Diff for /imach/src/imach.c between versions 1.18 and 1.143

version 1.18, 2002/02/20 17:17:09 version 1.143, 2014/01/26 09:45:38
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.143  2014/01/26 09:45:38  brouard
   individuals from different ages are interviewed on their health status    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   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    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.142  2014/01/26 03:57:36  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   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 1.141  2014/01/26 02:42:01  brouard
   is a covariate. If you want to have a more complex model than "constant and    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.140  2011/09/02 10:37:54  brouard
   More covariates you add, less is the speed of the convergence.    Summary: times.h is ok with mingw32 now.
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.139  2010/06/14 07:50:17  brouard
   delay between waves is not identical for each individual, or if some    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   individual missed an interview, the information is not rounded or lost, but    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.138  2010/04/30 18:19:40  brouard
   observed in state i at age x+h conditional to the observed state i at age    *** empty log message ***
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.137  2010/04/29 18:11:38  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    (Module): Checking covariates for more complex models
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    than V1+V2. A lot of change to be done. Unstable.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.136  2010/04/26 20:30:53  brouard
   Also this programme outputs the covariance matrix of the parameters but also    (Module): merging some libgsl code. Fixing computation
   of the life expectancies. It also computes the prevalence limits.    of likelione (using inter/intrapolation if mle = 0) in order to
      get same likelihood as if mle=1.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Some cleaning of code and comments added.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.135  2009/10/29 15:33:14  brouard
   from the European Union.    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.134  2009/10/29 13:18:53  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   **********************************************************************/  
      Revision 1.133  2009/07/06 10:21:25  brouard
 #include <math.h>    just nforces
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.132  2009/07/06 08:22:05  brouard
 #include <unistd.h>    Many tings
   
 #define MAXLINE 256    Revision 1.131  2009/06/20 16:22:47  brouard
 #define FILENAMELENGTH 80    Some dimensions resccaled
 /*#define DEBUG*/  
 #define windows    Revision 1.130  2009/05/26 06:44:34  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Max Covariate is now set to 20 instead of 8. A
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.129  2007/08/31 13:49:27  lievre
     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 NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.128  2006/06/30 13:02:05  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): Clarifications on computing e.j
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.127  2006/04/28 18:11:50  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Yes the sum of survivors was wrong since
 #define AGESUP 130    imach-114 because nhstepm was no more computed in the age
 #define AGEBASE 40    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 int nvar;    and then all the health expectancies with variances or standard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    deviation (needs data from the Hessian matrices) which slows the
 int npar=NPARMAX;    computation.
 int nlstate=2; /* Number of live states */    In the future we should be able to stop the program is only health
 int ndeath=1; /* Number of dead states */    expectancies and graph are needed without standard deviations.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 int *wav; /* Number of waves for this individuual 0 is possible */    imach-114 because nhstepm was no more computed in the age
 int maxwav; /* Maxim number of waves */    loop. Now we define nhstepma in the age loop.
 int jmin, jmax; /* min, max spacing between 2 waves */    Version 0.98h
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.125  2006/04/04 15:20:31  lievre
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Errors in calculation of health expectancies. Age was not initialized.
 double jmean; /* Mean space between 2 waves */    Forecasting file added.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.124  2006/03/22 17:13:53  lievre
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Parameters are printed with %lf instead of %f (more numbers after the comma).
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    The log-likelihood is printed in the log file
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.123  2006/03/20 10:52:43  brouard
  FILE  *ficresvij;    * imach.c (Module): <title> changed, corresponds to .htm file
   char fileresv[FILENAMELENGTH];    name. <head> headers where missing.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define NR_END 1    otherwise the weight is truncated).
 #define FREE_ARG char*    Modification of warning when the covariates values are not 0 or
 #define FTOL 1.0e-10    1.
     Version 0.98g
 #define NRANSI  
 #define ITMAX 200    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 #define TOL 2.0e-4    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 #define CGOLD 0.3819660    Modification of warning when the covariates values are not 0 or
 #define ZEPS 1.0e-10    1.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Version 0.98g
   
 #define GOLD 1.618034    Revision 1.121  2006/03/16 17:45:01  lievre
 #define GLIMIT 100.0    * imach.c (Module): Comments concerning covariates added
 #define TINY 1.0e-20  
     * imach.c (Module): refinements in the computation of lli if
 static double maxarg1,maxarg2;    status=-2 in order to have more reliable computation if stepm is
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    not 1 month. Version 0.98f
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.120  2006/03/16 15:10:38  lievre
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): refinements in the computation of lli if
 #define rint(a) floor(a+0.5)    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.119  2006/03/15 17:42:26  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 int imx;  
 int stepm;    Revision 1.118  2006/03/14 18:20:07  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 int m,nb;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Function pstamp added
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): Version 0.98d
 double **pmmij, ***probs, ***mobaverage;  
     Revision 1.117  2006/03/14 17:16:22  brouard
 double *weight;    (Module): varevsij Comments added explaining the second
 int **s; /* Status */    table of variances if popbased=1 .
 double *agedc, **covar, idx;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Function pstamp added
     (Module): Version 0.98d
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
 /**************** split *************************/    varian-covariance of ej. is needed (Saito).
 static  int split( char *path, char *dirc, char *name )  
 {    Revision 1.115  2006/02/27 12:17:45  brouard
    char *s;                             /* pointer */    (Module): One freematrix added in mlikeli! 0.98c
    int  l1, l2;                         /* length counters */  
     Revision 1.114  2006/02/26 12:57:58  brouard
    l1 = strlen( path );                 /* length of path */    (Module): Some improvements in processing parameter
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    filename with strsep.
    s = strrchr( path, '\\' );           /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.113  2006/02/24 14:20:24  brouard
 #if     defined(__bsd__)                /* get current working directory */    (Module): Memory leaks checks with valgrind and:
       extern char       *getwd( );    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.112  2006/01/30 09:55:26  brouard
       extern char       *getcwd( );    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.111  2006/01/25 20:38:18  brouard
 #endif    (Module): Lots of cleaning and bugs added (Gompertz)
          return( GLOCK_ERROR_GETCWD );    (Module): Comments can be added in data file. Missing date values
       }    can be a simple dot '.'.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.110  2006/01/25 00:51:50  brouard
       s++;                              /* after this, the filename */    (Module): Lots of cleaning and bugs added (Gompertz)
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.109  2006/01/24 19:37:15  brouard
       strcpy( name, s );                /* save file name */    (Module): Comments (lines starting with a #) are allowed in data.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.108  2006/01/19 18:05:42  lievre
    }    Gnuplot problem appeared...
    l1 = strlen( dirc );                 /* length of directory */    To be fixed
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */    Revision 1.107  2006/01/19 16:20:37  brouard
 }    Test existence of gnuplot in imach path
   
     Revision 1.106  2006/01/19 13:24:36  brouard
 /******************************************/    Some cleaning and links added in html output
   
 void replace(char *s, char*t)    Revision 1.105  2006/01/05 20:23:19  lievre
 {    *** empty log message ***
   int i;  
   int lg=20;    Revision 1.104  2005/09/30 16:11:43  lievre
   i=0;    (Module): sump fixed, loop imx fixed, and simplifications.
   lg=strlen(t);    (Module): If the status is missing at the last wave but we know
   for(i=0; i<= lg; i++) {    that the person is alive, then we can code his/her status as -2
     (s[i] = t[i]);    (instead of missing=-1 in earlier versions) and his/her
     if (t[i]== '\\') s[i]='/';    contributions to the likelihood is 1 - Prob of dying from last
   }    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 }    the healthy state at last known wave). Version is 0.98
   
 int nbocc(char *s, char occ)    Revision 1.103  2005/09/30 15:54:49  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   int i,j=0;  
   int lg=20;    Revision 1.102  2004/09/15 17:31:30  brouard
   i=0;    Add the possibility to read data file including tab characters.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.101  2004/09/15 10:38:38  brouard
   if  (s[i] == occ ) j++;    Fix on curr_time
   }  
   return j;    Revision 1.100  2004/07/12 18:29:06  brouard
 }    Add version for Mac OS X. Just define UNIX in Makefile
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.99  2004/06/05 08:57:40  brouard
 {    *** empty log message ***
   int i,lg,j,p=0;  
   i=0;    Revision 1.98  2004/05/16 15:05:56  brouard
   for(j=0; j<=strlen(t)-1; j++) {    New version 0.97 . First attempt to estimate force of mortality
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    directly from the data i.e. without the need of knowing the health
   }    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
   lg=strlen(t);    other analysis, in order to test if the mortality estimated from the
   for(j=0; j<p; j++) {    cross-longitudinal survey is different from the mortality estimated
     (u[j] = t[j]);    from other sources like vital statistic data.
   }  
      u[p]='\0';    The same imach parameter file can be used but the option for mle should be -3.
   
    for(j=0; j<= lg; j++) {    Agnès, who wrote this part of the code, tried to keep most of the
     if (j>=(p+1))(v[j-p-1] = t[j]);    former routines in order to include the new code within the former code.
   }  
 }    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
 /********************** nrerror ********************/  
     Current limitations:
 void nrerror(char error_text[])    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.
   fprintf(stderr,"ERREUR ...\n");    B) There is no computation of Life Expectancy nor Life Table.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.97  2004/02/20 13:25:42  lievre
 }    Version 0.96d. Population forecasting command line is (temporarily)
 /*********************** vector *******************/    suppressed.
 double *vector(int nl, int nh)  
 {    Revision 1.96  2003/07/15 15:38:55  brouard
   double *v;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    rewritten within the same printf. Workaround: many printfs.
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.95  2003/07/08 07:54:34  brouard
 }    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 /************************ free vector ******************/    matrix (cov(a12,c31) instead of numbers.
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.94  2003/06/27 13:00:02  brouard
   free((FREE_ARG)(v+nl-NR_END));    Just cleaning
 }  
     Revision 1.93  2003/06/25 16:33:55  brouard
 /************************ivector *******************************/    (Module): On windows (cygwin) function asctime_r doesn't
 int *ivector(long nl,long nh)    exist so I changed back to asctime which exists.
 {    (Module): Version 0.96b
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.92  2003/06/25 16:30:45  brouard
   if (!v) nrerror("allocation failure in ivector");    (Module): On windows (cygwin) function asctime_r doesn't
   return v-nl+NR_END;    exist so I changed back to asctime which exists.
 }  
     Revision 1.91  2003/06/25 15:30:29  brouard
 /******************free ivector **************************/    * imach.c (Repository): Duplicated warning errors corrected.
 void free_ivector(int *v, long nl, long nh)    (Repository): Elapsed time after each iteration is now output. It
 {    helps to forecast when convergence will be reached. Elapsed time
   free((FREE_ARG)(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.
   
 /******************* imatrix *******************************/    Revision 1.90  2003/06/24 12:34:15  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): Some bugs corrected for windows. Also, when
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.89  2003/06/24 12:30:52  brouard
      (Module): Some bugs corrected for windows. Also, when
   /* allocate pointers to rows */    mle=-1 a template is output in file "or"mypar.txt with the design
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    of the covariance matrix to be input.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.88  2003/06/23 17:54:56  brouard
   m -= nrl;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    
      Revision 1.87  2003/06/18 12:26:01  brouard
   /* allocate rows and set pointers to them */    Version 0.96
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.86  2003/06/17 20:04:08  brouard
   m[nrl] += NR_END;    (Module): Change position of html and gnuplot routines and added
   m[nrl] -= ncl;    routine fileappend.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.85  2003/06/17 13:12:43  brouard
      * imach.c (Repository): Check when date of death was earlier that
   /* return pointer to array of pointers to rows */    current date of interview. It may happen when the death was just
   return m;    prior to the death. In this case, dh was negative and likelihood
 }    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 /****************** free_imatrix *************************/    interview.
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Repository): Because some people have very long ID (first column)
       int **m;    we changed int to long in num[] and we added a new lvector for
       long nch,ncl,nrh,nrl;    memory allocation. But we also truncated to 8 characters (left
      /* free an int matrix allocated by imatrix() */    truncation)
 {    (Repository): No more line truncation errors.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.84  2003/06/13 21:44:43  brouard
 }    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 /******************* matrix *******************************/    many times. Probs is memory consuming and must be used with
 double **matrix(long nrl, long nrh, long ncl, long nch)    parcimony.
 {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.82  2003/06/05 15:57:20  brouard
   m += NR_END;    Add log in  imach.c and  fullversion number is now printed.
   m -= nrl;  
   */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /*
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");     Interpolated Markov Chain
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Short summary of the programme:
     
