xi,npar,ftol,&iter,&fret,func);    strcat(tmpout,fileres);
     return tmpout;
    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 subdirf2 ***********/
 }  char *subdirf2(char fileres[], char *preop)
   {
 /**** Computes Hessian and covariance matrix ***/    
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   double  **a,**y,*x,pd;    strcat(tmpout,"/");
   double **hess;    strcat(tmpout,preop);
   int i, j,jk;    strcat(tmpout,fileres);
   int *indx;    return tmpout;
   }
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  /*************** function subdirf3 ***********/
   void lubksb(double **a, int npar, int *indx, double b[]) ;  char *subdirf3(char fileres[], char *preop, char *preop2)
   void ludcmp(double **a, int npar, int *indx, double *d) ;  {
     
   hess=matrix(1,npar,1,npar);    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   printf("\nCalculation of the hessian matrix. Wait...\n");    strcat(tmpout,"/");
   for (i=1;i<=npar;i++){    strcat(tmpout,preop);
     printf("%d",i);fflush(stdout);    strcat(tmpout,preop2);
     hess[i][i]=hessii(p,ftolhess,i,delti);    strcat(tmpout,fileres);
     /*printf(" %f ",p[i]);*/    return tmpout;
     /*printf(" %lf ",hess[i][i]);*/  }
   }  
    /***************** f1dim *************************/
   for (i=1;i<=npar;i++) {  extern int ncom; 
     for (j=1;j<=npar;j++)  {  extern double *pcom,*xicom;
       if (j>i) {  extern double (*nrfunc)(double []); 
         printf(".%d%d",i,j);fflush(stdout);   
         hess[i][j]=hessij(p,delti,i,j);  double f1dim(double x) 
         hess[j][i]=hess[i][j];      { 
         /*printf(" %lf ",hess[i][j]);*/    int j; 
       }    double f;
     }    double *xt; 
   }   
   printf("\n");    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    f=(*nrfunc)(xt); 
      free_vector(xt,1,ncom); 
   a=matrix(1,npar,1,npar);    return f; 
   y=matrix(1,npar,1,npar);  } 
   x=vector(1,npar);  
   indx=ivector(1,npar);  /*****************brent *************************/
   for (i=1;i<=npar;i++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  { 
   ludcmp(a,npar,indx,&pd);    int iter; 
     double a,b,d,etemp;
   for (j=1;j<=npar;j++) {    double fu,fv,fw,fx;
     for (i=1;i<=npar;i++) x[i]=0;    double ftemp;
     x[j]=1;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     lubksb(a,npar,indx,x);    double e=0.0; 
     for (i=1;i<=npar;i++){   
       matcov[i][j]=x[i];    a=(ax < cx ? ax : cx); 
     }    b=(ax > cx ? ax : cx); 
   }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
   printf("\n#Hessian matrix#\n");    for (iter=1;iter<=ITMAX;iter++) { 
   for (i=1;i<=npar;i++) {      xm=0.5*(a+b); 
     for (j=1;j<=npar;j++) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       printf("%.3e ",hess[i][j]);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     }      printf(".");fflush(stdout);
     printf("\n");      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
       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);
   /* Recompute Inverse */      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);
   for (i=1;i<=npar;i++)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  #endif
   ludcmp(a,npar,indx,&pd);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
   /*  printf("\n#Hessian matrix recomputed#\n");        return fx; 
       } 
   for (j=1;j<=npar;j++) {      ftemp=fu;
     for (i=1;i<=npar;i++) x[i]=0;      if (fabs(e) > tol1) { 
     x[j]=1;        r=(x-w)*(fx-fv); 
     lubksb(a,npar,indx,x);        q=(x-v)*(fx-fw); 
     for (i=1;i<=npar;i++){        p=(x-v)*q-(x-w)*r; 
       y[i][j]=x[i];        q=2.0*(q-r); 
       printf("%.3e ",y[i][j]);        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     printf("\n");        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)); 
   free_matrix(a,1,npar,1,npar);        else { 
   free_matrix(y,1,npar,1,npar);          d=p/q; 
   free_vector(x,1,npar);          u=x+d; 
   free_ivector(indx,1,npar);          if (u-a < tol2 || b-u < tol2) 
   free_matrix(hess,1,npar,1,npar);            d=SIGN(tol1,xm-x); 
         } 
       } else { 
 }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 /*************** hessian matrix ****************/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 double hessii( double x[], double delta, int theta, double delti[])      fu=(*f)(u); 
 {      if (fu <= fx) { 
   int i;        if (u >= x) a=x; else b=x; 
   int l=1, lmax=20;        SHFT(v,w,x,u) 
   double k1,k2;          SHFT(fv,fw,fx,fu) 
   double p2[NPARMAX+1];          } else { 
   double res;            if (u < x) a=u; else b=u; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            if (fu <= fw || w == x) { 
   double fx;              v=w; 
   int k=0,kmax=10;              w=u; 
   double l1;              fv=fw; 
               fw=fu; 
   fx=func(x);            } else if (fu <= fv || v == x || v == w) { 
   for (i=1;i<=npar;i++) p2[i]=x[i];              v=u; 
   for(l=0 ; l <=lmax; l++){              fv=fu; 
     l1=pow(10,l);            } 
     delts=delt;          } 
     for(k=1 ; k <kmax; k=k+1){    } 
       delt = delta*(l1*k);    nrerror("Too many iterations in brent"); 
       p2[theta]=x[theta] +delt;    *xmin=x; 
       k1=func(p2)-fx;    return fx; 
       p2[theta]=x[theta]-delt;  } 
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */  /****************** mnbrak ***********************/
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
        void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 #ifdef DEBUG              double (*func)(double)) 
       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);  { 
 #endif    double ulim,u,r,q, dum;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double fu; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){   
         k=kmax;    *fa=(*func)(*ax); 
       }    *fb=(*func)(*bx); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    if (*fb > *fa) { 
         k=kmax; l=lmax*10.;      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        } 
         delts=delt;    *cx=(*bx)+GOLD*(*bx-*ax); 
       }    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { 
   }      r=(*bx-*ax)*(*fb-*fc); 
   delti[theta]=delts;      q=(*bx-*cx)*(*fb-*fa); 
   return res;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
          (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 double hessij( double x[], double delti[], int thetai,int thetaj)        fu=(*func)(u); 
 {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   int i;        fu=(*func)(u); 
   int l=1, l1, lmax=20;        if (fu < *fc) { 
   double k1,k2,k3,k4,res,fx;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double p2[NPARMAX+1];            SHFT(*fb,*fc,fu,(*func)(u)) 
   int k;            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   fx=func(x);        u=ulim; 
   for (k=1; k<=2; k++) {        fu=(*func)(u); 
     for (i=1;i<=npar;i++) p2[i]=x[i];      } else { 
     p2[thetai]=x[thetai]+delti[thetai]/k;        u=(*cx)+GOLD*(*cx-*bx); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        fu=(*func)(u); 
     k1=func(p2)-fx;      } 
        SHFT(*ax,*bx,*cx,u) 
     p2[thetai]=x[thetai]+delti[thetai]/k;        SHFT(*fa,*fb,*fc,fu) 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        } 
     k2=func(p2)-fx;  } 
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*************** linmin ************************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  int ncom; 
    double *pcom,*xicom;
     p2[thetai]=x[thetai]-delti[thetai]/k;  double (*nrfunc)(double []); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;   
     k4=func(p2)-fx;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  { 
 #ifdef DEBUG    double brent(double ax, double bx, double cx, 
     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);                 double (*f)(double), double tol, double *xmin); 
 #endif    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   return res;                double *fc, double (*func)(double)); 
 }    int j; 
     double xx,xmin,bx,ax; 
 /************** Inverse of matrix **************/    double fx,fb,fa;
 void ludcmp(double **a, int n, int *indx, double *d)   
 {    ncom=n; 
   int i,imax,j,k;    pcom=vector(1,n); 
   double big,dum,sum,temp;    xicom=vector(1,n); 
   double *vv;    nrfunc=func; 
      for (j=1;j<=n;j++) { 
   vv=vector(1,n);      pcom[j]=p[j]; 
   *d=1.0;      xicom[j]=xi[j]; 
   for (i=1;i<=n;i++) {    } 
     big=0.0;    ax=0.0; 
     for (j=1;j<=n;j++)    xx=1.0; 
       if ((temp=fabs(a[i][j])) > big) big=temp;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     vv[i]=1.0/big;  #ifdef DEBUG
   }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (j=1;j<=n;j++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (i=1;i<j;i++) {  #endif
       sum=a[i][j];    for (j=1;j<=n;j++) { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      xi[j] *= xmin; 
       a[i][j]=sum;      p[j] += xi[j]; 
     }    } 
     big=0.0;    free_vector(xicom,1,n); 
     for (i=j;i<=n;i++) {    free_vector(pcom,1,n); 
       sum=a[i][j];  } 
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  char *asc_diff_time(long time_sec, char ascdiff[])
       a[i][j]=sum;  {
       if ( (dum=vv[i]*fabs(sum)) >= big) {    long sec_left, days, hours, minutes;
         big=dum;    days = (time_sec) / (60*60*24);
         imax=i;    sec_left = (time_sec) % (60*60*24);
       }    hours = (sec_left) / (60*60) ;
     }    sec_left = (sec_left) %(60*60);
     if (j != imax) {    minutes = (sec_left) /60;
       for (k=1;k<=n;k++) {    sec_left = (sec_left) % (60);
         dum=a[imax][k];    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
         a[imax][k]=a[j][k];    return ascdiff;
         a[j][k]=dum;  }
       }  
       *d = -(*d);  /*************** powell ************************/
       vv[imax]=vv[j];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     }              double (*func)(double [])) 
     indx[j]=imax;  { 
     if (a[j][j] == 0.0) a[j][j]=TINY;    void linmin(double p[], double xi[], int n, double *fret, 
     if (j != n) {                double (*func)(double [])); 
       dum=1.0/(a[j][j]);    int i,ibig,j; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double del,t,*pt,*ptt,*xit;
     }    double fp,fptt;
   }    double *xits;
   free_vector(vv,1,n);  /* Doesn't work */    int niterf, itmp;
 ;  
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
 void lubksb(double **a, int n, int *indx, double b[])    xit=vector(1,n); 
 {    xits=vector(1,n); 
   int i,ii=0,ip,j;    *fret=(*func)(p); 
   double sum;    for (j=1;j<=n;j++) pt[j]=p[j]; 
      for (*iter=1;;++(*iter)) { 
   for (i=1;i<=n;i++) {      fp=(*fret); 
     ip=indx[i];      ibig=0; 
     sum=b[ip];      del=0.0; 
     b[ip]=b[i];      last_time=curr_time;
     if (ii)      (void) gettimeofday(&curr_time,&tzp);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      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);
     else if (sum) ii=i;      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);
     b[i]=sum;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   }     for (i=1;i<=n;i++) {
   for (i=n;i>=1;i--) {        printf(" %d %.12f",i, p[i]);
     sum=b[i];        fprintf(ficlog," %d %.12lf",i, p[i]);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        fprintf(ficrespow," %.12lf", p[i]);
     b[i]=sum/a[i][i];      }
   }      printf("\n");
 }      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
 /************ Frequencies ********************/      if(*iter <=3){
 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)        tm = *localtime(&curr_time.tv_sec);
 {  /* Some frequencies */        strcpy(strcurr,asctime(&tm));
    /*       asctime_r(&tm,strcurr); */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        forecast_time=curr_time; 
   double ***freq; /* Frequencies */        itmp = strlen(strcurr);
   double *pp;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double pos;          strcurr[itmp-1]='\0';
   FILE *ficresp;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   char fileresp[FILENAMELENGTH];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   pp=vector(1,nlstate);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
  probs= ma3x(1,130 ,1,8, 1,8);          tmf = *localtime(&forecast_time.tv_sec);
   strcpy(fileresp,"p");  /*      asctime_r(&tmf,strfor); */
   strcat(fileresp,fileres);          strcpy(strfor,asctime(&tmf));
   if((ficresp=fopen(fileresp,"w"))==NULL) {          itmp = strlen(strfor);
     printf("Problem with prevalence resultfile: %s\n", fileresp);          if(strfor[itmp-1]=='\n')
     exit(0);          strfor[itmp-1]='\0';
   }          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);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          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);
   j1=0;        }
       }
   j=cptcoveff;      for (i=1;i<=n;i++) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   for(k1=1; k1<=j;k1++){  #ifdef DEBUG
    for(i1=1; i1<=ncodemax[k1];i1++){        printf("fret=%lf \n",*fret);
        j1++;        fprintf(ficlog,"fret=%lf \n",*fret);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  #endif
          scanf("%d", i);*/        printf("%d",i);fflush(stdout);
         for (i=-1; i<=nlstate+ndeath; i++)          fprintf(ficlog,"%d",i);fflush(ficlog);
          for (jk=-1; jk<=nlstate+ndeath; jk++)          linmin(p,xit,n,fret,func); 
            for(m=agemin; m <= agemax+3; m++)        if (fabs(fptt-(*fret)) > del) { 
              freq[i][jk][m]=0;          del=fabs(fptt-(*fret)); 
                  ibig=i; 
        for (i=1; i<=imx; i++) {        } 
          bool=1;  #ifdef DEBUG
          if  (cptcovn>0) {        printf("%d %.12e",i,(*fret));
            for (z1=1; z1<=cptcoveff; z1++)        fprintf(ficlog,"%d %.12e",i,(*fret));
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for (j=1;j<=n;j++) {
                bool=0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
          }          printf(" x(%d)=%.12e",j,xit[j]);
           if (bool==1) {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
            for(m=fprev1; m<=lprev1; m++){        }
              if(agev[m][i]==0) agev[m][i]=agemax+1;        for(j=1;j<=n;j++) {
              if(agev[m][i]==1) agev[m][i]=agemax+2;          printf(" p=%.12e",p[j]);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          fprintf(ficlog," p=%.12e",p[j]);
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        }
            }        printf("\n");
          }        fprintf(ficlog,"\n");
        }  #endif
         if  (cptcovn>0) {      } 
          fprintf(ficresp, "\n#********** Variable ");      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  #ifdef DEBUG
        fprintf(ficresp, "**********\n#");        int k[2],l;
         }        k[0]=1;
        for(i=1; i<=nlstate;i++)        k[1]=-1;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        printf("Max: %.12e",(*func)(p));
        fprintf(ficresp, "\n");        fprintf(ficlog,"Max: %.12e",(*func)(p));
                for (j=1;j<=n;j++) {
   for(i=(int)agemin; i <= (int)agemax+3; i++){          printf(" %.12e",p[j]);
     if(i==(int)agemax+3)          fprintf(ficlog," %.12e",p[j]);
       printf("Total");        }
     else        printf("\n");
       printf("Age %d", i);        fprintf(ficlog,"\n");
     for(jk=1; jk <=nlstate ; jk++){        for(l=0;l<=1;l++) {
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          for (j=1;j<=n;j++) {
         pp[jk] += freq[jk][m][i];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     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, pos=0; m <=0 ; m++)          }
         pos += freq[jk][m][i];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if(pp[jk]>=1.e-10)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        }
       else  #endif
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
     }  
         free_vector(xit,1,n); 
      for(jk=1; jk <=nlstate ; jk++){        free_vector(xits,1,n); 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        free_vector(ptt,1,n); 
         pp[jk] += freq[jk][m][i];        free_vector(pt,1,n); 
      }        return; 
       } 
     for(jk=1,pos=0; jk <=nlstate ; jk++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       pos += pp[jk];      for (j=1;j<=n;j++) { 
     for(jk=1; jk <=nlstate ; jk++){        ptt[j]=2.0*p[j]-pt[j]; 
       if(pos>=1.e-5)        xit[j]=p[j]-pt[j]; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        pt[j]=p[j]; 
       else      } 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      fptt=(*func)(ptt); 
       if( i <= (int) agemax){      if (fptt < fp) { 
         if(pos>=1.e-5){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        if (t < 0.0) { 
           probs[i][jk][j1]= pp[jk]/pos;          linmin(p,xit,n,fret,func); 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          for (j=1;j<=n;j++) { 
         }            xi[j][ibig]=xi[j][n]; 
       else            xi[j][n]=xit[j]; 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          }
       }  #ifdef DEBUG
     }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(jk=-1; jk <=nlstate+ndeath; jk++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for(m=-1; m <=nlstate+ndeath; m++)          for(j=1;j<=n;j++){
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            printf(" %.12e",xit[j]);
     if(i <= (int) agemax)            fprintf(ficlog," %.12e",xit[j]);
       fprintf(ficresp,"\n");          }
     printf("\n");          printf("\n");
     }          fprintf(ficlog,"\n");
     }  #endif
  }        }
        } 
   fclose(ficresp);    } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  } 
   free_vector(pp,1,nlstate);  
   /**** Prevalence limit (stable or period prevalence)  ****************/
 }  /* End of Freq */  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 /************ Prevalence ********************/  {
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 {  /* Some frequencies */       matrix by transitions matrix until convergence is reached */
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, ii,j,k;
   double ***freq; /* Frequencies */    double min, max, maxmin, maxmax,sumnew=0.;
   double *pp;    double **matprod2();
   double pos;    double **out, cov[NCOVMAX+1], **pmij();
     double **newm;
   pp=vector(1,nlstate);    double agefin, delaymax=50 ; /* Max number of years to converge */
   probs= ma3x(1,130 ,1,8, 1,8);  
      for (ii=1;ii<=nlstate+ndeath;ii++)
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (j=1;j<=nlstate+ndeath;j++){
   j1=0;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        }
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}     cov[1]=1.;
     