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    This program computes Healthy Life Expectancies from
   return m;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 }    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 /*************************free matrix ************************/    case of a health survey which is our main interest) -2- at least a
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    second wave of interviews ("longitudinal") which measure each change
 {    (if any) in individual health status.  Health expectancies are
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    computed from the time spent in each health state according to a
   free((FREE_ARG)(m+nrl-NR_END));    model. More health states you consider, more time is necessary to reach the
 }    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 /******************* ma3x *******************************/    probability to be observed in state j at the second wave
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    conditional to be observed in state i at the first wave. Therefore
 {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    'age' is age and 'sex' is a covariate. If you want to have a more
   double ***m;    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    you to do it.  More covariates you add, slower the
   if (!m) nrerror("allocation failure 1 in matrix()");    convergence.
   m += NR_END;  
   m -= nrl;    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    identical for each individual. Also, if a individual missed an
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    intermediate interview, the information is lost, but taken into
   m[nrl] += NR_END;    account using an interpolation or extrapolation.  
   m[nrl] -= ncl;  
     hPijx is the probability to be observed in state i at age x+h
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    states. This elementary transition (by month, quarter,
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    semester or year) is modelled as a multinomial logistic.  The hPx
   m[nrl][ncl] += NR_END;    matrix is simply the matrix product of nh*stepm elementary matrices
   m[nrl][ncl] -= nll;    and the contribution of each individual to the likelihood is simply
   for (j=ncl+1; j<=nch; j++)    hPijx.
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Also this programme outputs the covariance matrix of the parameters but also
   for (i=nrl+1; i<=nrh; i++) {    of the life expectancies. It also computes the period (stable) prevalence. 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    
     for (j=ncl+1; j<=nch; j++)    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       m[i][j]=m[i][j-1]+nlay;             Institut national d'études démographiques, Paris.
   }    This software have been partly granted by Euro-REVES, a concerted action
   return m;    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 /*************************free ma3x ************************/    can be accessed at http://euroreves.ined.fr/imach .
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    
   free((FREE_ARG)(m+nrl-NR_END));    **********************************************************************/
 }  /*
     main
 /***************** f1dim *************************/    read parameterfile
 extern int ncom;    read datafile
 extern double *pcom,*xicom;    concatwav
 extern double (*nrfunc)(double []);    freqsummary
      if (mle >= 1)
 double f1dim(double x)      mlikeli
 {    print results files
   int j;    if mle==1 
   double f;       computes hessian
   double *xt;    read end of parameter file: agemin, agemax, bage, fage, estepm
          begin-prev-date,...
   xt=vector(1,ncom);    open gnuplot file
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    open html file
   f=(*nrfunc)(xt);    period (stable) prevalence
   free_vector(xt,1,ncom);     for age prevalim()
   return f;    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /*****************brent *************************/    health expectancies
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Variance-covariance of DFLE
 {    prevalence()
   int iter;     movingaverage()
   double a,b,d,etemp;    varevsij() 
   double fu,fv,fw,fx;    if popbased==1 varevsij(,popbased)
   double ftemp;    total life expectancies
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Variance of period (stable) prevalence
   double e=0.0;   end
    */
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);   
   for (iter=1;iter<=ITMAX;iter++) {  #include <math.h>
     xm=0.5*(a+b);  #include <stdio.h>
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #include <stdlib.h>
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #include <string.h>
     printf(".");fflush(stdout);  #include <unistd.h>
 #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);  #include <limits.h>
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #include <sys/types.h>
 #endif  #include <sys/stat.h>
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #include <errno.h>
       *xmin=x;  extern int errno;
       return fx;  
     }  #ifdef LINUX
     ftemp=fu;  #include <time.h>
     if (fabs(e) > tol1) {  #include "timeval.h"
       r=(x-w)*(fx-fv);  #else
       q=(x-v)*(fx-fw);  #include <sys/time.h>
       p=(x-v)*q-(x-w)*r;  #endif
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  #ifdef GSL
       q=fabs(q);  #include <gsl/gsl_errno.h>
       etemp=e;  #include <gsl/gsl_multimin.h>
       e=d;  #endif
       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));  /* #include <libintl.h> */
       else {  /* #define _(String) gettext (String) */
         d=p/q;  
         u=x+d;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  #define GNUPLOTPROGRAM "gnuplot"
       }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     } else {  #define FILENAMELENGTH 132
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     fu=(*f)(u);  
     if (fu <= fx) {  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
       if (u >= x) a=x; else b=x;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  #define NINTERVMAX 8
         } else {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
           if (u < x) a=u; else b=u;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
           if (fu <= fw || w == x) {  #define NCOVMAX 20 /* Maximum number of covariates */
             v=w;  #define MAXN 20000
             w=u;  #define YEARM 12. /* Number of months per year */
             fv=fw;  #define AGESUP 130
             fw=fu;  #define AGEBASE 40
           } else if (fu <= fv || v == x || v == w) {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
             v=u;  #ifdef UNIX
             fv=fu;  #define DIRSEPARATOR '/'
           }  #define CHARSEPARATOR "/"
         }  #define ODIRSEPARATOR '\\'
   }  #else
   nrerror("Too many iterations in brent");  #define DIRSEPARATOR '\\'
   *xmin=x;  #define CHARSEPARATOR "\\"
   return fx;  #define ODIRSEPARATOR '/'
 }  #endif
   
 /****************** mnbrak ***********************/  /* $Id$ */
   /* $State$ */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 {  char fullversion[]="$Revision$ $Date$"; 
   double ulim,u,r,q, dum;  char strstart[80];
   double fu;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
    int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   *fa=(*func)(*ax);  int nvar=0, nforce=0; /* Number of variables, number of forces */
   *fb=(*func)(*bx);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   if (*fb > *fa) {  int npar=NPARMAX;
     SHFT(dum,*ax,*bx,dum)  int nlstate=2; /* Number of live states */
       SHFT(dum,*fb,*fa,dum)  int ndeath=1; /* Number of dead states */
       }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   *cx=(*bx)+GOLD*(*bx-*ax);  int popbased=0;
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  int *wav; /* Number of waves for this individuual 0 is possible */
     r=(*bx-*ax)*(*fb-*fc);  int maxwav=0; /* Maxim number of waves */
     q=(*bx-*cx)*(*fb-*fa);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     ulim=(*bx)+GLIMIT*(*cx-*bx);                     to the likelihood and the sum of weights (done by funcone)*/
     if ((*bx-u)*(u-*cx) > 0.0) {  int mle=1, weightopt=0;
       fu=(*func)(u);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       fu=(*func)(u);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       if (fu < *fc) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  double jmean=1; /* Mean space between 2 waves */
           SHFT(*fb,*fc,fu,(*func)(u))  double **oldm, **newm, **savm; /* Working pointers to matrices */
           }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /*FILE *fic ; */ /* Used in readdata only */
       u=ulim;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       fu=(*func)(u);  FILE *ficlog, *ficrespow;
     } else {  int globpr=0; /* Global variable for printing or not */
       u=(*cx)+GOLD*(*cx-*bx);  double fretone; /* Only one call to likelihood */
       fu=(*func)(u);  long ipmx=0; /* Number of contributions */
     }  double sw; /* Sum of weights */
     SHFT(*ax,*bx,*cx,u)  char filerespow[FILENAMELENGTH];
       SHFT(*fa,*fb,*fc,fu)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       }  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /*************** linmin ************************/  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
 int ncom;  char filerese[FILENAMELENGTH];
 double *pcom,*xicom;  FILE *ficresstdeij;
 double (*nrfunc)(double []);  char fileresstde[FILENAMELENGTH];
    FILE *ficrescveij;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char filerescve[FILENAMELENGTH];
 {  FILE  *ficresvij;
   double brent(double ax, double bx, double cx,  char fileresv[FILENAMELENGTH];
                double (*f)(double), double tol, double *xmin);  FILE  *ficresvpl;
   double f1dim(double x);  char fileresvpl[FILENAMELENGTH];
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  char title[MAXLINE];
               double *fc, double (*func)(double));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int j;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double xx,xmin,bx,ax;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double fx,fb,fa;  char command[FILENAMELENGTH];
    int  outcmd=0;
   ncom=n;  
   pcom=vector(1,n);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   xicom=vector(1,n);  
   nrfunc=func;  char filelog[FILENAMELENGTH]; /* Log file */
   for (j=1;j<=n;j++) {  char filerest[FILENAMELENGTH];
     pcom[j]=p[j];  char fileregp[FILENAMELENGTH];
     xicom[j]=xi[j];  char popfile[FILENAMELENGTH];
   }  
   ax=0.0;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  struct timezone tzp;
 #ifdef DEBUG  extern int gettimeofday();
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 #endif  long time_value;
   for (j=1;j<=n;j++) {  extern long time();
     xi[j] *= xmin;  char strcurr[80], strfor[80];
     p[j] += xi[j];  
   }  char *endptr;
   free_vector(xicom,1,n);  long lval;
   free_vector(pcom,1,n);  double dval;
 }  
   #define NR_END 1
 /*************** powell ************************/  #define FREE_ARG char*
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define FTOL 1.0e-10
             double (*func)(double []))  
 {  #define NRANSI 
   void linmin(double p[], double xi[], int n, double *fret,  #define ITMAX 200 
               double (*func)(double []));  
   int i,ibig,j;  #define TOL 2.0e-4 
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  #define CGOLD 0.3819660 
   double *xits;  #define ZEPS 1.0e-10 
   pt=vector(1,n);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   ptt=vector(1,n);  
   xit=vector(1,n);  #define GOLD 1.618034 
   xits=vector(1,n);  #define GLIMIT 100.0 
   *fret=(*func)(p);  #define TINY 1.0e-20 
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  static double maxarg1,maxarg2;
     fp=(*fret);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     ibig=0;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     del=0.0;    
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for (i=1;i<=n;i++)  #define rint(a) floor(a+0.5)
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  static double sqrarg;
     for (i=1;i<=n;i++) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       fptt=(*fret);  int agegomp= AGEGOMP;
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  int imx; 
 #endif  int stepm=1;
       printf("%d",i);fflush(stdout);  /* Stepm, step in month: minimum step interpolation*/
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  int estepm;
         del=fabs(fptt-(*fret));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         ibig=i;  
       }  int m,nb;
 #ifdef DEBUG  long *num;
       printf("%d %.12e",i,(*fret));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       for (j=1;j<=n;j++) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  double **pmmij, ***probs;
         printf(" x(%d)=%.12e",j,xit[j]);  double *ageexmed,*agecens;
       }  double dateintmean=0;
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  double *weight;
       printf("\n");  int **s; /* Status */
 #endif  double *agedc;
     }  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {                    * covar=matrix(0,NCOVMAX,1,n); 
 #ifdef DEBUG                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       int k[2],l;  double  idx; 
       k[0]=1;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       k[1]=-1;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       printf("Max: %.12e",(*func)(p));  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       for (j=1;j<=n;j++)  double *lsurv, *lpop, *tpop;
         printf(" %.12e",p[j]);  
       printf("\n");  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       for(l=0;l<=1;l++) {  double ftolhess; /**< Tolerance for computing hessian */
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /**************** split *************************/
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         }  {
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 #endif    */ 
     char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
       free_vector(xit,1,n);  
       free_vector(xits,1,n);    l1 = strlen(path );                   /* length of path */
       free_vector(ptt,1,n);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       free_vector(pt,1,n);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       return;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     }      strcpy( name, path );               /* we got the fullname name because no directory */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     for (j=1;j<=n;j++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       ptt[j]=2.0*p[j]-pt[j];      /* get current working directory */
       xit[j]=p[j]-pt[j];      /*    extern  char* getcwd ( char *buf , int len);*/
       pt[j]=p[j];      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     }        return( GLOCK_ERROR_GETCWD );
     fptt=(*func)(ptt);      }
     if (fptt < fp) {      /* got dirc from getcwd*/
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      printf(" DIRC = %s \n",dirc);
       if (t < 0.0) {    } else {                              /* strip direcotry from path */
         linmin(p,xit,n,fret,func);      ss++;                               /* after this, the filename */
         for (j=1;j<=n;j++) {      l2 = strlen( ss );                  /* length of filename */
           xi[j][ibig]=xi[j][n];      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           xi[j][n]=xit[j];      strcpy( name, ss );         /* save file name */
         }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 #ifdef DEBUG      dirc[l1-l2] = 0;                    /* add zero */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      printf(" DIRC2 = %s \n",dirc);
         for(j=1;j<=n;j++)    }
           printf(" %.12e",xit[j]);    /* We add a separator at the end of dirc if not exists */
         printf("\n");    l1 = strlen( dirc );                  /* length of directory */
 #endif    if( dirc[l1-1] != DIRSEPARATOR ){
       }      dirc[l1] =  DIRSEPARATOR;
     }      dirc[l1+1] = 0; 
   }      printf(" DIRC3 = %s \n",dirc);
 }    }
     ss = strrchr( name, '.' );            /* find last / */
 /**** Prevalence limit ****************/    if (ss >0){
       ss++;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      strcpy(ext,ss);                     /* save extension */
 {      l1= strlen( name);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      l2= strlen(ss)+1;
      matrix by transitions matrix until convergence is reached */      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
   int i, ii,j,k;    }
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();    return( 0 );                          /* we're done */
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /******************************************/
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  void replace_back_to_slash(char *s, char*t)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
     }    int i;
     int lg=0;
    cov[1]=1.;    i=0;
      lg=strlen(t);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for(i=0; i<= lg; i++) {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      (s[i] = t[i]);
     newm=savm;      if (t[i]== '\\') s[i]='/';
     /* Covariates have to be included here again */    }
      cov[2]=agefin;  }
    
       for (k=1; k<=cptcovn;k++) {  char *trimbb(char *out, char *in)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    char *s;
       }    s=out;
       for (k=1; k<=cptcovage;k++)    while (*in != '\0'){
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       for (k=1; k<=cptcovprod;k++)        in++;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      }
       *out++ = *in++;
       /*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]);*/    *out='\0';
     return s;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   
     savm=oldm;  char *cutv(char *blocc, char *alocc, char *in, char occ)
     oldm=newm;  {
     maxmax=0.;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     for(j=1;j<=nlstate;j++){       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       min=1.;       gives blocc="abcdef2ghi" and alocc="j".
       max=0.;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       for(i=1; i<=nlstate; i++) {    */
         sumnew=0;    char *s, *t;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    t=in;s=in;
         prlim[i][j]= newm[i][j]/(1-sumnew);    while (*in != '\0'){
         max=FMAX(max,prlim[i][j]);      while( *in == occ){
         min=FMIN(min,prlim[i][j]);        *blocc++ = *in++;
       }        s=in;
       maxmin=max-min;      }
       maxmax=FMAX(maxmax,maxmin);      *blocc++ = *in++;
     }    }
     if(maxmax < ftolpl){    if (s == t) /* occ not found */
       return prlim;      *(blocc-(in-s))='\0';
     }    else
   }      *(blocc-(in-s)-1)='\0';
 }    in=s;
     while ( *in != '\0'){
 /*************** transition probabilities ***************/      *alocc++ = *in++;
     }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {    *alocc='\0';
   double s1, s2;    return s;
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   int nbocc(char *s, char occ)
     for(i=1; i<= nlstate; i++){  {
     for(j=1; j<i;j++){    int i,j=0;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    int lg=20;
         /*s2 += param[i][j][nc]*cov[nc];*/    i=0;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    lg=strlen(s);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    for(i=0; i<= lg; i++) {
       }    if  (s[i] == occ ) j++;
       ps[i][j]=s2;    }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    return j;
     }  }
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* void cutv(char *u,char *v, char*t, char occ) */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /* { */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       ps[i][j]=(s2);  /*      gives u="abcdef2ghi" and v="j" *\/ */
     }  /*   int i,lg,j,p=0; */
   }  /*   i=0; */
     /*ps[3][2]=1;*/  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
   for(i=1; i<= nlstate; i++){  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
      s1=0;  /*   } */
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  /*   for(j=0; j<p; j++) { */
     for(j=i+1; j<=nlstate+ndeath; j++)  /*     (u[j] = t[j]); */
       s1+=exp(ps[i][j]);  /*   } */
     ps[i][i]=1./(s1+1.);  /*      u[p]='\0'; */
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /*    for(j=0; j<= lg; j++) { */
     for(j=i+1; j<=nlstate+ndeath; j++)  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /*   } */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /* } */
   } /* end i */  
   /********************** nrerror ********************/
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  void nrerror(char error_text[])
       ps[ii][jj]=0;  {
       ps[ii][ii]=1;    fprintf(stderr,"ERREUR ...\n");
     }    fprintf(stderr,"%s\n",error_text);
   }    exit(EXIT_FAILURE);
   }
   /*********************** vector *******************/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double *vector(int nl, int nh)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
      printf("%lf ",ps[ii][jj]);    double *v;
    }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     printf("\n ");    if (!v) nrerror("allocation failure in vector");
     }    return v-nl+NR_END;
     printf("\n ");printf("%lf ",cov[2]);*/  }
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /************************ free vector ******************/
   goto end;*/  void free_vector(double*v, int nl, int nh)
     return ps;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /**************** Product of 2 matrices ******************/  
   /************************ivector *******************************/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  int *ivector(long nl,long nh)
 {  {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    int *v;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* in, b, out are matrice of pointers which should have been initialized    if (!v) nrerror("allocation failure in ivector");
      before: only the contents of out is modified. The function returns    return v-nl+NR_END;
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /******************free ivector **************************/
     for(k=ncolol; k<=ncoloh; k++)  void free_ivector(int *v, long nl, long nh)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    free((FREE_ARG)(v+nl-NR_END));
   }
   return out;  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
   {
 /************* Higher Matrix Product ***************/    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    if (!v) nrerror("allocation failure in ivector");
 {    return 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.  /******************free lvector **************************/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  void free_lvector(long *v, long nl, long nh)
      (typically every 2 years instead of every month which is too big).  {
      Model is determined by parameters x and covariates have to be    free((FREE_ARG)(v+nl-NR_END));
      included manually here.  }
   
      */  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
   int i, j, d, h, k;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double **out, cov[NCOVMAX];  { 
   double **newm;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
   /* Hstepm could be zero and should return the unit matrix */    
   for (i=1;i<=nlstate+ndeath;i++)    /* allocate pointers to rows */ 
     for (j=1;j<=nlstate+ndeath;j++){    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    m += NR_END; 
     }    m -= nrl; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    
   for(h=1; h <=nhstepm; h++){    
     for(d=1; d <=hstepm; d++){    /* allocate rows and set pointers to them */ 
       newm=savm;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       /* Covariates have to be included here again */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       cov[1]=1.;    m[nrl] += NR_END; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    m[nrl] -= ncl; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    
       for (k=1; k<=cptcovage;k++)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    
       for (k=1; k<=cptcovprod;k++)    /* return pointer to array of pointers to rows */ 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    return m; 
   } 
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /****************** free_imatrix *************************/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  void free_imatrix(m,nrl,nrh,ncl,nch)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        int **m;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        long nch,ncl,nrh,nrl; 
       savm=oldm;       /* free an int matrix allocated by imatrix() */ 
       oldm=newm;  { 
     }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     for(i=1; i<=nlstate+ndeath; i++)    free((FREE_ARG) (m+nrl-NR_END)); 
       for(j=1;j<=nlstate+ndeath;j++) {  } 
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /******************* matrix *******************************/
          */  double **matrix(long nrl, long nrh, long ncl, long nch)
       }  {
   } /* end h */    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   return po;    double **m;
 }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /*************** log-likelihood *************/    m += NR_END;
 double func( double *x)    m -= nrl;
 {  
   int i, ii, j, k, mi, d, kk;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double **out;    m[nrl] += NR_END;
   double sw; /* Sum of weights */    m[nrl] -= ncl;
   double lli; /* Individual log likelihood */  
   long ipmx;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   /*extern weight */    return m;
   /* We are differentiating ll according to initial status */    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/     */
   /*for(i=1;i<imx;i++)  }
     printf(" %d\n",s[4][i]);  
   */  /*************************free matrix ************************/
   cov[1]=1.;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
   for(k=1; k<=nlstate; k++) ll[k]=0.;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    free((FREE_ARG)(m+nrl-NR_END));
     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++)  /******************* ma3x *******************************/
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       for(d=0; d<dh[mi][i]; d++){  {
         newm=savm;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    double ***m;
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         }    if (!m) nrerror("allocation failure 1 in matrix()");
            m += NR_END;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    m -= nrl;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         oldm=newm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
            m[nrl] += NR_END;
            m[nrl] -= ncl;
       } /* end mult */  
          for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       ipmx +=1;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       sw += weight[i];    m[nrl][ncl] += NR_END;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    m[nrl][ncl] -= nll;
     } /* end of wave */    for (j=ncl+1; j<=nch; j++) 
   } /* end of individual */      m[nrl][j]=m[nrl][j-1]+nlay;
     