  for(k1=1; k1<=j;k1++){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(i1=1; i1<=ncodemax[k1];i1++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       j1++;      newm=savm;
        /* Covariates have to be included here again */
       for (i=-1; i<=nlstate+ndeath; i++)        cov[2]=agefin;
         for (jk=-1; jk<=nlstate+ndeath; jk++)        
           for(m=agemin; m <= agemax+3; m++)      for (k=1; k<=cptcovn;k++) {
           freq[i][jk][m]=0;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
              /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
       for (i=1; i<=imx; i++) {      }
         bool=1;      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         if  (cptcovn>0) {      for (k=1; k<=cptcovprod;k++)
           for (z1=1; z1<=cptcoveff; z1++)        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      
               bool=0;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
               }      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         if (bool==1) {      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
           for(m=fprev1; m<=lprev1; m++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
             if(agev[m][i]==0) agev[m][i]=agemax+1;      
             if(agev[m][i]==1) agev[m][i]=agemax+2;      savm=oldm;
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      oldm=newm;
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      maxmax=0.;
           }      for(j=1;j<=nlstate;j++){
         }        min=1.;
       }        max=0.;
        for(i=(int)agemin; i <= (int)agemax+3; i++){        for(i=1; i<=nlstate; i++) {
         for(jk=1; jk <=nlstate ; jk++){          sumnew=0;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
             pp[jk] += freq[jk][m][i];          prlim[i][j]= newm[i][j]/(1-sumnew);
         }          max=FMAX(max,prlim[i][j]);
         for(jk=1; jk <=nlstate ; jk++){          min=FMIN(min,prlim[i][j]);
           for(m=-1, pos=0; m <=0 ; m++)        }
             pos += freq[jk][m][i];        maxmin=max-min;
         }        maxmax=FMAX(maxmax,maxmin);
              }
          for(jk=1; jk <=nlstate ; jk++){      if(maxmax < ftolpl){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        return prlim;
              pp[jk] += freq[jk][m][i];      }
          }    }
            }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
   /*************** transition probabilities ***************/ 
          for(jk=1; jk <=nlstate ; jk++){            
            if( i <= (int) agemax){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
              if(pos>=1.e-5){  {
                probs[i][jk][j1]= pp[jk]/pos;    /* 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
            }       model to the ncovmodel covariates (including constant and age).
          }       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
                 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
   }       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
         Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       Outputs ps[i][j] the probability to be observed in j being in j according to
   free_vector(pp,1,nlstate);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
      */
 }  /* End of Freq */    double s1, lnpijopii;
 /************* Waves Concatenation ***************/    /*double t34;*/
     int i,j,j1, nc, ii, jj;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {      for(i=1; i<= nlstate; i++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for(j=1; j<i;j++){
      Death is a valid wave (if date is known).          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            /*lnpijopii += param[i][j][nc]*cov[nc];*/
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
      and mw[mi+1][i]. dh depends on stepm.  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
      */          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   int i, mi, m;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        }
      double sum=0., jmean=0.;*/        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   int j, k=0,jk, ju, jl;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   double sum=0.;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   jmin=1e+5;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   jmax=-1;          }
   jmean=0.;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   for(i=1; i<=imx; i++){        }
     mi=0;      }
     m=firstpass;      
     while(s[m][i] <= nlstate){      for(i=1; i<= nlstate; i++){
       if(s[m][i]>=1)        s1=0;
         mw[++mi][i]=m;        for(j=1; j<i; j++){
       if(m >=lastpass)          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         break;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       else        }
         m++;        for(j=i+1; j<=nlstate+ndeath; j++){
     }/* end while */          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     if (s[m][i] > nlstate){          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       mi++;     /* Death is another wave */        }
       /* if(mi==0)  never been interviewed correctly before death */        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
          /* Only death is a correct wave */        ps[i][i]=1./(s1+1.);
       mw[mi][i]=m;        /* Computing other pijs */
     }        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
     wav[i]=mi;        for(j=i+1; j<=nlstate+ndeath; j++)
     if(mi==0)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   }      } /* end i */
       