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for (i=nrl+1; i<=nrh; i++) {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for (j=ncl+1; j<=nch; j++) 
   return -l;        m[i][j]=m[i][j-1]+nlay;
 }    }
     return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 /*********** Maximum Likelihood Estimation ***************/             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  }
 {  
   int i,j, iter;  /*************************free ma3x ************************/
   double **xi,*delti;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double fret;  {
   xi=matrix(1,npar,1,npar);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   for (i=1;i<=npar;i++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for (j=1;j<=npar;j++)    free((FREE_ARG)(m+nrl-NR_END));
       xi[i][j]=(i==j ? 1.0 : 0.0);  }
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
 /**** Computes Hessian and covariance matrix ***/    return tmpout;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  /*************** function subdirf2 ***********/
   double **hess;  char *subdirf2(char fileres[], char *preop)
   int i, j,jk;  {
   int *indx;    
     /* Caution optionfilefiname is hidden */
   double hessii(double p[], double delta, int theta, double delti[]);    strcpy(tmpout,optionfilefiname);
   double hessij(double p[], double delti[], int i, int j);    strcat(tmpout,"/");
   void lubksb(double **a, int npar, int *indx, double b[]) ;    strcat(tmpout,preop);
   void ludcmp(double **a, int npar, int *indx, double *d) ;    strcat(tmpout,fileres);
     return tmpout;
   hess=matrix(1,npar,1,npar);  }
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*************** function subdirf3 ***********/
   for (i=1;i<=npar;i++){  char *subdirf3(char fileres[], char *preop, char *preop2)
     printf("%d",i);fflush(stdout);  {
     hess[i][i]=hessii(p,ftolhess,i,delti);    
     /*printf(" %f ",p[i]);*/    /* Caution optionfilefiname is hidden */
     /*printf(" %lf ",hess[i][i]);*/    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/");
      strcat(tmpout,preop);
   for (i=1;i<=npar;i++) {    strcat(tmpout,preop2);
     for (j=1;j<=npar;j++)  {    strcat(tmpout,fileres);
       if (j>i) {    return tmpout;
         printf(".%d%d",i,j);fflush(stdout);  }
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      /***************** f1dim *************************/
         /*printf(" %lf ",hess[i][j]);*/  extern int ncom; 
       }  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
   }   
   printf("\n");  double f1dim(double x) 
   { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    int j; 
      double f;
   a=matrix(1,npar,1,npar);    double *xt; 
   y=matrix(1,npar,1,npar);   
   x=vector(1,npar);    xt=vector(1,ncom); 
   indx=ivector(1,npar);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for (i=1;i<=npar;i++)    f=(*nrfunc)(xt); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    free_vector(xt,1,ncom); 
   ludcmp(a,npar,indx,&pd);    return f; 
   } 
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /*****************brent *************************/
     x[j]=1;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     lubksb(a,npar,indx,x);  { 
     for (i=1;i<=npar;i++){    int iter; 
       matcov[i][j]=x[i];    double a,b,d,etemp;
     }    double fu,fv,fw,fx;
   }    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
   printf("\n#Hessian matrix#\n");    double e=0.0; 
   for (i=1;i<=npar;i++) {   
     for (j=1;j<=npar;j++) {    a=(ax < cx ? ax : cx); 
       printf("%.3e ",hess[i][j]);    b=(ax > cx ? ax : cx); 
     }    x=w=v=bx; 
     printf("\n");    fw=fv=fx=(*f)(x); 
   }    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
   /* Recompute Inverse */      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for (i=1;i<=npar;i++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      printf(".");fflush(stdout);
   ludcmp(a,npar,indx,&pd);      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
   /*  printf("\n#Hessian matrix recomputed#\n");      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);
       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 (j=1;j<=npar;j++) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for (i=1;i<=npar;i++) x[i]=0;  #endif
     x[j]=1;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     lubksb(a,npar,indx,x);        *xmin=x; 
     for (i=1;i<=npar;i++){        return fx; 
       y[i][j]=x[i];      } 
       printf("%.3e ",y[i][j]);      ftemp=fu;
     }      if (fabs(e) > tol1) { 
     printf("\n");        r=(x-w)*(fx-fv); 
   }        q=(x-v)*(fx-fw); 
   */        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   free_matrix(a,1,npar,1,npar);        if (q > 0.0) p = -p; 
   free_matrix(y,1,npar,1,npar);        q=fabs(q); 
   free_vector(x,1,npar);        etemp=e; 
   free_ivector(indx,1,npar);        e=d; 
   free_matrix(hess,1,npar,1,npar);        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)); 
         else { 
 }          d=p/q; 
           u=x+d; 
 /*************** hessian matrix ****************/          if (u-a < tol2 || b-u < tol2) 
 double hessii( double x[], double delta, int theta, double delti[])            d=SIGN(tol1,xm-x); 
 {        } 
   int i;      } else { 
   int l=1, lmax=20;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double k1,k2;      } 
   double p2[NPARMAX+1];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double res;      fu=(*f)(u); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      if (fu <= fx) { 
   double fx;        if (u >= x) a=x; else b=x; 
   int k=0,kmax=10;        SHFT(v,w,x,u) 
   double l1;          SHFT(fv,fw,fx,fu) 
           } else { 
   fx=func(x);            if (u < x) a=u; else b=u; 
   for (i=1;i<=npar;i++) p2[i]=x[i];            if (fu <= fw || w == x) { 
   for(l=0 ; l <=lmax; l++){              v=w; 
     l1=pow(10,l);              w=u; 
     delts=delt;              fv=fw; 
     for(k=1 ; k <kmax; k=k+1){              fw=fu; 
       delt = delta*(l1*k);            } else if (fu <= fv || v == x || v == w) { 
       p2[theta]=x[theta] +delt;              v=u; 
       k1=func(p2)-fx;              fv=fu; 
       p2[theta]=x[theta]-delt;            } 
       k2=func(p2)-fx;          } 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    } 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    nrerror("Too many iterations in brent"); 
          *xmin=x; 
 #ifdef DEBUG    return fx; 
       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  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  /****************** mnbrak ***********************/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       }              double (*func)(double)) 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  { 
         k=kmax; l=lmax*10.;    double ulim,u,r,q, dum;
       }    double fu; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){   
         delts=delt;    *fa=(*func)(*ax); 
       }    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
   }      SHFT(dum,*ax,*bx,dum) 
   delti[theta]=delts;        SHFT(dum,*fb,*fa,dum) 
   return res;        } 
      *cx=(*bx)+GOLD*(*bx-*ax); 
 }    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 double hessij( double x[], double delti[], int thetai,int thetaj)      r=(*bx-*ax)*(*fb-*fc); 
 {      q=(*bx-*cx)*(*fb-*fa); 
   int i;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   int l=1, l1, lmax=20;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double k1,k2,k3,k4,res,fx;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double p2[NPARMAX+1];      if ((*bx-u)*(u-*cx) > 0.0) { 
   int k;        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   fx=func(x);        fu=(*func)(u); 
   for (k=1; k<=2; k++) {        if (fu < *fc) { 
     for (i=1;i<=npar;i++) p2[i]=x[i];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     p2[thetai]=x[thetai]+delti[thetai]/k;            SHFT(*fb,*fc,fu,(*func)(u)) 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            } 
     k1=func(p2)-fx;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
          u=ulim; 
     p2[thetai]=x[thetai]+delti[thetai]/k;        fu=(*func)(u); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } else { 
     k2=func(p2)-fx;        u=(*cx)+GOLD*(*cx-*bx); 
          fu=(*func)(u); 
     p2[thetai]=x[thetai]-delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      SHFT(*ax,*bx,*cx,u) 
     k3=func(p2)-fx;        SHFT(*fa,*fb,*fc,fu) 
          } 
     p2[thetai]=x[thetai]-delti[thetai]/k;  } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  /*************** linmin ************************/
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  int ncom; 
     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 *pcom,*xicom;
 #endif  double (*nrfunc)(double []); 
   }   
   return res;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 }  { 
     double brent(double ax, double bx, double cx, 
 /************** Inverse of matrix **************/                 double (*f)(double), double tol, double *xmin); 
 void ludcmp(double **a, int n, int *indx, double *d)    double f1dim(double x); 
 {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   int i,imax,j,k;                double *fc, double (*func)(double)); 
   double big,dum,sum,temp;    int j; 
   double *vv;    double xx,xmin,bx,ax; 
      double fx,fb,fa;
   vv=vector(1,n);   
   *d=1.0;    ncom=n; 
   for (i=1;i<=n;i++) {    pcom=vector(1,n); 
     big=0.0;    xicom=vector(1,n); 
     for (j=1;j<=n;j++)    nrfunc=func; 
       if ((temp=fabs(a[i][j])) > big) big=temp;    for (j=1;j<=n;j++) { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      pcom[j]=p[j]; 
     vv[i]=1.0/big;      xicom[j]=xi[j]; 
   }    } 
   for (j=1;j<=n;j++) {    ax=0.0; 
     for (i=1;i<j;i++) {    xx=1.0; 
       sum=a[i][j];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       a[i][j]=sum;  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     big=0.0;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (i=j;i<=n;i++) {  #endif
       sum=a[i][j];    for (j=1;j<=n;j++) { 
       for (k=1;k<j;k++)      xi[j] *= xmin; 
         sum -= a[i][k]*a[k][j];      p[j] += xi[j]; 
       a[i][j]=sum;    } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    free_vector(xicom,1,n); 
         big=dum;    free_vector(pcom,1,n); 
         imax=i;  } 
       }  
     }  char *asc_diff_time(long time_sec, char ascdiff[])
     if (j != imax) {  {
       for (k=1;k<=n;k++) {    long sec_left, days, hours, minutes;
         dum=a[imax][k];    days = (time_sec) / (60*60*24);
         a[imax][k]=a[j][k];    sec_left = (time_sec) % (60*60*24);
         a[j][k]=dum;    hours = (sec_left) / (60*60) ;
       }    sec_left = (sec_left) %(60*60);
       *d = -(*d);    minutes = (sec_left) /60;
       vv[imax]=vv[j];    sec_left = (sec_left) % (60);
     }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     indx[j]=imax;    return ascdiff;
     if (a[j][j] == 0.0) a[j][j]=TINY;  }
     if (j != n) {  
       dum=1.0/(a[j][j]);  /*************** powell ************************/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     }              double (*func)(double [])) 
   }  { 
   free_vector(vv,1,n);  /* Doesn't work */    void linmin(double p[], double xi[], int n, double *fret, 
 ;                double (*func)(double [])); 
 }    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 void lubksb(double **a, int n, int *indx, double b[])    double fp,fptt;
 {    double *xits;
   int i,ii=0,ip,j;    int niterf, itmp;
   double sum;  
      pt=vector(1,n); 
   for (i=1;i<=n;i++) {    ptt=vector(1,n); 
     ip=indx[i];    xit=vector(1,n); 
     sum=b[ip];    xits=vector(1,n); 
     b[ip]=b[i];    *fret=(*func)(p); 
     if (ii)    for (j=1;j<=n;j++) pt[j]=p[j]; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    for (*iter=1;;++(*iter)) { 
     else if (sum) ii=i;      fp=(*fret); 
     b[i]=sum;      ibig=0; 
   }      del=0.0; 
   for (i=n;i>=1;i--) {      last_time=curr_time;
     sum=b[i];      (void) gettimeofday(&curr_time,&tzp);
     for (j=i+1;j<=n;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);
     b[i]=sum/a[i][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);
   }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
 }     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
 /************ Frequencies ********************/        fprintf(ficlog," %d %.12lf",i, p[i]);
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint, int boolprev, double dateprev1,double dateprev2)        fprintf(ficrespow," %.12lf", p[i]);
 {  /* Some frequencies */      }
        printf("\n");
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      fprintf(ficlog,"\n");
   double ***freq; /* Frequencies */      fprintf(ficrespow,"\n");fflush(ficrespow);
   double *pp;      if(*iter <=3){
   double pos, k2;        tm = *localtime(&curr_time.tv_sec);
   FILE *ficresp;        strcpy(strcurr,asctime(&tm));
   char fileresp[FILENAMELENGTH];  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
   pp=vector(1,nlstate);        itmp = strlen(strcurr);
   probs= ma3x(1,130 ,1,8, 1,8);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   strcpy(fileresp,"p");          strcurr[itmp-1]='\0';
   strcat(fileresp,fileres);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   if((ficresp=fopen(fileresp,"w"))==NULL) {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(niterf=10;niterf<=30;niterf+=10){
     exit(0);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   }          tmf = *localtime(&forecast_time.tv_sec);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*      asctime_r(&tmf,strfor); */
   j1=0;          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
   j=cptcoveff;          if(strfor[itmp-1]=='\n')
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          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);
   for(k1=1; k1<=j;k1++){          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);
    for(i1=1; i1<=ncodemax[k1];i1++){        }
        j1++;      }
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      for (i=1;i<=n;i++) { 
          scanf("%d", i);*/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         for (i=-1; i<=nlstate+ndeath; i++)          fptt=(*fret); 
          for (jk=-1; jk<=nlstate+ndeath; jk++)    #ifdef DEBUG
            for(m=agemin; m <= agemax+3; m++)        printf("fret=%lf \n",*fret);
              freq[i][jk][m]=0;        fprintf(ficlog,"fret=%lf \n",*fret);
          #endif
        for (i=1; i<=imx; i++) {        printf("%d",i);fflush(stdout);
          bool=1;        fprintf(ficlog,"%d",i);fflush(ficlog);
          if  (cptcovn>0) {        linmin(p,xit,n,fret,func); 
            for (z1=1; z1<=cptcoveff; z1++)        if (fabs(fptt-(*fret)) > del) { 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          del=fabs(fptt-(*fret)); 
                bool=0;          ibig=i; 
          }        } 
          if (bool==1) {  #ifdef DEBUG
            if (boolprev==1){        printf("%d %.12e",i,(*fret));
              for(m=fprev1; m<=lprev1; m++){        fprintf(ficlog,"%d %.12e",i,(*fret));
                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;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          printf(" x(%d)=%.12e",j,xit[j]);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
              }        }
            }        for(j=1;j<=n;j++) {
            else {          printf(" p=%.12e",p[j]);
             for(m=firstpass; m<=lastpass; m++){          fprintf(ficlog," p=%.12e",p[j]);
              k2=anint[m][i]+(mint[m][i]/12.);        }
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        printf("\n");
              if(agev[m][i]==0) agev[m][i]=agemax+1;        fprintf(ficlog,"\n");
              if(agev[m][i]==1) agev[m][i]=agemax+2;  #endif
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      } 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
              }  #ifdef DEBUG
             }        int k[2],l;
            }        k[0]=1;
           }        k[1]=-1;
        }        printf("Max: %.12e",(*func)(p));
         if  (cptcovn>0) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
          fprintf(ficresp, "\n#********** Variable ");        for (j=1;j<=n;j++) {
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          printf(" %.12e",p[j]);
        fprintf(ficresp, "**********\n#");          fprintf(ficlog," %.12e",p[j]);
         }        }
        for(i=1; i<=nlstate;i++)        printf("\n");
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        fprintf(ficlog,"\n");
        fprintf(ficresp, "\n");        for(l=0;l<=1;l++) {
                  for (j=1;j<=n;j++) {
   for(i=(int)agemin; i <= (int)agemax+3; i++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     if(i==(int)agemax+3)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       printf("Total");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     else          }
       printf("Age %d", i);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
         pp[jk] += freq[jk][m][i];  #endif
     }  
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)        free_vector(xit,1,n); 
         pos += freq[jk][m][i];        free_vector(xits,1,n); 
       if(pp[jk]>=1.e-10)        free_vector(ptt,1,n); 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        free_vector(pt,1,n); 
       else        return; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      } 
     }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
      for(jk=1; jk <=nlstate ; jk++){        ptt[j]=2.0*p[j]-pt[j]; 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        xit[j]=p[j]-pt[j]; 
         pp[jk] += freq[jk][m][i];        pt[j]=p[j]; 
      }      } 
       fptt=(*func)(ptt); 
     for(jk=1,pos=0; jk <=nlstate ; jk++)      if (fptt < fp) { 
       pos += pp[jk];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for(jk=1; jk <=nlstate ; jk++){        if (t < 0.0) { 
       if(pos>=1.e-5)          linmin(p,xit,n,fret,func); 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          for (j=1;j<=n;j++) { 
       else            xi[j][ibig]=xi[j][n]; 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            xi[j][n]=xit[j]; 
       if( i <= (int) agemax){          }
         if(pos>=1.e-5){  #ifdef DEBUG
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           probs[i][jk][j1]= pp[jk]/pos;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           /*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++){
         }            printf(" %.12e",xit[j]);
       else            fprintf(ficlog," %.12e",xit[j]);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          }
       }          printf("\n");
     }          fprintf(ficlog,"\n");
     for(jk=-1; jk <=nlstate+ndeath; jk++)  #endif
       for(m=-1; m <=nlstate+ndeath; m++)        }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      } 
     if(i <= (int) agemax)    } 
       fprintf(ficresp,"\n");  } 
     printf("\n");  
     }  /**** Prevalence limit (stable or period prevalence)  ****************/
     }  
  }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    {
   fclose(ficresp);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       matrix by transitions matrix until convergence is reached */
   free_vector(pp,1,nlstate);  
     int i, ii,j,k;
 }  /* End of Freq */    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
 /************ Prevalence ********************/    double **out, cov[NCOVMAX+1], **pmij();
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1, double **mint,double **anint,int boolprev, double dateprev1, double dateprev2)    double **newm;
 {  /* Some frequencies */    double agefin, delaymax=50 ; /* Max number of years to converge */
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***freq; /* Frequencies */      for (j=1;j<=nlstate+ndeath;j++){
   double *pp;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2;      }
   
   pp=vector(1,nlstate);     cov[1]=1.;
   probs= ma3x(1,130 ,1,8, 1,8);   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   j1=0;      newm=savm;
        /* Covariates have to be included here again */
   j=cptcoveff;      cov[2]=agefin;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      
        for (k=1; k<=cptcovn;k++) {
  for(k1=1; k1<=j;k1++){        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(i1=1; i1<=ncodemax[k1];i1++){        /*        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]]);*/
       j1++;      }
        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for (i=-1; i<=nlstate+ndeath; i++)        for (k=1; k<=cptcovprod;k++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           for(m=agemin; m <= agemax+3; m++)      
           freq[i][jk][m]=0;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
            /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       for (i=1; i<=imx; i++) {      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         bool=1;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
         if  (cptcovn>0) {      
           for (z1=1; z1<=cptcoveff; z1++)      savm=oldm;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      oldm=newm;
               bool=0;      maxmax=0.;
               }      for(j=1;j<=nlstate;j++){
         if (bool==1) {        min=1.;
           if (boolprev==1){        max=0.;
             for(m=fprev1; m<=lprev1; m++){        for(i=1; i<=nlstate; i++) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;          sumnew=0;
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
               freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          prlim[i][j]= newm[i][j]/(1-sumnew);
               freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          max=FMAX(max,prlim[i][j]);
             }          min=FMIN(min,prlim[i][j]);
           }        }
           else {        maxmin=max-min;
             for(m=firstpass; m<=lastpass; m++){        maxmax=FMAX(maxmax,maxmin);
               k2=anint[m][i]+(mint[m][i]/12.);      }
               if ((k2>=dateprev1) && (k2<=dateprev2)) {      if(maxmax < ftolpl){
                 if(agev[m][i]==0) agev[m][i]=agemax+1;        return prlim;
                 if(agev[m][i]==1) agev[m][i]=agemax+2;      }
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    }
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  }
               }  
             }  /*************** transition probabilities ***************/ 
           }  
         }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       }  {
         for(i=(int)agemin; i <= (int)agemax+3; i++){    /* According to parameters values stored in x and the covariate's values stored in cov,
           for(jk=1; jk <=nlstate ; jk++){       computes the probability to be observed in state j being in state i by appying the
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)       model to the ncovmodel covariates (including constant and age).
               pp[jk] += freq[jk][m][i];       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
           for(jk=1; jk <=nlstate ; jk++){       ncth covariate in the global vector x is given by the formula:
             for(m=-1, pos=0; m <=0 ; m++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
             pos += freq[jk][m][i];       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.
          for(jk=1; jk <=nlstate ; jk++){       Outputs ps[i][j] the probability to be observed in j being in j according to
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
              pp[jk] += freq[jk][m][i];    */
          }    double s1, lnpijopii;
              /*double t34;*/
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    int i,j,j1, nc, ii, jj;
   
          for(jk=1; jk <=nlstate ; jk++){                for(i=1; i<= nlstate; i++){
            if( i <= (int) agemax){        for(j=1; j<i;j++){
              if(pos>=1.e-5){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                probs[i][jk][j1]= pp[jk]/pos;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
              }            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
            }  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
          }          }
                    ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     }        }
   }        for(j=i+1; j<=nlstate+ndeath;j++){
            for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
              /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   free_vector(pp,1,nlstate);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
            }
 }  /* End of Freq */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 /************* Waves Concatenation ***************/        }
       }
 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.        s1=0;
      Death is a valid wave (if date is known).        for(j=1; j<i; j++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
      and mw[mi+1][i]. dh depends on stepm.        }
      */        for(j=i+1; j<=nlstate+ndeath; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   int i, mi, m;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        }
      double sum=0., jmean=0.;*/        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
   int j, k=0,jk, ju, jl;        /* Computing other pijs */
   double sum=0.;        for(j=1; j<i; j++)
   jmin=1e+5;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   jmax=-1;        for(j=i+1; j<=nlstate+ndeath; j++)
   jmean=0.;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(i=1; i<=imx; i++){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     mi=0;      } /* end i */
     m=firstpass;      
     while(s[m][i] <= nlstate){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       if(s[m][i]>=1)        for(jj=1; jj<= nlstate+ndeath; jj++){
         mw[++mi][i]=m;          ps[ii][jj]=0;
       if(m >=lastpass)          ps[ii][ii]=1;
         break;        }
       else      }
         m++;      
     }/* end while */  
     if (s[m][i] > nlstate){  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       mi++;     /* Death is another wave */  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       /* if(mi==0)  never been interviewed correctly before death */  /*         printf("ddd %lf ",ps[ii][jj]); */
          /* Only death is a correct wave */  /*       } */
       mw[mi][i]=m;  /*       printf("\n "); */
     }  /*        } */
   /*        printf("\n ");printf("%lf ",cov[2]); */
     wav[i]=mi;         /*
     if(mi==0)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        goto end;*/
   }      return ps;
   }
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){  /**************** Product of 2 matrices ******************/
       if (stepm <=0)  
         dh[mi][i]=1;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       else{  {
         if (s[mw[mi+1][i]][i] > nlstate) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           if (agedc[i] < 2*AGESUP) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    /* in, b, out are matrice of pointers which should have been initialized 
           if(j==0) j=1;  /* Survives at least one month after exam */       before: only the contents of out is modified. The function returns
           k=k+1;       a pointer to pointers identical to out */
           if (j >= jmax) jmax=j;    long i, j, k;
           if (j <= jmin) jmin=j;    for(i=nrl; i<= nrh; i++)
           sum=sum+j;      for(k=ncolol; k<=ncoloh; k++)
           /* if (j<10) printf("j=%d num=%d ",j,i); */        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           }          out[i][k] +=in[i][j]*b[j][k];
         }  
         else{    return out;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  }
           k=k+1;  
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;  /************* Higher Matrix Product ***************/
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  
           sum=sum+j;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         }  {
         jk= j/stepm;    /* Computes the transition matrix starting at age 'age' over 
         jl= j -jk*stepm;       'nhstepm*hstepm*stepm' months (i.e. until
         ju= j -(jk+1)*stepm;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         if(jl <= -ju)       nhstepm*hstepm matrices. 
           dh[mi][i]=jk;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         else       (typically every 2 years instead of every month which is too big 
           dh[mi][i]=jk+1;       for the memory).
         if(dh[mi][i]==0)       Model is determined by parameters x and covariates have to be 
           dh[mi][i]=1; /* At least one step */       included manually here. 
       }  
     }       */
   }  
   jmean=sum/k;    int i, j, d, h, k;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    double **out, cov[NCOVMAX+1];
  }    double **newm;
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)    /* Hstepm could be zero and should return the unit matrix */
 {    for (i=1;i<=nlstate+ndeath;i++)
   int Ndum[20],ij=1, k, j, i;      for (j=1;j<=nlstate+ndeath;j++){
   int cptcode=0;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   cptcoveff=0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
        }
   for (k=0; k<19; k++) Ndum[k]=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (k=1; k<=7; k++) ncodemax[k]=0;    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        newm=savm;
     for (i=1; i<=imx; i++) {        /* Covariates have to be included here again */
       ij=(int)(covar[Tvar[j]][i]);        cov[1]=1.;
       Ndum[ij]++;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        for (k=1; k<=cptcovn;k++) 
       if (ij > cptcode) cptcode=ij;          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 (i=0; i<=cptcode; i++) {        for (k=1; k<=cptcovprod;k++)
       if(Ndum[i]!=0) ncodemax[j]++;          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);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for (i=1; i<=ncodemax[j]; i++) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       for (k=0; k<=19; k++) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (Ndum[k] != 0) {        savm=oldm;
           nbcode[Tvar[j]][ij]=k;        oldm=newm;
           ij++;      }
         }      for(i=1; i<=nlstate+ndeath; i++)
         if (ij > ncodemax[j]) break;        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]);*/
   }          }
       /*printf("h=%d ",h);*/
  for (k=0; k<19; k++) Ndum[k]=0;    } /* end h */
   /*     printf("\n H=%d \n",h); */
  for (i=1; i<=ncovmodel-2; i++) {    return po;
       ij=Tvar[i];  }
       Ndum[ij]++;  
     }  
   /*************** log-likelihood *************/
  ij=1;  double func( double *x)
  for (i=1; i<=10; i++) {  {
    if((Ndum[i]!=0) && (i<=ncov)){    int i, ii, j, k, mi, d, kk;
      Tvaraff[ij]=i;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      ij++;    double **out;
    }    double sw; /* Sum of weights */
  }    double lli; /* Individual log likelihood */
      int s1, s2;
     cptcoveff=ij-1;    double bbh, survp;
 }    long ipmx;
     /*extern weight */
 /*********** Health Expectancies ****************/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   /* Health expectancies */    */
   int i, j, nhstepm, hstepm, h;    cov[1]=1.;
   double age, agelim,hf;  
   double ***p3mat;    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   fprintf(ficreseij,"# Health expectancies\n");    if(mle==1){
   fprintf(ficreseij,"# Age");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=nlstate;i++)        /* Computes the values of the ncovmodel covariates of the model
     for(j=1; j<=nlstate;j++)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       fprintf(ficreseij," %1d-%1d",i,j);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   fprintf(ficreseij,"\n");           to be observed in j being in i according to the model.
          */
   hstepm=1*YEARM; /*  Every j years of age (in month) */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   agelim=AGESUP;           has been calculated etc */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for(mi=1; mi<= wav[i]-1; mi++){
     /* nhstepm age range expressed in number of stepm */          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            for (j=1;j<=nlstate+ndeath;j++){
     /* Typically if 20 years = 20*12/6=40 stepm */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) hstepm=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(d=0; d<dh[mi][i]; d++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            newm=savm;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
             }
     for(i=1; i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<=nlstate;j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            savm=oldm;
           eij[i][j][(int)age] +=p3mat[i][j][h];            oldm=newm;
         }          } /* end mult */
            
     hf=1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     if (stepm >= YEARM) hf=stepm/YEARM;          /* But now since version 0.9 we anticipate for bias at large stepm.
     fprintf(ficreseij,"%.0f",age );           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for(i=1; i<=nlstate;i++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for(j=1; j<=nlstate;j++){           * the nearest (and in case of equal distance, to the lowest) interval but now
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     fprintf(ficreseij,"\n");           * probability in order to take into account the bias as a fraction of the way
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   }           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
 /************ Variance ******************/           */
 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)          s1=s[mw[mi][i]][i];
 {          s2=s[mw[mi+1][i]][i];
   /* Variance of health expectancies */          bbh=(double)bh[mi][i]/(double)stepm; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          /* bias bh is positive if real duration
   double **newm;           * is higher than the multiple of stepm and negative otherwise.
   double **dnewm,**doldm;           */
   int i, j, nhstepm, hstepm, h;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int k, cptcode;          if( s2 > nlstate){ 
   double *xp;            /* i.e. if s2 is a death state and if the date of death is known 
   double **gp, **gm;               then the contribution to the likelihood is the probability to 
   double ***gradg, ***trgradg;               die between last step unit time and current  step unit time, 
   double ***p3mat;               which is also equal to probability to die before dh 
   double age,agelim;               minus probability to die before dh-stepm . 
   int theta;               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
    fprintf(ficresvij,"# Covariances of life expectancies\n");          health state: the date of the interview describes the actual state
   fprintf(ficresvij,"# Age");          and not the date of a change in health state. The former idea was
   for(i=1; i<=nlstate;i++)          to consider that at each interview the state was recorded
     for(j=1; j<=nlstate;j++)          (healthy, disable or death) and IMaCh was corrected; but when we
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          introduced the exact date of death then we should have modified
   fprintf(ficresvij,"\n");          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
   xp=vector(1,npar);          stepm. It is no more the probability to die between last interview
   dnewm=matrix(1,nlstate,1,npar);          and month of death but the probability to survive from last
   doldm=matrix(1,nlstate,1,nlstate);          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
   hstepm=1*YEARM; /* Every year of age */          Jackson for correcting this bug.  Former versions increased
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          mortality artificially. The bad side is that we add another loop
   agelim = AGESUP;          which slows down the processing. The difference can be up to 10%
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          lower mortality.
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            */
     if (stepm >= YEARM) hstepm=1;            lli=log(out[s1][s2] - savm[s1][s2]);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          } else if  (s2==-2) {
     gp=matrix(0,nhstepm,1,nlstate);            for (j=1,survp=0. ; j<=nlstate; j++) 
     gm=matrix(0,nhstepm,1,nlstate);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
     for(theta=1; theta <=npar; theta++){            lli= log(survp);
       for(i=1; i<=npar; i++){ /* Computes gradient */          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          
       }          else if  (s2==-4) { 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for (j=3,survp=0. ; j<=nlstate; j++)  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
       if (popbased==1) {          } 
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];          else if  (s2==-5) { 
       }            for (j=1,survp=0. ; j<=2; j++)  
                    survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<= nlstate; j++){            lli= log(survp); 
         for(h=0; h<=nhstepm; h++){          } 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          else{
         }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
              } 
       for(i=1; i<=npar; i++) /* Computes gradient */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          /*if(lli ==000.0)*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            /*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); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ipmx +=1;
           sw += weight[i];
       if (popbased==1) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1; i<=nlstate;i++)        } /* end of wave */
           prlim[i][i]=probs[(int)age][i][ij];      } /* end of individual */
       }    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<= nlstate; j++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(h=0; h<=nhstepm; h++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
       for(j=1; j<= nlstate; j++)          for(d=0; d<=dh[mi][i]; d++){
         for(h=0; h<=nhstepm; h++){            newm=savm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
     } /* End theta */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(h=0; h<=nhstepm; h++)            savm=oldm;
       for(j=1; j<=nlstate;j++)            oldm=newm;
         for(theta=1; theta <=npar; theta++)          } /* end mult */
           trgradg[h][j][theta]=gradg[h][theta][j];        
           s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       for(j=1;j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
         vareij[i][j][(int)age] =0.;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for(h=0;h<=nhstepm;h++){          ipmx +=1;
       for(k=0;k<=nhstepm;k++){          sw += weight[i];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        } /* end of wave */
         for(i=1;i<=nlstate;i++)      } /* end of individual */
           for(j=1;j<=nlstate;j++)    }  else if(mle==3){  /* exponential inter-extrapolation */
             vareij[i][j][(int)age] += doldm[i][j];      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++){
     h=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (stepm >= YEARM) h=stepm/YEARM;            for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresvij,"%.0f ",age );              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++){            }
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
     fprintf(ficresvij,"\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_matrix(gp,0,nhstepm,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
     free_matrix(gm,0,nhstepm,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   } /* End age */            savm=oldm;
              oldm=newm;
   free_vector(xp,1,npar);          } /* end mult */
   free_matrix(doldm,1,nlstate,1,npar);        
   free_matrix(dnewm,1,nlstate,1,nlstate);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 /************ Variance of prevlim ******************/          ipmx +=1;
 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)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Variance of prevalence limit */        } /* end of wave */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } /* end of individual */
   double **newm;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double **dnewm,**doldm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j, nhstepm, hstepm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int k, cptcode;        for(mi=1; mi<= wav[i]-1; mi++){
   double *xp;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double *gp, *gm;            for (j=1;j<=nlstate+ndeath;j++){
   double **gradg, **trgradg;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age,agelim;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int theta;            }
              for(d=0; d<dh[mi][i]; d++){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            newm=savm;
   fprintf(ficresvpl,"# Age");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresvpl," %1d-%1d",i,i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficresvpl,"\n");            }
           
   xp=vector(1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   dnewm=matrix(1,nlstate,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   doldm=matrix(1,nlstate,1,nlstate);            savm=oldm;
              oldm=newm;
   hstepm=1*YEARM; /* Every year of age */          } /* end mult */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        
   agelim = AGESUP;          s1=s[mw[mi][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          s2=s[mw[mi+1][i]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          if( s2 > nlstate){ 
     if (stepm >= YEARM) hstepm=1;            lli=log(out[s1][s2] - savm[s1][s2]);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }else{
     gradg=matrix(1,npar,1,nlstate);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gp=vector(1,nlstate);          }
     gm=vector(1,nlstate);          ipmx +=1;
           sw += weight[i];
     for(theta=1; theta <=npar; theta++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*      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]); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } /* end of wave */
       }      } /* end of individual */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(i=1;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         gp[i] = prlim[i][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            for(mi=1; mi<= wav[i]-1; mi++){
       for(i=1; i<=npar; i++) /* Computes gradient */          for (ii=1;ii<=nlstate+ndeath;ii++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for (j=1;j<=nlstate+ndeath;j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         gm[i] = prlim[i][i];            }
           for(d=0; d<dh[mi][i]; d++){
       for(i=1;i<=nlstate;i++)            newm=savm;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     } /* End theta */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     trgradg =matrix(1,nlstate,1,npar);            }
           