   for(i=1; i<=imx; i++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for(mi=1; mi<wav[i];mi++){        for(jj=1; jj<= nlstate+ndeath; jj++){
       if (stepm <=0)          ps[ii][jj]=0;
         dh[mi][i]=1;          ps[ii][ii]=1;
       else{        }
         if (s[mw[mi+1][i]][i] > nlstate) {      }
           if (agedc[i] < 2*AGESUP) {      
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
           k=k+1;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
           if (j >= jmax) jmax=j;  /*         printf("ddd %lf ",ps[ii][jj]); */
           if (j <= jmin) jmin=j;  /*       } */
           sum=sum+j;  /*       printf("\n "); */
           /* if (j<10) printf("j=%d num=%d ",j,i); */  /*        } */
           }  /*        printf("\n ");printf("%lf ",cov[2]); */
         }         /*
         else{        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        goto end;*/
           k=k+1;      return ps;
           if (j >= jmax) jmax=j;  }
           else if (j <= jmin)jmin=j;  
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /**************** Product of 2 matrices ******************/
           sum=sum+j;  
         }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         jk= j/stepm;  {
         jl= j -jk*stepm;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         ju= j -(jk+1)*stepm;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         if(jl <= -ju)    /* in, b, out are matrice of pointers which should have been initialized 
           dh[mi][i]=jk;       before: only the contents of out is modified. The function returns
         else       a pointer to pointers identical to out */
           dh[mi][i]=jk+1;    long i, j, k;
         if(dh[mi][i]==0)    for(i=nrl; i<= nrh; i++)
           dh[mi][i]=1; /* At least one step */      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];
   }  
   jmean=sum/k;    return out;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  }
  }  
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  /************* Higher Matrix Product ***************/
 {  
   int Ndum[20],ij=1, k, j, i;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   int cptcode=0;  {
   cptcoveff=0;    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
   for (k=0; k<19; k++) Ndum[k]=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   for (k=1; k<=7; k++) ncodemax[k]=0;       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {       (typically every 2 years instead of every month which is too big 
     for (i=1; i<=imx; i++) {       for the memory).
       ij=(int)(covar[Tvar[j]][i]);       Model is determined by parameters x and covariates have to be 
       Ndum[ij]++;       included manually here. 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;       */
     }  
     int i, j, d, h, k;
     for (i=0; i<=cptcode; i++) {    double **out, cov[NCOVMAX+1];
       if(Ndum[i]!=0) ncodemax[j]++;    double **newm;
     }  
     ij=1;    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
     for (i=1; i<=ncodemax[j]; i++) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
       for (k=0; k<=19; k++) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
         if (Ndum[k] != 0) {      }
           nbcode[Tvar[j]][ij]=k;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           ij++;    for(h=1; h <=nhstepm; h++){
         }      for(d=1; d <=hstepm; d++){
         if (ij > ncodemax[j]) break;        newm=savm;
       }          /* Covariates have to be included here again */
     }        cov[1]=1.;
   }          cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
  for (k=0; k<19; k++) Ndum[k]=0;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
  for (i=1; i<=ncovmodel-2; i++) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       ij=Tvar[i];        for (k=1; k<=cptcovprod;k++)
       Ndum[ij]++;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }  
   
  ij=1;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
  for (i=1; i<=10; i++) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
    if((Ndum[i]!=0) && (i<=ncov)){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
      Tvaraff[ij]=i;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
      ij++;        savm=oldm;
    }        oldm=newm;
  }      }
        for(i=1; i<=nlstate+ndeath; i++)
     cptcoveff=ij-1;        for(j=1;j<=nlstate+ndeath;j++) {
 }          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
 /*********** Health Expectancies ****************/        }
       /*printf("h=%d ",h);*/
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    } /* end h */
 {  /*     printf("\n H=%d \n",h); */
   /* Health expectancies */    return po;
   int i, j, nhstepm, hstepm, h;  }
   double age, agelim,hf;  
   double ***p3mat;  
    /*************** log-likelihood *************/
   fprintf(ficreseij,"# Health expectancies\n");  double func( double *x)
   fprintf(ficreseij,"# Age");  {
   for(i=1; i<=nlstate;i++)    int i, ii, j, k, mi, d, kk;
     for(j=1; j<=nlstate;j++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       fprintf(ficreseij," %1d-%1d",i,j);    double **out;
   fprintf(ficreseij,"\n");    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
   hstepm=1*YEARM; /*  Every j years of age (in month) */    int s1, s2;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double bbh, survp;
     long ipmx;
   agelim=AGESUP;    /*extern weight */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* We are differentiating ll according to initial status */
     /* nhstepm age range expressed in number of stepm */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    /*for(i=1;i<imx;i++) 
     /* Typically if 20 years = 20*12/6=40 stepm */      printf(" %d\n",s[4][i]);
     if (stepm >= YEARM) hstepm=1;    */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    cov[1]=1.;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for(k=1; k<=nlstate; k++) ll[k]=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);      if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
     for(i=1; i<=nlstate;i++)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       for(j=1; j<=nlstate;j++)           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){           to be observed in j being in i according to the model.
           eij[i][j][(int)age] +=p3mat[i][j][h];         */
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     hf=1;           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     if (stepm >= YEARM) hf=stepm/YEARM;           has been calculated etc */
     fprintf(ficreseij,"%.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(ficreseij," %.4f", hf*eij[i][j][(int)age]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficreseij,"\n");            }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /************ Variance ******************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
 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)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Variance of health expectancies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            savm=oldm;
   double **newm;            oldm=newm;
   double **dnewm,**doldm;          } /* end mult */
   int i, j, nhstepm, hstepm, h;        
   int k, cptcode;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double *xp;          /* But now since version 0.9 we anticipate for bias at large stepm.
   double **gp, **gm;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double ***gradg, ***trgradg;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double ***p3mat;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double age,agelim;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int theta;           * (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
    fprintf(ficresvij,"# Covariances of life expectancies\n");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   fprintf(ficresvij,"# Age");           * -stepm/2 to stepm/2 .
   for(i=1; i<=nlstate;i++)           * For stepm=1 the results are the same as for previous versions of Imach.
     for(j=1; j<=nlstate;j++)           * For stepm > 1 the results are less biased than in previous versions. 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);           */
   fprintf(ficresvij,"\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   xp=vector(1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   dnewm=matrix(1,nlstate,1,npar);          /* bias bh is positive if real duration
   doldm=matrix(1,nlstate,1,nlstate);           * is higher than the multiple of stepm and negative otherwise.
             */
   hstepm=1*YEARM; /* Every year of age */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          if( s2 > nlstate){ 
   agelim = AGESUP;            /* i.e. if s2 is a death state and if the date of death is known 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */               then the contribution to the likelihood is the probability to 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */               die between last step unit time and current  step unit time, 
     if (stepm >= YEARM) hstepm=1;               which is also equal to probability to die before dh 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */               minus probability to die before dh-stepm . 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);               In version up to 0.92 likelihood was computed
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          as if date of death was unknown. Death was treated as any other
     gp=matrix(0,nhstepm,1,nlstate);          health state: the date of the interview describes the actual state
     gm=matrix(0,nhstepm,1,nlstate);          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
     for(theta=1; theta <=npar; theta++){          (healthy, disable or death) and IMaCh was corrected; but when we
       for(i=1; i<=npar; i++){ /* Computes gradient */          introduced the exact date of death then we should have modified
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          the contribution of an exact death to the likelihood. This new
       }          contribution is smaller and very dependent of the step unit
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            stepm. It is no more the probability to die between last interview
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
       if (popbased==1) {          probability to die within a month. Thanks to Chris
         for(i=1; i<=nlstate;i++)          Jackson for correcting this bug.  Former versions increased
           prlim[i][i]=probs[(int)age][i][ij];          mortality artificially. The bad side is that we add another loop
       }          which slows down the processing. The difference can be up to 10%
                lower mortality.
       for(j=1; j<= nlstate; j++){            */
         for(h=0; h<=nhstepm; h++){            lli=log(out[s1][s2] - savm[s1][s2]);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }          } else if  (s2==-2) {
       }            for (j=1,survp=0. ; j<=nlstate; j++) 
                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(i=1; i<=npar; i++) /* Computes gradient */            /*survp += out[s1][j]; */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            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, gm[h][j]=0.;i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            lli= log(survp); 
         }          } 
       }          
           else{
       for(j=1; j<= nlstate; j++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for(h=0; h<=nhstepm; h++){            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          } 
         }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     } /* End theta */          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          ipmx +=1;
           sw += weight[i];
     for(h=0; h<=nhstepm; h++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<=nlstate;j++)        } /* end of wave */
         for(theta=1; theta <=npar; theta++)      } /* end of individual */
           trgradg[h][j][theta]=gradg[h][theta][j];    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1;i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(j=1;j<=nlstate;j++)        for(mi=1; mi<= wav[i]-1; mi++){
         vareij[i][j][(int)age] =0.;          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(h=0;h<=nhstepm;h++){            for (j=1;j<=nlstate+ndeath;j++){
       for(k=0;k<=nhstepm;k++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            }
         for(i=1;i<=nlstate;i++)          for(d=0; d<=dh[mi][i]; d++){
           for(j=1;j<=nlstate;j++)            newm=savm;
             vareij[i][j][(int)age] += doldm[i][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     h=1;            }
     if (stepm >= YEARM) h=stepm/YEARM;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficresvij,"%.0f ",age );                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)            savm=oldm;
       for(j=1; j<=nlstate;j++){            oldm=newm;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          } /* end mult */
       }        
     fprintf(ficresvij,"\n");          s1=s[mw[mi][i]][i];
     free_matrix(gp,0,nhstepm,1,nlstate);          s2=s[mw[mi+1][i]][i];
     free_matrix(gm,0,nhstepm,1,nlstate);          bbh=(double)bh[mi][i]/(double)stepm; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          ipmx +=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sw += weight[i];
   } /* End age */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   free_vector(xp,1,npar);      } /* end of individual */
   free_matrix(doldm,1,nlstate,1,npar);    }  else if(mle==3){  /* exponential inter-extrapolation */
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************ Variance of prevlim ******************/            for (j=1;j<=nlstate+ndeath;j++){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Variance of prevalence limit */            }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(d=0; d<dh[mi][i]; d++){
   double **newm;            newm=savm;
   double **dnewm,**doldm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, j, nhstepm, hstepm;            for (kk=1; kk<=cptcovage;kk++) {
   int k, cptcode;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *xp;            }
   double *gp, *gm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **gradg, **trgradg;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double age,agelim;            savm=oldm;
   int theta;            oldm=newm;
              } /* end mult */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        
   fprintf(ficresvpl,"# Age");          s1=s[mw[mi][i]][i];
   for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       fprintf(ficresvpl," %1d-%1d",i,i);          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficresvpl,"\n");          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
   xp=vector(1,npar);          sw += weight[i];
   dnewm=matrix(1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   doldm=matrix(1,nlstate,1,nlstate);        } /* end of wave */
        } /* end of individual */
   hstepm=1*YEARM; /* Every year of age */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   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 */        for(mi=1; mi<= wav[i]-1; mi++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (stepm >= YEARM) hstepm=1;            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=matrix(1,npar,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gp=vector(1,nlstate);            }
     gm=vector(1,nlstate);          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for(theta=1; theta <=npar; theta++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (kk=1; kk<=cptcovage;kk++) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          
       for(i=1;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         gp[i] = prlim[i][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       for(i=1; i<=npar; i++) /* Computes gradient */            oldm=newm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          } /* end mult */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        
       for(i=1;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
         gm[i] = prlim[i][i];          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
       for(i=1;i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          }else{
     } /* End theta */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
     trgradg =matrix(1,nlstate,1,npar);          ipmx +=1;
           sw += weight[i];
     for(j=1; j<=nlstate;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(theta=1; theta <=npar; theta++)  /*      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]); */
         trgradg[j][theta]=gradg[theta][j];        } /* end of wave */
       } /* end of individual */
     for(i=1;i<=nlstate;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       varpl[i][(int)age] =0.;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficresvpl,"%.0f ",age );              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)            }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          for(d=0; d<dh[mi][i]; d++){
     fprintf(ficresvpl,"\n");            newm=savm;
     free_vector(gp,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_vector(gm,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
     free_matrix(gradg,1,npar,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_matrix(trgradg,1,nlstate,1,npar);            }
   } /* 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 one-step probabilities  ******************/          s2=s[mw[mi+1][i]][i];
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 {          ipmx +=1;
   int i, j;          sw += weight[i];
   int k=0, cptcode;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **dnewm,**doldm;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   double *xp;        } /* end of wave */
   double *gp, *gm;      } /* end of individual */
   double **gradg, **trgradg;    } /* End of if */
   double age,agelim, cov[NCOVMAX];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   int theta;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   char fileresprob[FILENAMELENGTH];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   strcpy(fileresprob,"prob");  }
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  /*************** log-likelihood *************/
     printf("Problem with resultfile: %s\n", fileresprob);  double funcone( double *x)
   }  {
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    /* Same as likeli but slower because of a lot of printf and if */
      int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   xp=vector(1,npar);    double **out;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double lli; /* Individual log likelihood */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double llt;
      int s1, s2;
   cov[1]=1;    double bbh, survp;
   for (age=bage; age<=fage; age ++){    /*extern weight */
     cov[2]=age;    /* We are differentiating ll according to initial status */
     gradg=matrix(1,npar,1,9);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     trgradg=matrix(1,9,1,npar);    /*for(i=1;i<imx;i++) 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      printf(" %d\n",s[4][i]);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    */
        cov[1]=1.;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
       k=0;        for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<= (nlstate+ndeath); i++){          for (j=1;j<=nlstate+ndeath;j++){
         for(j=1; j<=(nlstate+ndeath);j++){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            k=k+1;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           gp[k]=pmmij[i][j];          }
         }        for(d=0; d<dh[mi][i]; d++){
       }          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++)          for (kk=1; kk<=cptcovage;kk++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       k=0;          savm=oldm;
       for(i=1; i<=(nlstate+ndeath); i++){          oldm=newm;
         for(j=1; j<=(nlstate+ndeath);j++){        } /* end mult */
           k=k+1;        
           gm[k]=pmmij[i][j];        s1=s[mw[mi][i]][i];
         }        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
              /* bias is positive if real duration
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)         * is higher than the multiple of stepm and negative otherwise.
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];           */
     }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        } else if  (s2==-2) {
       for(theta=1; theta <=npar; theta++)          for (j=1,survp=0. ; j<=nlstate; j++) 
       trgradg[j][theta]=gradg[theta][j];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        }else if (mle==1){
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
      pmij(pmmij,cov,ncovmodel,x,nlstate);          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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
      k=0;          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 */
      for(i=1; i<=(nlstate+ndeath); i++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
        for(j=1; j<=(nlstate+ndeath);j++){          lli=log(out[s1][s2]); /* Original formula */
          k=k+1;        } else{  /* mle=0 back to 1 */
          gm[k]=pmmij[i][j];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         }          /*lli=log(out[s1][s2]); */ /* Original formula */
      }        } /* End of if */
              ipmx +=1;
      /*printf("\n%d ",(int)age);        sw += weight[i];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
      }*/   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   fprintf(ficresprob,"\n%d ",(int)age);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            llt +=ll[k]*gipmx/gsw;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }
   }          fprintf(ficresilk," %10.6f\n", -llt);
         }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      } /* end of wave */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    } /* end of individual */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  free_vector(xp,1,npar);    if(globpr==0){ /* First time we count the contributions and weights */
 fclose(ficresprob);      gipmx=ipmx;
  exit(0);      gsw=sw;
 }    }
     return -l;
 /***********************************************/  }
 /**************** Main Program *****************/  
 /***********************************************/  
   /*************** function likelione ***********/
 /*int main(int argc, char *argv[])*/  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 int main()  {
 {    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       to check the exact contribution to the likelihood.
   double agedeb, agefin,hf;       Plotting could be done.
   double agemin=1.e20, agemax=-1.e20;     */
     int k;
   double fret;  
   double **xi,tmp,delta;    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   double dum; /* Dummy variable */      strcat(fileresilk,fileres);
   double ***p3mat;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   int *indx;        printf("Problem with resultfile: %s\n", fileresilk);
   char line[MAXLINE], linepar[MAXLINE];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   char title[MAXLINE];      }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      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");
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   char filerest[FILENAMELENGTH];      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   char fileregp[FILENAMELENGTH];      for(k=1; k<=nlstate; k++) 
   char popfile[FILENAMELENGTH];        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   int firstobs=1, lastobs=10;    }
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;    *fretone=(*funcone)(p);
   int ju,jl, mi;    if(*globpri !=0){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      fclose(ficresilk);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;      fflush(fichtm); 
   int hstepm, nhstepm;    } 
   int *popage;    return;
   }
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;  
   double **prlim;  /*********** Maximum Likelihood Estimation ***************/
   double *severity;  
   double ***param; /* Matrix of parameters */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double  *p;  {
   double **matcov; /* Matrix of covariance */    int i,j, iter;
   double ***delti3; /* Scale */    double **xi;
   double *delti; /* Scale */    double fret;
   double ***eij, ***vareij;    double fretone; /* Only one call to likelihood */
   double **varpl; /* Variances of prevalence limits by age */    /*  char filerespow[FILENAMELENGTH];*/
   double *epj, vepp;    xi=matrix(1,npar,1,npar);
   double kk1, kk2;    for (i=1;i<=npar;i++)
   double *popeffectif,*popcount;      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
   char z[1]="c", occ;      printf("Problem with resultfile: %s\n", filerespow);
 #include <sys/time.h>      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 #include <time.h>    }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   /* long total_usecs;    for (i=1;i<=nlstate;i++)
   struct timeval start_time, end_time;      for(j=1;j<=nlstate+ndeath;j++)
          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficrespow,"\n");
   
     powell(p,xi,npar,ftol,&iter,&fret,func);
   printf("\nIMACH, Version 0.7");  
   printf("\nEnter the parameter file name: ");    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
 #ifdef windows    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   scanf("%s",pathtot);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   getcwd(pathcd, size);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  }
   /* cutv(path,optionfile,pathtot,'\\');*/  
   /**** Computes Hessian and covariance matrix ***/
 split(pathtot, path,optionfile);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   chdir(path);  {
   replace(pathc,path);    double  **a,**y,*x,pd;
 #endif    double **hess;
 #ifdef unix    int i, j,jk;
   scanf("%s",optionfile);    int *indx;
 #endif  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
 /*-------- arguments in the command line --------*/    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[]) ;
   strcpy(fileres,"r");    void ludcmp(double **a, int npar, int *indx, double *d) ;
   strcat(fileres, optionfile);    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   /*---------arguments file --------*/  
     printf("\nCalculation of the hessian matrix. Wait...\n");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     printf("Problem with optionfile %s\n",optionfile);    for (i=1;i<=npar;i++){
     goto end;      printf("%d",i);fflush(stdout);
   }      fprintf(ficlog,"%d",i);fflush(ficlog);
      
   strcpy(filereso,"o");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   strcat(filereso,fileres);      
   if((ficparo=fopen(filereso,"w"))==NULL) {      /*  printf(" %f ",p[i]);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }    }
     