     for(j=1; j<=nlstate;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(theta=1; theta <=npar; theta++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         trgradg[j][theta]=gradg[theta][j];            savm=oldm;
             oldm=newm;
     for(i=1;i<=nlstate;i++)          } /* end mult */
       varpl[i][(int)age] =0.;        
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          s1=s[mw[mi][i]][i];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          s2=s[mw[mi+1][i]][i];
     for(i=1;i<=nlstate;i++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          ipmx +=1;
           sw += weight[i];
     fprintf(ficresvpl,"%.0f ",age );          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1; i<=nlstate;i++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        } /* end of wave */
     fprintf(ficresvpl,"\n");      } /* end of individual */
     free_vector(gp,1,nlstate);    } /* End of if */
     free_vector(gm,1,nlstate);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     free_matrix(gradg,1,npar,1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     free_matrix(trgradg,1,nlstate,1,npar);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   } /* End age */    return -l;
   }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  /*************** log-likelihood *************/
   free_matrix(dnewm,1,nlstate,1,nlstate);  double funcone( double *x)
   {
 }    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
 /************ Variance of one-step probabilities  ******************/    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double **out;
 {    double lli; /* Individual log likelihood */
   int i, j;    double llt;
   int k=0, cptcode;    int s1, s2;
   double **dnewm,**doldm;    double bbh, survp;
   double *xp;    /*extern weight */
   double *gp, *gm;    /* We are differentiating ll according to initial status */
   double **gradg, **trgradg;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double age,agelim, cov[NCOVMAX];    /*for(i=1;i<imx;i++) 
   int theta;      printf(" %d\n",s[4][i]);
   char fileresprob[FILENAMELENGTH];    */
     cov[1]=1.;
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   xp=vector(1,npar);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          }
          for(d=0; d<dh[mi][i]; d++){
   cov[1]=1;          newm=savm;
   for (age=bage; age<=fage; age ++){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     cov[2]=age;          for (kk=1; kk<=cptcovage;kk++) {
     gradg=matrix(1,npar,1,9);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     trgradg=matrix(1,9,1,npar);          }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
     for(theta=1; theta <=npar; theta++){          oldm=newm;
       for(i=1; i<=npar; i++)        } /* end mult */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        
              s1=s[mw[mi][i]][i];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
       k=0;        /* bias is positive if real duration
       for(i=1; i<= (nlstate+ndeath); i++){         * is higher than the multiple of stepm and negative otherwise.
         for(j=1; j<=(nlstate+ndeath);j++){         */
            k=k+1;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           gp[k]=pmmij[i][j];          lli=log(out[s1][s2] - savm[s1][s2]);
         }        } 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++)          lli= log(survp);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }else if (mle==1){
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
       pmij(pmmij,cov,ncovmodel,xp,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 */
       k=0;        } else if(mle==3){  /* exponential inter-extrapolation */
       for(i=1; i<=(nlstate+ndeath); i++){          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(j=1; j<=(nlstate+ndeath);j++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           k=k+1;          lli=log(out[s1][s2]); /* Original formula */
           gm[k]=pmmij[i][j];        } else{  /* mle=0 back to 1 */
         }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }          /*lli=log(out[s1][s2]); */ /* Original formula */
              } /* End of if */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        ipmx +=1;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          sw += weight[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]); */
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        if(globpr){
       for(theta=1; theta <=npar; theta++)          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       trgradg[j][theta]=gradg[theta][j];   %11.6f %11.6f %11.6f ", \
                    num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
      pmij(pmmij,cov,ncovmodel,x,nlstate);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
      k=0;          fprintf(ficresilk," %10.6f\n", -llt);
      for(i=1; i<=(nlstate+ndeath); i++){        }
        for(j=1; j<=(nlstate+ndeath);j++){      } /* end of wave */
          k=k+1;    } /* end of individual */
          gm[k]=pmmij[i][j];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* 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 */
          if(globpr==0){ /* First time we count the contributions and weights */
      /*printf("\n%d ",(int)age);      gipmx=ipmx;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      gsw=sw;
            }
     return -l;
        printf("%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);  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  {
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /* This routine should help understanding what is done with 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);       the selection of individuals/waves and
   }       to check the exact contribution to the likelihood.
        Plotting could be done.
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));     */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    int k;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    if(*globpri !=0){ /* Just counts and sums, no printings */
 }      strcpy(fileresilk,"ilk"); 
  free_vector(xp,1,npar);      strcat(fileresilk,fileres);
 fclose(ficresprob);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
  exit(0);        printf("Problem with resultfile: %s\n", fileresilk);
 }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
 /***********************************************/      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
 /**************** Main Program *****************/      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
 /***********************************************/      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
 /*int main(int argc, char *argv[])*/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 int main()      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 {    }
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    *fretone=(*funcone)(p);
   double agedeb, agefin,hf;    if(*globpri !=0){
   double agemin=1.e20, agemax=-1.e20;      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double fret;      fflush(fichtm); 
   double **xi,tmp,delta;    } 
     return;
   double dum; /* Dummy variable */  }
   double ***p3mat;  
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];  /*********** Maximum Likelihood Estimation ***************/
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];  {
   char filerest[FILENAMELENGTH];    int i,j, iter;
   char fileregp[FILENAMELENGTH];    double **xi;
   char popfile[FILENAMELENGTH];    double fret;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    double fretone; /* Only one call to likelihood */
   int firstobs=1, lastobs=10;    /*  char filerespow[FILENAMELENGTH];*/
   int sdeb, sfin; /* Status at beginning and end */    xi=matrix(1,npar,1,npar);
   int c,  h , cpt,l;    for (i=1;i<=npar;i++)
   int ju,jl, mi;      for (j=1;j<=npar;j++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        xi[i][j]=(i==j ? 1.0 : 0.0);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;    strcpy(filerespow,"pow"); 
   int hstepm, nhstepm;    strcat(filerespow,fileres);
   int *popage,boolprev=0;/*boolprev=0 if date and zero if wave*/    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   double bage, fage, age, agelim, agebase;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double ftolpl=FTOL;    }
   double **prlim;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double *severity;    for (i=1;i<=nlstate;i++)
   double ***param; /* Matrix of parameters */      for(j=1;j<=nlstate+ndeath;j++)
   double  *p;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double **matcov; /* Matrix of covariance */    fprintf(ficrespow,"\n");
   double ***delti3; /* Scale */  
   double *delti; /* Scale */    powell(p,xi,npar,ftol,&iter,&fret,func);
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */    free_matrix(xi,1,npar,1,npar);
   double *epj, vepp;    fclose(ficrespow);
   double kk1, kk2;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double *popeffectif,*popcount;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double dateprev1, dateprev2;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";  }
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   char z[1]="c", occ;  {
 #include <sys/time.h>    double  **a,**y,*x,pd;
 #include <time.h>    double **hess;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int i, j,jk;
   char strfprev[10], strlprev[10];    int *indx;
   char strfprevfore[10], strlprevfore[10];  
   /* long total_usecs;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   struct timeval start_time, end_time;    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[]) ;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   printf("\nIMACH, Version 0.7");  
   printf("\nEnter the parameter file name: ");    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 #ifdef windows    for (i=1;i<=npar;i++){
   scanf("%s",pathtot);      printf("%d",i);fflush(stdout);
   getcwd(pathcd, size);      fprintf(ficlog,"%d",i);fflush(ficlog);
   /*cygwin_split_path(pathtot,path,optionfile);     
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   /* cutv(path,optionfile,pathtot,'\\');*/      
       /*  printf(" %f ",p[i]);
 split(pathtot, path,optionfile);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   chdir(path);    }
   replace(pathc,path);    
 #endif    for (i=1;i<=npar;i++) {
 #ifdef unix      for (j=1;j<=npar;j++)  {
   scanf("%s",optionfile);        if (j>i) { 
 #endif          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 /*-------- arguments in the command line --------*/          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
   strcpy(fileres,"r");          hess[j][i]=hess[i][j];    
   strcat(fileres, optionfile);          /*printf(" %lf ",hess[i][j]);*/
         }
   /*---------arguments file --------*/      }
     }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    printf("\n");
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficlog,"\n");
     goto end;  
   }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   strcpy(filereso,"o");    
   strcat(filereso,fileres);    a=matrix(1,npar,1,npar);
   if((ficparo=fopen(filereso,"w"))==NULL) {    y=matrix(1,npar,1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    x=vector(1,npar);
   }    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
   /* Reads comments: lines beginning with '#' */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   while((c=getc(ficpar))=='#' && c!= EOF){    ludcmp(a,npar,indx,&pd);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    for (j=1;j<=npar;j++) {
     puts(line);      for (i=1;i<=npar;i++) x[i]=0;
     fputs(line,ficparo);      x[j]=1;
   }      lubksb(a,npar,indx,x);
   ungetc(c,ficpar);      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   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#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,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,&popbased);      fprintf(ficlog,"\n");
   fprintf(ficparo,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);    }
    
   /* printf("%s %s",strfprev,strlprev);    /* Recompute Inverse */
      exit(0);*/    for (i=1;i<=npar;i++)
  while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ungetc(c,ficpar);    ludcmp(a,npar,indx,&pd);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /*  printf("\n#Hessian matrix recomputed#\n");
     fputs(line,ficparo);  
   }    for (j=1;j<=npar;j++) {
   ungetc(c,ficpar);      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
   fscanf(ficpar,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,&nforecast,&mobilav);      lubksb(a,npar,indx,x);
   fprintf(ficparo,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);      for (i=1;i<=npar;i++){ 
              y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
 while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficlog,"%.3e ",y[i][j]);
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);      printf("\n");
     puts(line);      fprintf(ficlog,"\n");
     fputs(line,ficparo);    }
   }    */
   ungetc(c,ficpar);  
      free_matrix(a,1,npar,1,npar);
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);    free_matrix(y,1,npar,1,npar);
      free_vector(x,1,npar);
   covar=matrix(0,NCOVMAX,1,n);    free_ivector(indx,1,npar);
   cptcovn=0;    free_matrix(hess,1,npar,1,npar);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   
   ncovmodel=2+cptcovn;  }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    /*************** hessian matrix ****************/
   /* Read guess parameters */  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    int i;
     ungetc(c,ficpar);    int l=1, lmax=20;
     fgets(line, MAXLINE, ficpar);    double k1,k2;
     puts(line);    double p2[MAXPARM+1]; /* identical to x */
     fputs(line,ficparo);    double res;
   }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   ungetc(c,ficpar);    double fx;
      int k=0,kmax=10;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double l1;
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){    fx=func(x);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (i=1;i<=npar;i++) p2[i]=x[i];
       fprintf(ficparo,"%1d%1d",i1,j1);    for(l=0 ; l <=lmax; l++){
       printf("%1d%1d",i,j);      l1=pow(10,l);
       for(k=1; k<=ncovmodel;k++){      delts=delt;
         fscanf(ficpar," %lf",&param[i][j][k]);      for(k=1 ; k <kmax; k=k+1){
         printf(" %lf",param[i][j][k]);        delt = delta*(l1*k);
         fprintf(ficparo," %lf",param[i][j][k]);        p2[theta]=x[theta] +delt;
       }        k1=func(p2)-fx;
       fscanf(ficpar,"\n");        p2[theta]=x[theta]-delt;
       printf("\n");        k2=func(p2)-fx;
       fprintf(ficparo,"\n");        /*res= (k1-2.0*fx+k2)/delt/delt; */
     }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  #ifdef DEBUGHESS
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   p=param[1][1];        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
   /* Reads comments: lines beginning with '#' */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   while((c=getc(ficpar))=='#' && c!= EOF){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     ungetc(c,ficpar);          k=kmax;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     fputs(line,ficparo);          k=kmax; l=lmax*10.;
   }        }
   ungetc(c,ficpar);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      }
   for(i=1; i <=nlstate; i++){    }
     for(j=1; j <=nlstate+ndeath-1; j++){    delti[theta]=delts;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    return res; 
       printf("%1d%1d",i,j);    
       fprintf(ficparo,"%1d%1d",i1,j1);  }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         printf(" %le",delti3[i][j][k]);  {
         fprintf(ficparo," %le",delti3[i][j][k]);    int i;
       }    int l=1, l1, lmax=20;
       fscanf(ficpar,"\n");    double k1,k2,k3,k4,res,fx;
       printf("\n");    double p2[MAXPARM+1];
       fprintf(ficparo,"\n");    int k;
     }  
   }    fx=func(x);
   delti=delti3[1][1];    for (k=1; k<=2; k++) {
        for (i=1;i<=npar;i++) p2[i]=x[i];
   /* Reads comments: lines beginning with '#' */      p2[thetai]=x[thetai]+delti[thetai]/k;
   while((c=getc(ficpar))=='#' && c!= EOF){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     ungetc(c,ficpar);      k1=func(p2)-fx;
     fgets(line, MAXLINE, ficpar);    
     puts(line);      p2[thetai]=x[thetai]+delti[thetai]/k;
     fputs(line,ficparo);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k2=func(p2)-fx;
   ungetc(c,ficpar);    
        p2[thetai]=x[thetai]-delti[thetai]/k;
   matcov=matrix(1,npar,1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for(i=1; i <=npar; i++){      k3=func(p2)-fx;
     fscanf(ficpar,"%s",&str);    
     printf("%s",str);      p2[thetai]=x[thetai]-delti[thetai]/k;
     fprintf(ficparo,"%s",str);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(j=1; j <=i; j++){      k4=func(p2)-fx;
       fscanf(ficpar," %le",&matcov[i][j]);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       printf(" %.5le",matcov[i][j]);  #ifdef DEBUG
       fprintf(ficparo," %.5le",matcov[i][j]);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     fscanf(ficpar,"\n");  #endif
     printf("\n");    }
     fprintf(ficparo,"\n");    return res;
   }  }
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  /************** Inverse of matrix **************/
       matcov[i][j]=matcov[j][i];  void ludcmp(double **a, int n, int *indx, double *d) 
      { 
   printf("\n");    int i,imax,j,k; 
     double big,dum,sum,temp; 
     double *vv; 
     /*-------- data file ----------*/   
     if((ficres =fopen(fileres,"w"))==NULL) {    vv=vector(1,n); 
       printf("Problem with resultfile: %s\n", fileres);goto end;    *d=1.0; 
     }    for (i=1;i<=n;i++) { 
     fprintf(ficres,"#%s\n",version);      big=0.0; 
          for (j=1;j<=n;j++) 
     if((fic=fopen(datafile,"r"))==NULL)    {        if ((temp=fabs(a[i][j])) > big) big=temp; 
       printf("Problem with datafile: %s\n", datafile);goto end;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }      vv[i]=1.0/big; 
     } 
     n= lastobs;    for (j=1;j<=n;j++) { 
     severity = vector(1,maxwav);      for (i=1;i<j;i++) { 
     outcome=imatrix(1,maxwav+1,1,n);        sum=a[i][j]; 
     num=ivector(1,n);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     moisnais=vector(1,n);        a[i][j]=sum; 
     annais=vector(1,n);      } 
     moisdc=vector(1,n);      big=0.0; 
     andc=vector(1,n);      for (i=j;i<=n;i++) { 
     agedc=vector(1,n);        sum=a[i][j]; 
     cod=ivector(1,n);        for (k=1;k<j;k++) 
     weight=vector(1,n);          sum -= a[i][k]*a[k][j]; 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        a[i][j]=sum; 
     mint=matrix(1,maxwav,1,n);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     anint=matrix(1,maxwav,1,n);          big=dum; 
     s=imatrix(1,maxwav+1,1,n);          imax=i; 
     adl=imatrix(1,maxwav+1,1,n);            } 
     tab=ivector(1,NCOVMAX);      } 
     ncodemax=ivector(1,8);      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     i=1;          dum=a[imax][k]; 
     while (fgets(line, MAXLINE, fic) != NULL)    {          a[imax][k]=a[j][k]; 
       if ((i >= firstobs) && (i <=lastobs)) {          a[j][k]=dum; 
                } 
         for (j=maxwav;j>=1;j--){        *d = -(*d); 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        vv[imax]=vv[j]; 
           strcpy(line,stra);      } 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      indx[j]=imax; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      if (a[j][j] == 0.0) a[j][j]=TINY; 
         }      if (j != n) { 
                dum=1.0/(a[j][j]); 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      } 
     } 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(vv,1,n);  /* Doesn't work */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  ;
   } 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncov;j>=1;j--){  void lubksb(double **a, int n, int *indx, double b[]) 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  { 
         }    int i,ii=0,ip,j; 
         num[i]=atol(stra);    double sum; 
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    for (i=1;i<=n;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])); ij=ij+1;}*/      ip=indx[i]; 
       sum=b[ip]; 
         i=i+1;      b[ip]=b[i]; 
       }      if (ii) 
     }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     /* printf("ii=%d", ij);      else if (sum) ii=i; 
        scanf("%d",i);*/      b[i]=sum; 
   imx=i-1; /* Number of individuals */    } 
     for (i=n;i>=1;i--) { 
   /* for (i=1; i<=imx; i++){      sum=b[i]; 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      b[i]=sum/a[i][i]; 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    } 
     }  } 
     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]));*/  
   void pstamp(FILE *fichier)
   /* Calculation of the number of parameter from char model*/  {
   Tvar=ivector(1,15);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   Tprod=ivector(1,15);  }
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);  /************ Frequencies ********************/
   Tage=ivector(1,15);        void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
      {  /* Some frequencies */
   if (strlen(model) >1){    
     j=0, j1=0, k1=1, k2=1;    int i, m, jk, k1,i1, j1, bool, z1,j;
     j=nbocc(model,'+');    int first;
     j1=nbocc(model,'*');    double ***freq; /* Frequencies */
     cptcovn=j+1;    double *pp, **prop;
     cptcovprod=j1;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        char fileresp[FILENAMELENGTH];
        