   /* Reads comments: lines beginning with '#' */    for (i=1;i<=npar;i++) {
   while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++)  {
     ungetc(c,ficpar);        if (j>i) { 
     fgets(line, MAXLINE, ficpar);          printf(".%d%d",i,j);fflush(stdout);
     puts(line);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     fputs(line,ficparo);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   }          
   ungetc(c,ficpar);          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
   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);        }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);      }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    }
 while((c=getc(ficpar))=='#' && c!= EOF){    printf("\n");
     ungetc(c,ficpar);    fprintf(ficlog,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fputs(line,ficparo);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   }    
   ungetc(c,ficpar);    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);    x=vector(1,npar);
   fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);    indx=ivector(1,npar);
      for (i=1;i<=npar;i++)
  while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ungetc(c,ficpar);    ludcmp(a,npar,indx,&pd);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for (j=1;j<=npar;j++) {
     fputs(line,ficparo);      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
   ungetc(c,ficpar);      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);        matcov[i][j]=x[i];
   fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);      }
          }
    
 while((c=getc(ficpar))=='#' && c!= EOF){    printf("\n#Hessian matrix#\n");
     ungetc(c,ficpar);    fprintf(ficlog,"\n#Hessian matrix#\n");
     fgets(line, MAXLINE, ficpar);    for (i=1;i<=npar;i++) { 
     puts(line);      for (j=1;j<=npar;j++) { 
     fputs(line,ficparo);        printf("%.3e ",hess[i][j]);
   }        fprintf(ficlog,"%.3e ",hess[i][j]);
   ungetc(c,ficpar);      }
        printf("\n");
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);      fprintf(ficlog,"\n");
      }
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;    /* Recompute Inverse */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   ncovmodel=2+cptcovn;    ludcmp(a,npar,indx,&pd);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      /*  printf("\n#Hessian matrix recomputed#\n");
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */    for (j=1;j<=npar;j++) {
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1;i<=npar;i++) x[i]=0;
     ungetc(c,ficpar);      x[j]=1;
     fgets(line, MAXLINE, ficpar);      lubksb(a,npar,indx,x);
     puts(line);      for (i=1;i<=npar;i++){ 
     fputs(line,ficparo);        y[i][j]=x[i];
   }        printf("%.3e ",y[i][j]);
   ungetc(c,ficpar);        fprintf(ficlog,"%.3e ",y[i][j]);
        }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      printf("\n");
     for(i=1; i <=nlstate; i++)      fprintf(ficlog,"\n");
     for(j=1; j <=nlstate+ndeath-1; j++){    }
       fscanf(ficpar,"%1d%1d",&i1,&j1);    */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);    free_matrix(a,1,npar,1,npar);
       for(k=1; k<=ncovmodel;k++){    free_matrix(y,1,npar,1,npar);
         fscanf(ficpar," %lf",&param[i][j][k]);    free_vector(x,1,npar);
         printf(" %lf",param[i][j][k]);    free_ivector(indx,1,npar);
         fprintf(ficparo," %lf",param[i][j][k]);    free_matrix(hess,1,npar,1,npar);
       }  
       fscanf(ficpar,"\n");  
       printf("\n");  }
       fprintf(ficparo,"\n");  
     }  /*************** hessian matrix ****************/
    double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  {
     int i;
   p=param[1][1];    int l=1, lmax=20;
      double k1,k2;
   /* Reads comments: lines beginning with '#' */    double p2[MAXPARM+1]; /* identical to x */
   while((c=getc(ficpar))=='#' && c!= EOF){    double res;
     ungetc(c,ficpar);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     fgets(line, MAXLINE, ficpar);    double fx;
     puts(line);    int k=0,kmax=10;
     fputs(line,ficparo);    double l1;
   }  
   ungetc(c,ficpar);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for(l=0 ; l <=lmax; l++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      l1=pow(10,l);
   for(i=1; i <=nlstate; i++){      delts=delt;
     for(j=1; j <=nlstate+ndeath-1; j++){      for(k=1 ; k <kmax; k=k+1){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        delt = delta*(l1*k);
       printf("%1d%1d",i,j);        p2[theta]=x[theta] +delt;
       fprintf(ficparo,"%1d%1d",i1,j1);        k1=func(p2)-fx;
       for(k=1; k<=ncovmodel;k++){        p2[theta]=x[theta]-delt;
         fscanf(ficpar,"%le",&delti3[i][j][k]);        k2=func(p2)-fx;
         printf(" %le",delti3[i][j][k]);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         fprintf(ficparo," %le",delti3[i][j][k]);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       }        
       fscanf(ficpar,"\n");  #ifdef DEBUGHESS
       printf("\n");        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficparo,"\n");        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   delti=delti3[1][1];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
            k=kmax;
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     ungetc(c,ficpar);          k=kmax; l=lmax*10.;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     fputs(line,ficparo);          delts=delt;
   }        }
   ungetc(c,ficpar);      }
      }
   matcov=matrix(1,npar,1,npar);    delti[theta]=delts;
   for(i=1; i <=npar; i++){    return res; 
     fscanf(ficpar,"%s",&str);    
     printf("%s",str);  }
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       fscanf(ficpar," %le",&matcov[i][j]);  {
       printf(" %.5le",matcov[i][j]);    int i;
       fprintf(ficparo," %.5le",matcov[i][j]);    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
     fscanf(ficpar,"\n");    double p2[MAXPARM+1];
     printf("\n");    int k;
     fprintf(ficparo,"\n");  
   }    fx=func(x);
   for(i=1; i <=npar; i++)    for (k=1; k<=2; k++) {
     for(j=i+1;j<=npar;j++)      for (i=1;i<=npar;i++) p2[i]=x[i];
       matcov[i][j]=matcov[j][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
          p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   printf("\n");      k1=func(p2)-fx;
     
       p2[thetai]=x[thetai]+delti[thetai]/k;
     /*-------- data file ----------*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if((ficres =fopen(fileres,"w"))==NULL) {      k2=func(p2)-fx;
       printf("Problem with resultfile: %s\n", fileres);goto end;    
     }      p2[thetai]=x[thetai]-delti[thetai]/k;
     fprintf(ficres,"#%s\n",version);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k3=func(p2)-fx;
     if((fic=fopen(datafile,"r"))==NULL)    {    
       printf("Problem with datafile: %s\n", datafile);goto end;      p2[thetai]=x[thetai]-delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
     n= lastobs;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     severity = vector(1,maxwav);  #ifdef DEBUG
     outcome=imatrix(1,maxwav+1,1,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);
     num=ivector(1,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);
     moisnais=vector(1,n);  #endif
     annais=vector(1,n);    }
     moisdc=vector(1,n);    return res;
     andc=vector(1,n);  }
     agedc=vector(1,n);  
     cod=ivector(1,n);  /************** Inverse of matrix **************/
     weight=vector(1,n);  void ludcmp(double **a, int n, int *indx, double *d) 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  { 
     mint=matrix(1,maxwav,1,n);    int i,imax,j,k; 
     anint=matrix(1,maxwav,1,n);    double big,dum,sum,temp; 
     s=imatrix(1,maxwav+1,1,n);    double *vv; 
     adl=imatrix(1,maxwav+1,1,n);       
     tab=ivector(1,NCOVMAX);    vv=vector(1,n); 
     ncodemax=ivector(1,8);    *d=1.0; 
     for (i=1;i<=n;i++) { 
     i=1;      big=0.0; 
     while (fgets(line, MAXLINE, fic) != NULL)    {      for (j=1;j<=n;j++) 
       if ((i >= firstobs) && (i <=lastobs)) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
              if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         for (j=maxwav;j>=1;j--){      vv[i]=1.0/big; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    } 
           strcpy(line,stra);    for (j=1;j<=n;j++) { 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for (i=1;i<j;i++) { 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        sum=a[i][j]; 
         }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                a[i][j]=sum; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      big=0.0; 
       for (i=j;i<=n;i++) { 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        sum=a[i][j]; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        a[i][j]=sum; 
         for (j=ncov;j>=1;j--){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          big=dum; 
         }          imax=i; 
         num[i]=atol(stra);        } 
              } 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      if (j != imax) { 
           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;}*/        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
         i=i+1;          a[imax][k]=a[j][k]; 
       }          a[j][k]=dum; 
     }        } 
     /* printf("ii=%d", ij);        *d = -(*d); 
        scanf("%d",i);*/        vv[imax]=vv[j]; 
   imx=i-1; /* Number of individuals */      } 
       indx[j]=imax; 
   /* for (i=1; i<=imx; i++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      if (j != n) { 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        dum=1.0/(a[j][j]); 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     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]));*/    } 
     free_vector(vv,1,n);  /* Doesn't work */
   /* Calculation of the number of parameter from char model*/  ;
   Tvar=ivector(1,15);  } 
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);  void lubksb(double **a, int n, int *indx, double b[]) 
   Tvard=imatrix(1,15,1,2);  { 
   Tage=ivector(1,15);          int i,ii=0,ip,j; 
        double sum; 
   if (strlen(model) >1){   
     j=0, j1=0, k1=1, k2=1;    for (i=1;i<=n;i++) { 
     j=nbocc(model,'+');      ip=indx[i]; 
     j1=nbocc(model,'*');      sum=b[ip]; 
     cptcovn=j+1;      b[ip]=b[i]; 
     cptcovprod=j1;      if (ii) 
            for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
          else if (sum) ii=i; 
     strcpy(modelsav,model);      b[i]=sum; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    } 
       printf("Error. Non available option model=%s ",model);    for (i=n;i>=1;i--) { 
       goto end;      sum=b[i]; 
     }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
          b[i]=sum/a[i][i]; 
     for(i=(j+1); i>=1;i--){    } 
       cutv(stra,strb,modelsav,'+');  } 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  void pstamp(FILE *fichier)
       /*scanf("%d",i);*/  {
       if (strchr(strb,'*')) {    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         cutv(strd,strc,strb,'*');  }
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;  /************ Frequencies ********************/
           cutv(strb,stre,strd,'V');  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[])
           Tvar[i]=atoi(stre);  {  /* Some frequencies */
           cptcovage++;    
             Tage[cptcovage]=i;    int i, m, jk, k1,i1, j1, bool, z1,j;
             /*printf("stre=%s ", stre);*/    int first;
         }    double ***freq; /* Frequencies */
         else if (strcmp(strd,"age")==0) {    double *pp, **prop;
           cptcovprod--;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           cutv(strb,stre,strc,'V');    char fileresp[FILENAMELENGTH];
           Tvar[i]=atoi(stre);    
           cptcovage++;    pp=vector(1,nlstate);
           Tage[cptcovage]=i;    prop=matrix(1,nlstate,iagemin,iagemax+3);
         }    strcpy(fileresp,"p");
         else {    strcat(fileresp,fileres);
           cutv(strb,stre,strc,'V');    if((ficresp=fopen(fileresp,"w"))==NULL) {
           Tvar[i]=ncov+k1;      printf("Problem with prevalence resultfile: %s\n", fileresp);
           cutv(strb,strc,strd,'V');      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           Tprod[k1]=i;      exit(0);
           Tvard[k1][1]=atoi(strc);    }
           Tvard[k1][2]=atoi(stre);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           Tvar[cptcovn+k2]=Tvard[k1][1];    j1=0;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    
           for (k=1; k<=lastobs;k++)    j=cptcoveff;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           k1++;  
           k2=k2+2;    first=1;
         }  
       }    for(k1=1; k1<=j;k1++){
       else {      for(i1=1; i1<=ncodemax[k1];i1++){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        j1++;
        /*  scanf("%d",i);*/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       cutv(strd,strc,strb,'V');          scanf("%d", i);*/
       Tvar[i]=atoi(strc);        for (i=-5; i<=nlstate+ndeath; i++)  
       }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       strcpy(modelsav,stra);              for(m=iagemin; m <= iagemax+3; m++)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);              freq[i][jk][m]=0;
         scanf("%d",i);*/  
     }      for (i=1; i<=nlstate; i++)  
 }        for(m=iagemin; m <= iagemax+3; m++)
            prop[i][m]=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);        dateintsum=0;
   scanf("%d ",i);*/        k2cpt=0;
     fclose(fic);        for (i=1; i<=imx; i++) {
           bool=1;
     /*  if(mle==1){*/          if  (cptcovn>0) {
     if (weightopt != 1) { /* Maximisation without weights*/            for (z1=1; z1<=cptcoveff; z1++) 
       for(i=1;i<=n;i++) weight[i]=1.0;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     }                bool=0;
     /*-calculation of age at interview from date of interview and age at death -*/          }
     agev=matrix(1,maxwav,1,imx);          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
    for (i=1; i<=imx; i++)              k2=anint[m][i]+(mint[m][i]/12.);
      for(m=2; (m<= maxwav); m++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
          anint[m][i]=9999;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
          s[m][i]=-1;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
        }                if (m<lastpass) {
                      freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for (i=1; i<=imx; i++)  {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                }
       for(m=1; (m<= maxwav); m++){                
         if(s[m][i] >0){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           if (s[m][i] == nlstate+1) {                  dateintsum=dateintsum+k2;
             if(agedc[i]>0)                  k2cpt++;
               if(moisdc[i]!=99 && andc[i]!=9999)                }
               agev[m][i]=agedc[i];                /*}*/
             else {            }
               if (andc[i]!=9999){          }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        }
               agev[m][i]=-1;         
               }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             }        pstamp(ficresp);
           }        if  (cptcovn>0) {
           else if(s[m][i] !=9){ /* Should no more exist */          fprintf(ficresp, "\n#********** Variable "); 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if(mint[m][i]==99 || anint[m][i]==9999)          fprintf(ficresp, "**********\n#");
               agev[m][i]=1;        }
             else if(agev[m][i] <agemin){        for(i=1; i<=nlstate;i++) 
               agemin=agev[m][i];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        fprintf(ficresp, "\n");
             }        
             else if(agev[m][i] >agemax){        for(i=iagemin; i <= iagemax+3; i++){
               agemax=agev[m][i];          if(i==iagemax+3){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            fprintf(ficlog,"Total");
             }          }else{
             /*agev[m][i]=anint[m][i]-annais[i];*/            if(first==1){
             /*   agev[m][i] = age[i]+2*m;*/              first=0;
           }              printf("See log file for details...\n");
           else { /* =9 */            }
             agev[m][i]=1;            fprintf(ficlog,"Age %d", i);
             s[m][i]=-1;          }
           }          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         else /*= 0 Unknown */              pp[jk] += freq[jk][m][i]; 
           agev[m][i]=1;          }
       }          for(jk=1; jk <=nlstate ; jk++){
                for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
     for (i=1; i<=imx; i++)  {            if(pp[jk]>=1.e-10){
       for(m=1; (m<= maxwav); m++){              if(first==1){
         if (s[m][i] > (nlstate+ndeath)) {                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           printf("Error: Wrong value in nlstate or ndeath\n");                }
           goto end;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }            }else{
       }              if(first==1)
     }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            }
           }
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);          for(jk=1; jk <=nlstate ; jk++){
     free_vector(moisnais,1,n);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     free_vector(annais,1,n);              pp[jk] += freq[jk][m][i];
     free_matrix(mint,1,maxwav,1,n);          }       
     free_matrix(anint,1,maxwav,1,n);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     free_vector(moisdc,1,n);            pos += pp[jk];
     free_vector(andc,1,n);            posprop += prop[jk][i];
           }
              for(jk=1; jk <=nlstate ; jk++){
     wav=ivector(1,imx);            if(pos>=1.e-5){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              if(first==1)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     /* Concatenates waves */            }else{
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       Tcode=ivector(1,100);            }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            if( i <= iagemax){
       ncodemax[1]=1;              if(pos>=1.e-5){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                      /*probs[i][jk][j1]= pp[jk]/pos;*/
    codtab=imatrix(1,100,1,10);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
    h=0;              }
    m=pow(2,cptcoveff);              else
                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
    for(k=1;k<=cptcoveff; k++){            }
      for(i=1; i <=(m/pow(2,k));i++){          }
        for(j=1; j <= ncodemax[k]; j++){          
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
            h++;            for(m=-1; m <=nlstate+ndeath; m++)
            if (h>m) h=1;codtab[h][k]=j;              if(freq[jk][m][i] !=0 ) {
          }              if(first==1)
        }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
    }              }
           if(i <= iagemax)
             fprintf(ficresp,"\n");
    /*for(i=1; i <=m ;i++){          if(first==1)
      for(k=1; k <=cptcovn; k++){            printf("Others in log...\n");
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          fprintf(ficlog,"\n");
      }        }
      printf("\n");      }
    }    }
    scanf("%d",i);*/    dateintmean=dateintsum/k2cpt; 
       
    /* Calculates basic frequencies. Computes observed prevalence at single age    fclose(ficresp);
        and prints on file fileres'p'. */    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* End of Freq */
     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 */  /************ Prevalence ********************/
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  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)
        {  
     /* For Powell, parameters are in a vector p[] starting at p[1]    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       in each health status at the date of interview (if between dateprev1 and dateprev2).
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */       We still use firstpass and lastpass as another selection.
     */
     if(mle==1){   
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    int i, m, jk, k1, i1, j1, bool, z1,j;
     }    double ***freq; /* Frequencies */
        double *pp, **prop;
     /*--------- results files --------------*/    double pos,posprop; 
     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);    double  y2; /* in fractional years */
    fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);    int iagemin, iagemax;
    fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);  
     iagemin= (int) agemin;
    jk=1;    iagemax= (int) agemax;
    fprintf(ficres,"# Parameters\n");    /*pp=vector(1,nlstate);*/
    printf("# Parameters\n");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
    for(i=1,jk=1; i <=nlstate; i++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      for(k=1; k <=(nlstate+ndeath); k++){    j1=0;
        if (k != i)    
          {    j=cptcoveff;
            printf("%d%d ",i,k);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
            fprintf(ficres,"%1d%1d ",i,k);    
            for(j=1; j <=ncovmodel; j++){    for(k1=1; k1<=j;k1++){
              printf("%f ",p[jk]);      for(i1=1; i1<=ncodemax[k1];i1++){
              fprintf(ficres,"%f ",p[jk]);        j1++;
              jk++;        
            }        for (i=1; i<=nlstate; i++)  
            printf("\n");          for(m=iagemin; m <= iagemax+3; m++)
            fprintf(ficres,"\n");            prop[i][m]=0.0;
          }       
      }        for (i=1; i<=imx; i++) { /* Each individual */
    }          bool=1;
  if(mle==1){          if  (cptcovn>0) {
     /* Computing hessian and covariance matrix */            for (z1=1; z1<=cptcoveff; z1++) 
     ftolhess=ftol; /* Usually correct */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     hesscov(matcov, p, npar, delti, ftolhess, func);                bool=0;
  }          } 
     fprintf(ficres,"# Scales\n");          if (bool==1) { 
     printf("# Scales\n");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
      for(i=1,jk=1; i <=nlstate; i++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for(j=1; j <=nlstate+ndeath; j++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         if (j!=i) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           fprintf(ficres,"%1d%1d",i,j);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           printf("%1d%1d",i,j);                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(k=1; k<=ncovmodel;k++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             printf(" %.5e",delti[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," %.5e",delti[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++){  
              