     strcpy(modelsav,model);    pp=vector(1,nlstate);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    prop=matrix(1,nlstate,iagemin,iagemax+3);
       printf("Error. Non available option model=%s ",model);    strcpy(fileresp,"p");
       goto end;    strcat(fileresp,fileres);
     }    if((ficresp=fopen(fileresp,"w"))==NULL) {
          printf("Problem with prevalence resultfile: %s\n", fileresp);
     for(i=(j+1); i>=1;i--){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       cutv(stra,strb,modelsav,'+');      exit(0);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       /*scanf("%d",i);*/    j1=0;
       if (strchr(strb,'*')) {    
         cutv(strd,strc,strb,'*');    j=cptcoveff;
         if (strcmp(strc,"age")==0) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    first=1;
           Tvar[i]=atoi(stre);  
           cptcovage++;    for(k1=1; k1<=j;k1++){   /* Loop on covariates */
             Tage[cptcovage]=i;      for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
             /*printf("stre=%s ", stre);*/        j1++;
         }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         else if (strcmp(strd,"age")==0) {          scanf("%d", i);*/
           cptcovprod--;        for (i=-5; i<=nlstate+ndeath; i++)  
           cutv(strb,stre,strc,'V');          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           Tvar[i]=atoi(stre);            for(m=iagemin; m <= iagemax+3; m++)
           cptcovage++;              freq[i][jk][m]=0;
           Tage[cptcovage]=i;        
         }        for (i=1; i<=nlstate; i++)  
         else {          for(m=iagemin; m <= iagemax+3; m++)
           cutv(strb,stre,strc,'V');            prop[i][m]=0;
           Tvar[i]=ncov+k1;        
           cutv(strb,strc,strd,'V');        dateintsum=0;
           Tprod[k1]=i;        k2cpt=0;
           Tvard[k1][1]=atoi(strc);        for (i=1; i<=imx; i++) {
           Tvard[k1][2]=atoi(stre);          bool=1;
           Tvar[cptcovn+k2]=Tvard[k1][1];          if  (cptcovn>0) {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];            for (z1=1; z1<=cptcoveff; z1++) 
           for (k=1; k<=lastobs;k++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                bool=0;
           k1++;          }
           k2=k2+2;          if (bool==1){
         }            for(m=firstpass; m<=lastpass; m++){
       }              k2=anint[m][i]+(mint[m][i]/12.);
       else {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
        /*  scanf("%d",i);*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       cutv(strd,strc,strb,'V');                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       Tvar[i]=atoi(strc);                if (m<lastpass) {
       }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       strcpy(modelsav,stra);                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                }
         scanf("%d",i);*/                
     }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 }                  dateintsum=dateintsum+k2;
                    k2cpt++;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                }
   printf("cptcovprod=%d ", cptcovprod);                /*}*/
   scanf("%d ",i);*/            }
     fclose(fic);          }
         }
     /*  if(mle==1){*/         
     if (weightopt != 1) { /* Maximisation without weights*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for(i=1;i<=n;i++) weight[i]=1.0;        pstamp(ficresp);
     }        if  (cptcovn>0) {
     /*-calculation of age at interview from date of interview and age at death -*/          fprintf(ficresp, "\n#********** Variable "); 
     agev=matrix(1,maxwav,1,imx);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
    for (i=1; i<=imx; i++)          fprintf(ficlog, "\n#********** Variable "); 
      for(m=2; (m<= maxwav); m++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          fprintf(ficlog, "**********\n#");
          anint[m][i]=9999;        }
          s[m][i]=-1;        for(i=1; i<=nlstate;i++) 
        }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
            fprintf(ficresp, "\n");
     for (i=1; i<=imx; i++)  {        
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(i=iagemin; i <= iagemax+3; i++){
       for(m=1; (m<= maxwav); m++){          if(i==iagemax+3){
         if(s[m][i] >0){            fprintf(ficlog,"Total");
           if (s[m][i] == nlstate+1) {          }else{
             if(agedc[i]>0)            if(first==1){
               if(moisdc[i]!=99 && andc[i]!=9999)              first=0;
               agev[m][i]=agedc[i];              printf("See log file for details...\n");
             else {            }
               if (andc[i]!=9999){            fprintf(ficlog,"Age %d", i);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          }
               agev[m][i]=-1;          for(jk=1; jk <=nlstate ; jk++){
               }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             }              pp[jk] += freq[jk][m][i]; 
           }          }
           else if(s[m][i] !=9){ /* Should no more exist */          for(jk=1; jk <=nlstate ; jk++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            for(m=-1, pos=0; m <=0 ; m++)
             if(mint[m][i]==99 || anint[m][i]==9999)              pos += freq[jk][m][i];
               agev[m][i]=1;            if(pp[jk]>=1.e-10){
             else if(agev[m][i] <agemin){              if(first==1){
               agemin=agev[m][i];                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              }
             }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             else if(agev[m][i] >agemax){            }else{
               agemax=agev[m][i];              if(first==1)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             /*agev[m][i]=anint[m][i]-annais[i];*/            }
             /*   agev[m][i] = age[i]+2*m;*/          }
           }  
           else { /* =9 */          for(jk=1; jk <=nlstate ; jk++){
             agev[m][i]=1;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             s[m][i]=-1;              pp[jk] += freq[jk][m][i];
           }          }       
         }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         else /*= 0 Unknown */            pos += pp[jk];
           agev[m][i]=1;            posprop += prop[jk][i];
       }          }
              for(jk=1; jk <=nlstate ; jk++){
     }            if(pos>=1.e-5){
     for (i=1; i<=imx; i++)  {              if(first==1)
       for(m=1; (m<= maxwav); m++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         if (s[m][i] > (nlstate+ndeath)) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           printf("Error: Wrong value in nlstate or ndeath\n");              }else{
           goto end;              if(first==1)
         }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }            }
             if( i <= iagemax){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     free_vector(severity,1,maxwav);                /*probs[i][jk][j1]= pp[jk]/pos;*/
     free_imatrix(outcome,1,maxwav+1,1,n);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     free_vector(moisnais,1,n);              }
     free_vector(annais,1,n);              else
     /* free_matrix(mint,1,maxwav,1,n);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
        free_matrix(anint,1,maxwav,1,n);*/            }
     free_vector(moisdc,1,n);          }
     free_vector(andc,1,n);          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
                for(m=-1; m <=nlstate+ndeath; m++)
     wav=ivector(1,imx);              if(freq[jk][m][i] !=0 ) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              if(first==1)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                    fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     /* Concatenates waves */              }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          if(i <= iagemax)
             fprintf(ficresp,"\n");
           if(first==1)
       Tcode=ivector(1,100);            printf("Others in log...\n");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          fprintf(ficlog,"\n");
       ncodemax[1]=1;        }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      }
          }
    codtab=imatrix(1,100,1,10);    dateintmean=dateintsum/k2cpt; 
    h=0;   
    m=pow(2,cptcoveff);    fclose(ficresp);
      free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
    for(k=1;k<=cptcoveff; k++){    free_vector(pp,1,nlstate);
      for(i=1; i <=(m/pow(2,k));i++){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        for(j=1; j <= ncodemax[k]; j++){    /* End of Freq */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  }
            h++;  
            if (h>m) h=1;codtab[h][k]=j;  /************ Prevalence ********************/
          }  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)
        }  {  
      }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
    }       in each health status at the date of interview (if between dateprev1 and dateprev2).
           We still use firstpass and lastpass as another selection.
    /* Calculates basic frequencies. Computes observed prevalence at single age    */
        and prints on file fileres'p'. */   
     int i, m, jk, k1, i1, j1, bool, z1,j;
     if ((nbocc(strfprev,'/')==1) && (nbocc(strlprev,'/')==1)){    double ***freq; /* Frequencies */
      boolprev=0;    double *pp, **prop;
      cutv(stra,strb,strfprev,'/');    double pos,posprop; 
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);    double  y2; /* in fractional years */
      cutv(stra,strb,strlprev,'/');    int iagemin, iagemax;
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);  
    }    iagemin= (int) agemin;
        iagemax= (int) agemax;
    else if ((nbocc(strfprev,'/')==0) &&(nbocc(strlprev,'/')==0)){    /*pp=vector(1,nlstate);*/
      boolprev=1;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
      fprev=atoi(strfprev); lprev=atoi(strlprev);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    }    j1=0;
     else {    
       printf("Error in statement lprevalence or fprevalence\n");    j=cptcoveff;
       goto end;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }    
        for(k1=1; k1<=j;k1++){
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint,boolprev,dateprev1,dateprev2);      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i<=nlstate; i++)  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(m=iagemin; m <= iagemax+3; m++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            prop[i][m]=0.0;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       
              for (i=1; i<=imx; i++) { /* Each individual */
     /* For Powell, parameters are in a vector p[] starting at p[1]          bool=1;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          if  (cptcovn>0) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     if(mle==1){                bool=0;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          } 
     }          if (bool==1) { 
                for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     /*--------- results files --------------*/              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     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);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
    fprintf(ficres,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
    fprintf(ficres,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
    jk=1;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
    fprintf(ficres,"# Parameters\n");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
    printf("# Parameters\n");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
    for(i=1,jk=1; i <=nlstate; i++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
      for(k=1; k <=(nlstate+ndeath); k++){                } 
        if (k != i)              }
          {            } /* end selection of waves */
            printf("%d%d ",i,k);          }
            fprintf(ficres,"%1d%1d ",i,k);        }
            for(j=1; j <=ncovmodel; j++){        for(i=iagemin; i <= iagemax+3; i++){  
              printf("%f ",p[jk]);          
              fprintf(ficres,"%f ",p[jk]);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
              jk++;            posprop += prop[jk][i]; 
            }          } 
            printf("\n");  
            fprintf(ficres,"\n");          for(jk=1; jk <=nlstate ; jk++){     
          }            if( i <=  iagemax){ 
      }              if(posprop>=1.e-5){ 
    }                probs[i][jk][j1]= prop[jk][i]/posprop;
  if(mle==1){              } else
     /* Computing hessian and covariance matrix */                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
     ftolhess=ftol; /* Usually correct */            } 
     hesscov(matcov, p, npar, delti, ftolhess, func);          }/* end jk */ 
  }        }/* end i */ 
     fprintf(ficres,"# Scales\n");      } /* end i1 */
     printf("# Scales\n");    } /* end k1 */
      for(i=1,jk=1; i <=nlstate; i++){    
       for(j=1; j <=nlstate+ndeath; j++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         if (j!=i) {    /*free_vector(pp,1,nlstate);*/
           fprintf(ficres,"%1d%1d",i,j);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           printf("%1d%1d",i,j);  }  /* End of prevalence */
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);  /************* Waves Concatenation ***************/
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           }  {
           printf("\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           fprintf(ficres,"\n");       Death is a valid wave (if date is known).
         }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      }       and mw[mi+1][i]. dh depends on stepm.
           */
     k=1;  
     fprintf(ficres,"# Covariance\n");    int i, mi, m;
     printf("# Covariance\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for(i=1;i<=npar;i++){       double sum=0., jmean=0.;*/
       /*  if (k>nlstate) k=1;    int first;
       i1=(i-1)/(ncovmodel*nlstate)+1;    int j, k=0,jk, ju, jl;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double sum=0.;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    first=0;
       fprintf(ficres,"%3d",i);    jmin=1e+5;
       printf("%3d",i);    jmax=-1;
       for(j=1; j<=i;j++){    jmean=0.;
         fprintf(ficres," %.5e",matcov[i][j]);    for(i=1; i<=imx; i++){
         printf(" %.5e",matcov[i][j]);      mi=0;
       }      m=firstpass;
       fprintf(ficres,"\n");      while(s[m][i] <= nlstate){
       printf("\n");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       k++;          mw[++mi][i]=m;
     }        if(m >=lastpass)
              break;
     while((c=getc(ficpar))=='#' && c!= EOF){        else
       ungetc(c,ficpar);          m++;
       fgets(line, MAXLINE, ficpar);      }/* end while */
       puts(line);      if (s[m][i] > nlstate){
       fputs(line,ficparo);        mi++;     /* Death is another wave */
     }        /* if(mi==0)  never been interviewed correctly before death */
     ungetc(c,ficpar);           /* Only death is a correct wave */
          mw[mi][i]=m;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      }
      