     k=1;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fprintf(ficres,"# Covariance\n");            posprop += prop[jk][i]; 
     printf("# Covariance\n");          } 
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;          for(jk=1; jk <=nlstate ; jk++){     
       i1=(i-1)/(ncovmodel*nlstate)+1;            if( i <=  iagemax){ 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              if(posprop>=1.e-5){ 
       printf("%s%d%d",alph[k],i1,tab[i]);*/                probs[i][jk][j1]= prop[jk][i]/posprop;
       fprintf(ficres,"%3d",i);              } else
       printf("%3d",i);                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
       for(j=1; j<=i;j++){            } 
         fprintf(ficres," %.5e",matcov[i][j]);          }/* end jk */ 
         printf(" %.5e",matcov[i][j]);        }/* end i */ 
       }      } /* end i1 */
       fprintf(ficres,"\n");    } /* end k1 */
       printf("\n");    
       k++;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     }    /*free_vector(pp,1,nlstate);*/
        free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     while((c=getc(ficpar))=='#' && c!= EOF){  }  /* End of prevalence */
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  /************* Waves Concatenation ***************/
       puts(line);  
       fputs(line,ficparo);  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)
     }  {
     ungetc(c,ficpar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         Death is a valid wave (if date is known).
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     if (fage <= 2) {       and mw[mi+1][i]. dh depends on stepm.
       bage = agemin;       */
       fage = agemax;  
     }    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       double sum=0., jmean=0.;*/
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int first;
     int j, k=0,jk, ju, jl;
        double sum=0.;
 /*------------ gnuplot -------------*/    first=0;
 chdir(pathcd);    jmin=1e+5;
   if((ficgp=fopen("graph.plt","w"))==NULL) {    jmax=-1;
     printf("Problem with file graph.gp");goto end;    jmean=0.;
   }    for(i=1; i<=imx; i++){
 #ifdef windows      mi=0;
   fprintf(ficgp,"cd \"%s\" \n",pathc);      m=firstpass;
 #endif      while(s[m][i] <= nlstate){
 m=pow(2,cptcoveff);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
            mw[++mi][i]=m;
  /* 1eme*/        if(m >=lastpass)
   for (cpt=1; cpt<= nlstate ; cpt ++) {          break;
    for (k1=1; k1<= m ; k1 ++) {        else
           m++;
 #ifdef windows      }/* end while */
     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 (s[m][i] > nlstate){
 #endif        mi++;     /* Death is another wave */
 #ifdef unix        /* if(mi==0)  never been interviewed correctly before death */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);           /* Only death is a correct wave */
 #endif        mw[mi][i]=m;
       }
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      wav[i]=mi;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if(mi==0){
 }        nbwarn++;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        if(first==0){
     for (i=1; i<= nlstate ; i ++) {          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          first=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        if(first==1){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
      for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      } /* end mi==0 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } /* End individuals */
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    for(i=1; i<=imx; i++){
 #ifdef unix      for(mi=1; mi<wav[i];mi++){
 fprintf(ficgp,"\nset ter gif small size 400,300");        if (stepm <=0)
 #endif          dh[mi][i]=1;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        else{
    }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   }            if (agedc[i] < 2*AGESUP) {
   /*2 eme*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
   for (k1=1; k1<= m ; k1 ++) {              else if(j<0){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);                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]);
     for (i=1; i<= nlstate+1 ; i ++) {                j=1; /* Temporary Dangerous patch */
       k=2*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);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for (j=1; j<= nlstate+1 ; j ++) {                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");              k=k+1;
 }                if (j >= jmax){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                jmax=j;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                ijmax=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 <= jmin){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                jmin=j;
         else fprintf(ficgp," \%%*lf (\%%*lf)");                ijmin=i;
 }                }
       fprintf(ficgp,"\" t\"\" w l 0,");              sum=sum+j;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       for (j=1; j<= nlstate+1 ; j ++) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }            else{
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       else fprintf(ficgp,"\" t\"\" w l 0,");  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            k=k+1;
   }            if (j >= jmax) {
                jmax=j;
   /*3eme*/              ijmax=i;
             }
   for (k1=1; k1<= m ; k1 ++) {            else if (j <= jmin){
     for (cpt=1; cpt<= nlstate ; cpt ++) {              jmin=j;
       k=2+nlstate*(cpt-1);              ijmin=i;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);            }
       for (i=1; i< nlstate ; i ++) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         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);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       }            if(j<0){
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              nberr++;
     }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }              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]);
              }
   /* CV preval stat */            sum=sum+j;
   for (k1=1; k1<= m ; k1 ++) {          }
     for (cpt=1; cpt<nlstate ; cpt ++) {          jk= j/stepm;
       k=3;          jl= j -jk*stepm;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          ju= j -(jk+1)*stepm;
       for (i=1; i< nlstate ; i ++)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         fprintf(ficgp,"+$%d",k+i+1);            if(jl==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              dh[mi][i]=jk;
                    bh[mi][i]=0;
       l=3+(nlstate+ndeath)*cpt;            }else{ /* We want a negative bias in order to only have interpolation ie
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                    * to avoid the price of an extra matrix product in likelihood */
       for (i=1; i< nlstate ; i ++) {              dh[mi][i]=jk+1;
         l=3+(nlstate+ndeath)*cpt;              bh[mi][i]=ju;
         fprintf(ficgp,"+$%d",l+i+1);            }
       }          }else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              if(jl <= -ju){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              dh[mi][i]=jk;
     }              bh[mi][i]=jl;       /* bias is positive if real duration
   }                                     * is higher than the multiple of stepm and negative otherwise.
                                    */
   /* proba elementaires */            }
    for(i=1,jk=1; i <=nlstate; i++){            else{
     for(k=1; k <=(nlstate+ndeath); k++){              dh[mi][i]=jk+1;
       if (k != i) {              bh[mi][i]=ju;
         for(j=1; j <=ncovmodel; j++){            }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/            if(dh[mi][i]==0){
           /*fprintf(ficgp,"%s",alph[1]);*/              dh[mi][i]=1; /* At least one step */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              bh[mi][i]=ju; /* At least one step */
           jk++;              /*  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,"\n");            }
         }          } /* end if mle */
       }        }
     }      } /* end wave */
     }    }
     jmean=sum/k;
   for(jk=1; jk <=m; jk++) {    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(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    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);
    i=1;   }
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;  /*********** Tricode ****************************/
      for(k=1; k<=(nlstate+ndeath); k++) {  void tricode(int *Tvar, int **nbcode, int imx)
        if (k != k2){  {
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /* Uses cptcovn+2*cptcovprod as the number of covariates */
 ij=1;    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int modmaxcovj=0; /* Modality max of covariates j */
             ij++;    cptcoveff=0; 
           }   
           else    for (k=0; k<maxncov; k++) Ndum[k]=0;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
         }  
           fprintf(ficgp,")/(1");    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(k1=1; k1 <=nlstate; k1++){                                   modality of this covariate Vj*/ 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
 ij=1;                                        modality of the nth covariate of individual i. */
           for(j=3; j <=ncovmodel; j++){        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        if (ij > modmaxcovj) modmaxcovj=ij; 
             ij++;        /* getting the maximum value of the modality of the covariate
           }           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
           else           female is 1, then modmaxcovj=1.*/
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      }
           }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           fprintf(ficgp,")");      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
         }        if( Ndum[i] != 0 )
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          ncodemax[j]++; 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        /* Number of modalities of the j th covariate. In fact
         i=i+ncovmodel;           ncodemax[j]=2 (dichotom. variables only) but it could be more for
        }           historical reasons */
      }      } /* Ndum[-1] number of undefined modalities */
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   }      ij=1; 
          for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
   fclose(ficgp);        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
              if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
 chdir(path);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                           k is a modality. If we have model=V1+V1*sex 
     free_ivector(wav,1,imx);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            ij++;
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            }
     free_ivector(num,1,n);          if (ij > ncodemax[j]) break; 
     free_vector(agedc,1,n);        }  /* end of loop on */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      } /* end of loop on modality */ 
     fclose(ficparo);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     fclose(ficres);    
     /*  }*/    for (k=0; k< maxncov; k++) Ndum[k]=0;
        
    /*________fin mle=1_________*/    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.*/
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
       Ndum[ij]++;
     /* No more information from the sample is required now */   }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){   ij=1;
     ungetc(c,ficpar);   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     fgets(line, MAXLINE, ficpar);     if((Ndum[i]!=0) && (i<=ncovcol)){
     puts(line);       Tvaraff[ij]=i; /*For printing */
     fputs(line,ficparo);       ij++;
   }     }
   ungetc(c,ficpar);   }
     ij--;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);   cptcoveff=ij; /*Number of simple covariates*/
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/  /*********** Health Expectancies ****************/
   
   strcpy(optionfilehtm,optionfile);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  {
     printf("Problem with %s \n",optionfilehtm);goto end;    /* Health expectancies, no variances */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    double age, agelim, hf;
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    double ***p3mat;
 Total number of observations=%d <br>    double eip;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  
 <hr  size=\"2\" color=\"#EC5E5E\">    pstamp(ficreseij);
 <li>Outputs files<br><br>\n    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    fprintf(ficreseij,"# Age");
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    for(i=1; i<=nlstate;i++){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      for(j=1; j<=nlstate;j++){
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        fprintf(ficreseij," e%1d%1d ",i,j);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      fprintf(ficreseij," e%1d. ",i);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    }
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    fprintf(ficreseij,"\n");
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    
 <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);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
  fprintf(fichtm," <li>Graphs</li><p>");    }
     else  hstepm=estepm;   
  m=cptcoveff;    /* We compute the life expectancy from trapezoids spaced every estepm months
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
  j1=0;     * we are calculating an estimate of the Life Expectancy assuming a linear 
  for(k1=1; k1<=m;k1++){     * progression in between and thus overestimating or underestimating according
    for(i1=1; i1<=ncodemax[k1];i1++){     * to the curvature of the survival function. If, for the same date, we 
        j1++;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
        if (cptcovn > 0) {     * to compare the new estimate of Life expectancy with the same linear 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");     * hypothesis. A more precise result, taking into account a more precise
          for (cpt=1; cpt<=cptcoveff;cpt++)     * curvature will be obtained if estepm is as small as stepm. */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /* 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. 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>       nhstepm is the number of hstepm from age to agelim 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);           nstepm is the number of stepm from age to agelin. 
        for(cpt=1; cpt<nlstate;cpt++){       Look at hpijx to understand the reason of that which relies in memory size
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>       and note for a fixed period like estepm months */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    /* 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
     for(cpt=1; cpt<=nlstate;cpt++) {       means that if the survival funtion is printed only each two years of age and if
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 interval) in state (%d): v%s%d%d.gif <br>       results. So we changed our mind and took the option of the best precision.
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      */
      }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    agelim=AGESUP;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    /* If stepm=6 months */
      }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
      fprintf(fichtm,"\n<br>- Total life expectancy by age and         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 health expectancies in states (1) and (2): e%s%d.gif<br>      
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  /* nhstepm age range expressed in number of stepm */
 fprintf(fichtm,"\n</body>");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
    }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  }    /* if (stepm >= YEARM) hstepm=1;*/
 fclose(fichtm);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*--------------- Prevalence limit --------------*/  
      for (age=bage; age<=fage; age ++){ 
   strcpy(filerespl,"pl");      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   strcat(filerespl,fileres);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      /* if (stepm >= YEARM) hstepm=1;*/
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      /* If stepm=6 months */
   fprintf(ficrespl,"#Prevalence limit\n");      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   fprintf(ficrespl,"#Age ");         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      
   fprintf(ficrespl,"\n");      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        
   prlim=matrix(1,nlstate,1,nlstate);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("%d|",(int)age);fflush(stdout);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      /* Computing expectancies */
   k=0;      for(i=1; i<=nlstate;i++)
   agebase=agemin;        for(j=1; j<=nlstate;j++)
   agelim=agemax;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   ftolpl=1.e-10;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   i1=cptcoveff;            
   if (cptcovn < 1){i1=1;}            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;      fprintf(ficreseij,"%3.0f",age );
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      for(i=1; i<=nlstate;i++){
         fprintf(ficrespl,"\n#******");        eip=0;
         for(j=1;j<=cptcoveff;j++)        for(j=1; j<=nlstate;j++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          eip +=eij[i][j][(int)age];
         fprintf(ficrespl,"******\n");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
                }
         for (age=agebase; age<=agelim; age++){        fprintf(ficreseij,"%9.4f", eip );
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      }
           fprintf(ficrespl,"%.0f",age );      fprintf(ficreseij,"\n");
           for(i=1; i<=nlstate;i++)      
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    printf("\n");
       }    fprintf(ficlog,"\n");
     }    
   fclose(ficrespl);  }
   
   /*------------- h Pij x at various ages ------------*/  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[] )
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    /* Covariances of health expectancies eij and of total life expectancies according
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;     to initial status i, ei. .
   }    */
   printf("Computing pij: result on file '%s' \n", filerespij);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      int nhstepma, nstepma; /* Decreasing with age */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double age, agelim, hf;
   /*if (stepm<=24) stepsize=2;*/    double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   agelim=AGESUP;    double *xp, *xm;
   hstepm=stepsize*YEARM; /* Every year of age */    double **gp, **gm;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double ***gradg, ***trgradg;
      int theta;
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    double eip, vip;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         fprintf(ficrespij,"\n#****** ");    xp=vector(1,npar);
         for(j=1;j<=cptcoveff;j++)    xm=vector(1,npar);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dnewm=matrix(1,nlstate*nlstate,1,npar);
         fprintf(ficrespij,"******\n");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
            
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    pstamp(ficresstdeij);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficresstdeij,"# Age");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=nlstate;i++){
           oldm=oldms;savm=savms;      for(j=1; j<=nlstate;j++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
           fprintf(ficrespij,"# Age");      fprintf(ficresstdeij," e%1d. ",i);
           for(i=1; i<=nlstate;i++)    }
             for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficresstdeij,"\n");
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");    pstamp(ficrescveij);
           for (h=0; h<=nhstepm; h++){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficrescveij,"# Age");
             for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)      for(j=1; j<=nlstate;j++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        cptj= (j-1)*nlstate+i;
             fprintf(ficrespij,"\n");        for(i2=1; i2<=nlstate;i2++)
           }          for(j2=1; j2<=nlstate;j2++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cptj2= (j2-1)*nlstate+i2;
           fprintf(ficrespij,"\n");            if(cptj2 <= cptj)
         }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     }          }
   }      }
     fprintf(ficrescveij,"\n");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    
     if(estepm < stepm){
   fclose(ficrespij);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   /*---------- Forecasting ------------------*/    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   strcpy(fileresf,"f");     * This is mainly to measure the difference between two models: for example
   strcat(fileresf,fileres);     * if stepm=24 months pijx are given only every 2 years and by summing them
   if((ficresf=fopen(fileresf,"w"))==NULL) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;     * progression in between and thus overestimating or underestimating according
   }     * to the curvature of the survival function. If, for the same date, we 
   printf("Computing forecasting: result on file '%s' \n", fileresf);     * 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 
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
  free_matrix(agev,1,maxwav,1,imx);  
   /* Mobile average */    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   if (mobilav==1) {       Look at hpijx to understand the reason of that which relies in memory size
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       and note for a fixed period like estepm months */
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       for (i=1; i<=nlstate;i++)       survival function given by stepm (the optimization length). Unfortunately it
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)       means that if the survival funtion is printed only each two years of age and if
           mobaverage[(int)agedeb][i][cptcod]=0.;       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.
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    */
       for (i=1; i<=nlstate;i++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){    /* If stepm=6 months */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    /* nhstepm age range expressed in number of stepm */
           }    agelim=AGESUP;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }    /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }    
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (stepm<=12) stepsize=1;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   agelim=AGESUP;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   hstepm=stepsize*YEARM; /* Every year of age */    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  
      for (age=bage; age<=fage; age ++){ 
   if (popforecast==1) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     if((ficpop=fopen(popfile,"r"))==NULL)    {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       printf("Problem with population file : %s\n",popfile);goto end;      /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      /* If stepm=6 months */
     popcount=vector(0,AGESUP);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     i=1;        
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       {  
         i=i+1;      /* Computing  Variances of health expectancies */
       }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     imx=i;         decrease memory allocation */
        for(theta=1; theta <=npar; theta++){
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(i=1; i<=npar; i++){ 
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       k=k+1;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficresf,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++) {        for(j=1; j<= nlstate; j++){
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(i=1; i<=nlstate; i++){
       }            for(h=0; h<=nhstepm-1; h++){
       fprintf(ficresf,"******\n");              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            }
       if (popforecast==1)  fprintf(ficresf," [Population]");          }
         }
       for (agedeb=fage; agedeb>=bage; agedeb--){       
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);        for(ij=1; ij<= nlstate*nlstate; ij++)
        if (mobilav==1) {          for(h=0; h<=nhstepm-1; h++){
         for(j=1; j<=nlstate;j++)            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);          }
         }      }/* End theta */
         else {      
           for(j=1; j<=nlstate;j++)      
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);      for(h=0; h<=nhstepm-1; h++)
         }          for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");            trgradg[h][j][theta]=gradg[h][theta][j];
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);      
       }  
             for(ij=1;ij<=nlstate*nlstate;ij++)
       for (cpt=1; cpt<=nforecast;cpt++) {        for(ji=1;ji<=nlstate*nlstate;ji++)
         fprintf(ficresf,"\n");          varhe[ij][ji][(int)age] =0.;
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       printf("%d|",(int)age);fflush(stdout);
         nhstepm = nhstepm/hstepm;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         oldm=oldms;savm=savms;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(ij=1;ij<=nlstate*nlstate;ij++)
                            for(ji=1;ji<=nlstate*nlstate;ji++)
         for (h=0; h<=nhstepm; h++){              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
                }
          if (h*hstepm/YEARM*stepm==cpt)      }
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);  
                /* Computing expectancies */
                hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
          for(j=1; j<=nlstate+ndeath;j++) {      for(i=1; i<=nlstate;i++)
            kk1=0.;kk2=0;        for(j=1; j<=nlstate;j++)
            for(i=1; i<=nlstate;i++) {                  for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              if (mobilav==1)            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];            
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];  
             }          }
            if (h*hstepm/YEARM*stepm==cpt) {  
              fprintf(ficresf," %.3f", kk1);      fprintf(ficresstdeij,"%3.0f",age );
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);      for(i=1; i<=nlstate;i++){
            }        eip=0.;
           }        vip=0.;
         }        for(j=1; j<=nlstate;j++){
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          eip += eij[i][j][(int)age];
                  for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
       }            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
       }          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     }        }
   }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
   if (popforecast==1) {      fprintf(ficresstdeij,"\n");
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);      fprintf(ficrescveij,"%3.0f",age );
     free_vector(popcount,0,AGESUP);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   free_imatrix(s,1,maxwav+1,1,n);          cptj= (j-1)*nlstate+i;
   free_vector(weight,1,n);          for(i2=1; i2<=nlstate;i2++)
   fclose(ficresf);            for(j2=1; j2<=nlstate;j2++){
   /*---------- Health expectancies and variances ------------*/              cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
   strcpy(filerest,"t");                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   strcat(filerest,fileres);            }
   if((ficrest=fopen(filerest,"w"))==NULL) {        }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fprintf(ficrescveij,"\n");
   }     
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   strcpy(filerese,"e");    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   strcat(filerese,fileres);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    printf("\n");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fprintf(ficlog,"\n");
   
  strcpy(fileresv,"v");    free_vector(xm,1,npar);
   strcat(fileresv,fileres);    free_vector(xp,1,npar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  }
   
   k=0;  /************ Variance ******************/
   for(cptcov=1;cptcov<=i1;cptcov++){  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[])
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  {
       k=k+1;    /* Variance of health expectancies */
       fprintf(ficrest,"\n#****** ");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       for(j=1;j<=cptcoveff;j++)    /* double **newm;*/
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **dnewm,**doldm;
       fprintf(ficrest,"******\n");    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
       fprintf(ficreseij,"\n#****** ");    int k, cptcode;
       for(j=1;j<=cptcoveff;j++)    double *xp;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double **gp, **gm;  /* for var eij */
       fprintf(ficreseij,"******\n");    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
       fprintf(ficresvij,"\n#****** ");    double *gpp, *gmp; /* for var p point j */
       for(j=1;j<=cptcoveff;j++)    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double ***p3mat;
       fprintf(ficresvij,"******\n");    double age,agelim, hf;
     double ***mobaverage;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int theta;
       oldm=oldms;savm=savms;    char digit[4];
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      char digitp[25];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    char fileresprobmorprev[FILENAMELENGTH];
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
          if(popbased==1){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      if(mobilav!=0)
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        strcpy(digitp,"-populbased-mobilav-");
       fprintf(ficrest,"\n");      else strcpy(digitp,"-populbased-nomobil-");
            }
       hf=1;    else 
       if (stepm >= YEARM) hf=stepm/YEARM;      strcpy(digitp,"-stablbased-");
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){    if (mobilav!=0) {
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (popbased==1) {      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           for(i=1; i<=nlstate;i++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             prlim[i][i]=probs[(int)age][i][k];        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }      }
            }
         fprintf(ficrest," %.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    strcpy(fileresprobmorprev,"prmorprev"); 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    sprintf(digit,"%-d",ij);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           epj[nlstate+1] +=epj[j];    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         }    strcat(fileresprobmorprev,fileres);
         for(i=1, vepp=0.;i <=nlstate;i++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           for(j=1;j <=nlstate;j++)      printf("Problem with resultfile: %s\n", fileresprobmorprev);
             vepp += vareij[i][j][(int)age];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    }
         for(j=1;j <=nlstate;j++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));   
         }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficrest,"\n");    pstamp(ficresprobmorprev);
       }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              fprintf(ficresprobmorprev," p.%-d SE",j);
              for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
  fclose(ficreseij);    fprintf(ficresprobmorprev,"\n");
  fclose(ficresvij);    fprintf(ficgp,"\n# Routine varevsij");
   fclose(ficrest);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   fclose(ficpar);    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");
   free_vector(epj,1,nlstate+1);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*  scanf("%d ",i); */  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /*------- Variance limit prevalence------*/      pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
 strcpy(fileresvpl,"vpl");    if(popbased==1)
   strcat(fileresvpl,fileres);      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((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    else
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     exit(0);    fprintf(ficresvij,"# Age");
   }    for(i=1; i<=nlstate;i++)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
  k=0;    fprintf(ficresvij,"\n");
  for(cptcov=1;cptcov<=i1;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    xp=vector(1,npar);
      k=k+1;    dnewm=matrix(1,nlstate,1,npar);
      fprintf(ficresvpl,"\n#****** ");    doldm=matrix(1,nlstate,1,nlstate);
      for(j=1;j<=cptcoveff;j++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      fprintf(ficresvpl,"******\n");  
          gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    gpp=vector(nlstate+1,nlstate+ndeath);
      oldm=oldms;savm=savms;    gmp=vector(nlstate+1,nlstate+ndeath);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    }    
  }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   fclose(ficresvpl);    }
     else  hstepm=estepm;   
   /*---------- End : free ----------------*/    /* For example we decided to compute the life expectancy with the smallest unit */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /* 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 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);       nstepm is the number of stepm from age to agelin. 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       Look at function hpijx to understand why (it is linked to memory size questions) */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       means that if the survival funtion is printed every two years of age and if
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       results. So we changed our mind and took the option of the best precision.
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   free_matrix(matcov,1,npar,1,npar);    agelim = AGESUP;
   free_vector(delti,1,npar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("End of Imach\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
  end:        }
 #ifdef windows        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  chdir(pathcd);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 #endif  
          if (popbased==1) {
  system("..\\gp37mgw\\wgnuplot graph.plt");          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
 #ifdef windows              prlim[i][i]=probs[(int)age][i][ij];
   while (z[0] != 'q') {          }else{ /* mobilav */ 
     chdir(pathcd);            for(i=1; i<=nlstate;i++)
     printf("\nType e to edit output files, c to start again, and q for exiting: ");              prlim[i][i]=mobaverage[(int)age][i][ij];
     scanf("%s",z);          }
     if (z[0] == 'c') system("./imach");        }
     else if (z[0] == 'e') {    
       chdir(path);        for(j=1; j<= nlstate; j++){
       system(optionfilehtm);          for(h=0; h<=nhstepm; h++){
     }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     else if (z[0] == 'q') exit(0);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
 #endif        }
 }        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 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(1,8); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); /* 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); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             codtab[h][k]=j;
             codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       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=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*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.1.16  
changed lines
  Added in v.1.142

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