     if (fage <= 2) {      wav[i]=mi;
       bage = agemin;      if(mi==0){
       fage = agemax;        nbwarn++;
     }        if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          first=1;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        }
         if(first==1){
              fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
 /*------------ gnuplot -------------*/        }
 chdir(pathcd);      } /* end mi==0 */
   if((ficgp=fopen("graph.plt","w"))==NULL) {    } /* End individuals */
     printf("Problem with file graph.gp");goto end;  
   }    for(i=1; i<=imx; i++){
 #ifdef windows      for(mi=1; mi<wav[i];mi++){
   fprintf(ficgp,"cd \"%s\" \n",pathc);        if (stepm <=0)
 #endif          dh[mi][i]=1;
 m=pow(2,cptcoveff);        else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
  /* 1eme*/            if (agedc[i] < 2*AGESUP) {
   for (cpt=1; cpt<= nlstate ; cpt ++) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
    for (k1=1; k1<= m ; k1 ++) {              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
 #ifdef windows                nberr++;
     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);                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]);
 #endif                j=1; /* Temporary Dangerous patch */
 #ifdef unix                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,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                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]);
 #endif                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);
               }
 for (i=1; i<= nlstate ; i ++) {              k=k+1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if (j >= jmax){
   else fprintf(ficgp," \%%*lf (\%%*lf)");                jmax=j;
 }                ijmax=i;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              }
     for (i=1; i<= nlstate ; i ++) {              if (j <= jmin){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                jmin=j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                ijmin=i;
 }              }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              sum=sum+j;
      for (i=1; i<= nlstate ; i ++) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }            }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          else{
 #ifdef unix            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 fprintf(ficgp,"\nset ter gif small size 400,300");  /*        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]); */
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            k=k+1;
    }            if (j >= jmax) {
   }              jmax=j;
   /*2 eme*/              ijmax=i;
             }
   for (k1=1; k1<= m ; k1 ++) {            else if (j <= jmin){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              jmin=j;
                  ijmin=i;
     for (i=1; i<= nlstate+1 ; i ++) {            }
       k=2*i;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            /*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]);*/
       for (j=1; j<= nlstate+1 ; j ++) {            if(j<0){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              nberr++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              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]);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            sum=sum+j;
     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 ++) {          jk= j/stepm;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          jl= j -jk*stepm;
         else fprintf(ficgp," \%%*lf (\%%*lf)");          ju= j -(jk+1)*stepm;
 }            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       fprintf(ficgp,"\" t\"\" w l 0,");            if(jl==0){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              dh[mi][i]=jk;
       for (j=1; j<= nlstate+1 ; j ++) {              bh[mi][i]=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }else{ /* We want a negative bias in order to only have interpolation ie
   else fprintf(ficgp," \%%*lf (\%%*lf)");                    * to avoid the price of an extra matrix product in likelihood */
 }                dh[mi][i]=jk+1;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              bh[mi][i]=ju;
       else fprintf(ficgp,"\" t\"\" w l 0,");            }
     }          }else{
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            if(jl <= -ju){
   }              dh[mi][i]=jk;
                bh[mi][i]=jl;       /* bias is positive if real duration
   /*3eme*/                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
   for (k1=1; k1<= m ; k1 ++) {            }
     for (cpt=1; cpt<= nlstate ; cpt ++) {            else{
       k=2+nlstate*(cpt-1);              dh[mi][i]=jk+1;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);              bh[mi][i]=ju;
       for (i=1; i< nlstate ; 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);            if(dh[mi][i]==0){
       }              dh[mi][i]=1; /* At least one step */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              bh[mi][i]=ju; /* At least one step */
     }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   }            }
            } /* end if mle */
   /* CV preval stat */        }
   for (k1=1; k1<= m ; k1 ++) {      } /* end wave */
     for (cpt=1; cpt<nlstate ; cpt ++) {    }
       k=3;    jmean=sum/k;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
       for (i=1; i< nlstate ; i ++)    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
         fprintf(ficgp,"+$%d",k+i+1);   }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
        /*********** Tricode ****************************/
       l=3+(nlstate+ndeath)*cpt;  void tricode(int *Tvar, int **nbcode, int imx)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  {
       for (i=1; i< nlstate ; i ++) {    /* Uses cptcovn+2*cptcovprod as the number of covariates */
         l=3+(nlstate+ndeath)*cpt;    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
         fprintf(ficgp,"+$%d",l+i+1);  
       }    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      int modmaxcovj=0; /* Modality max of covariates j */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    cptcoveff=0; 
     }   
   }      for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
     for(k=1; k <=(nlstate+ndeath); k++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
       if (k != i) {                                 modality of this covariate Vj*/ 
         for(j=1; j <=ncovmodel; j++){        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/                                        modality of the nth covariate of individual i. */
           /*fprintf(ficgp,"%s",alph[1]);*/        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           jk++;        if (ij > modmaxcovj) modmaxcovj=ij; 
           fprintf(ficgp,"\n");        /* 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
       }           female is 1, then modmaxcovj=1.*/
     }      }
     }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
   for(jk=1; jk <=m; jk++) {        if( Ndum[i] != 0 )
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          ncodemax[j]++; 
    i=1;        /* Number of modalities of the j th covariate. In fact
    for(k2=1; k2<=nlstate; k2++) {           ncodemax[j]=2 (dichotom. variables only) but it could be more for
      k3=i;           historical reasons */
      for(k=1; k<=(nlstate+ndeath); k++) {      } /* Ndum[-1] number of undefined modalities */
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
 ij=1;      ij=1; 
         for(j=3; j <=ncovmodel; j++) {      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             ij++;            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
           }                                       k is a modality. If we have model=V1+V1*sex 
           else                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            ij++;
         }          }
           fprintf(ficgp,")/(1");          if (ij > ncodemax[j]) break; 
                }  /* end of loop on */
         for(k1=1; k1 <=nlstate; k1++){        } /* end of loop on modality */ 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
 ij=1;    
           for(j=3; j <=ncovmodel; j++){    for (k=0; k< maxncov; k++) Ndum[k]=0;
           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]]]);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
             ij++;     /* 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 */
           else     Ndum[ij]++;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   }
           }  
           fprintf(ficgp,")");   ij=1;
         }   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);     if((Ndum[i]!=0) && (i<=ncovcol)){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");       Tvaraff[ij]=i; /*For printing */
         i=i+ncovmodel;       ij++;
        }     }
      }   }
    }   ij--;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);   cptcoveff=ij; /*Number of simple covariates*/
   }  }
      
   fclose(ficgp);  /*********** Health Expectancies ****************/
      
 chdir(path);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
      
     free_ivector(wav,1,imx);  {
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    /* Health expectancies, no variances */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     free_ivector(num,1,n);    int nhstepma, nstepma; /* Decreasing with age */
     free_vector(agedc,1,n);    double age, agelim, hf;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    double ***p3mat;
     fclose(ficparo);    double eip;
     fclose(ficres);  
     /*  }*/    pstamp(ficreseij);
        fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
    /*________fin mle=1_________*/    fprintf(ficreseij,"# Age");
        for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
          fprintf(ficreseij," e%1d%1d ",i,j);
     /* No more information from the sample is required now */      }
   /* Reads comments: lines beginning with '#' */      fprintf(ficreseij," e%1d. ",i);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    fprintf(ficreseij,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    
     fputs(line,ficparo);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   ungetc(c,ficpar);    }
      else  hstepm=estepm;   
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    /* We compute the life expectancy from trapezoids spaced every estepm months
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);     * This is mainly to measure the difference between two models: for example
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     * if stepm=24 months pijx are given only every 2 years and by summing them
 /*--------- index.htm --------*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   strcpy(optionfilehtm,optionfile);     * to the curvature of the survival function. If, for the same date, we 
   strcat(optionfilehtm,".htm");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {     * to compare the new estimate of Life expectancy with the same linear 
     printf("Problem with %s \n",optionfilehtm);goto end;     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    /* For example we decided to compute the life expectancy with the smallest unit */
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 Total number of observations=%d <br>       nhstepm is the number of hstepm from age to agelim 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>       nstepm is the number of stepm from age to agelin. 
 <hr  size=\"2\" color=\"#EC5E5E\">       Look at hpijx to understand the reason of that which relies in memory size
 <li>Outputs files<br><br>\n       and note for a fixed period like estepm months */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>       survival function given by stepm (the optimization length). Unfortunately it
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>       means that if the survival funtion is printed only each two years of age and if
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>       results. So we changed our mind and took the option of the best precision.
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    agelim=AGESUP;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    /* If stepm=6 months */
 <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);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  fprintf(fichtm," <li>Graphs</li><p>");      
   /* nhstepm age range expressed in number of stepm */
  m=cptcoveff;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
  j1=0;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  for(k1=1; k1<=m;k1++){    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;    for (age=bage; age<=fage; age ++){ 
        if (cptcovn > 0) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
          for (cpt=1; cpt<=cptcoveff;cpt++)      /* if (stepm >= YEARM) hstepm=1;*/
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }      /* If stepm=6 months */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      /* Computed by stepm unit matrices, product of hstepma matrices, stored
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);             in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
        for(cpt=1; cpt<nlstate;cpt++){      
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      
        }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for(cpt=1; cpt<=nlstate;cpt++) {      
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      printf("%d|",(int)age);fflush(stdout);
 interval) in state (%d): v%s%d%d.gif <br>      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        
      }      /* Computing expectancies */
      for(cpt=1; cpt<=nlstate;cpt++) {      for(i=1; i<=nlstate;i++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        for(j=1; j<=nlstate;j++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
      }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            
 health expectancies in states (1) and (2): e%s%d.gif<br>            /* 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]);*/
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  
 fprintf(fichtm,"\n</body>");          }
    }  
  }      fprintf(ficreseij,"%3.0f",age );
 fclose(fichtm);      for(i=1; i<=nlstate;i++){
         eip=0;
   /*--------------- Prevalence limit --------------*/        for(j=1; j<=nlstate;j++){
            eip +=eij[i][j][(int)age];
   strcpy(filerespl,"pl");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   strcat(filerespl,fileres);        }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        fprintf(ficreseij,"%9.4f", eip );
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      }
   }      fprintf(ficreseij,"\n");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      
   fprintf(ficrespl,"#Prevalence limit\n");    }
   fprintf(ficrespl,"#Age ");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    printf("\n");
   fprintf(ficrespl,"\n");    fprintf(ficlog,"\n");
      
   prlim=matrix(1,nlstate,1,nlstate);  }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  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[] )
   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 */    /* Covariances of health expectancies eij and of total life expectancies according
   k=0;     to initial status i, ei. .
   agebase=agemin;    */
   agelim=agemax;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   ftolpl=1.e-10;    int nhstepma, nstepma; /* Decreasing with age */
   i1=cptcoveff;    double age, agelim, hf;
   if (cptcovn < 1){i1=1;}    double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   for(cptcov=1;cptcov<=i1;cptcov++){    double *xp, *xm;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double **gp, **gm;
         k=k+1;    double ***gradg, ***trgradg;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    int theta;
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)    double eip, vip;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            xp=vector(1,npar);
         for (age=agebase; age<=agelim; age++){    xm=vector(1,npar);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    dnewm=matrix(1,nlstate*nlstate,1,npar);
           fprintf(ficrespl,"%.0f",age );    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           for(i=1; i<=nlstate;i++)    
           fprintf(ficrespl," %.5f", prlim[i][i]);    pstamp(ficresstdeij);
           fprintf(ficrespl,"\n");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         }    fprintf(ficresstdeij,"# Age");
       }    for(i=1; i<=nlstate;i++){
     }      for(j=1; j<=nlstate;j++)
   fclose(ficrespl);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
   /*------------- h Pij x at various ages ------------*/    }
      fprintf(ficresstdeij,"\n");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    pstamp(ficrescveij);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   }    fprintf(ficrescveij,"# Age");
   printf("Computing pij: result on file '%s' \n", filerespij);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;        cptj= (j-1)*nlstate+i;
   /*if (stepm<=24) stepsize=2;*/        for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
   agelim=AGESUP;            cptj2= (j2-1)*nlstate+i2;
   hstepm=stepsize*YEARM; /* Every year of age */            if(cptj2 <= cptj)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
            }
   k=0;      }
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficrescveij,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    if(estepm < stepm){
         fprintf(ficrespij,"\n#****** ");      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(j=1;j<=cptcoveff;j++)    }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    else  hstepm=estepm;   
         fprintf(ficrespij,"******\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
             * This is mainly to measure the difference between two models: for example
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     * if stepm=24 months pijx are given only every 2 years and by summing them
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     * we are calculating an estimate of the Life Expectancy assuming a linear 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */     * progression in between and thus overestimating or underestimating according
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * to the curvature of the survival function. If, for the same date, we 
           oldm=oldms;savm=savms;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * to compare the new estimate of Life expectancy with the same linear 
           fprintf(ficrespij,"# Age");     * hypothesis. A more precise result, taking into account a more precise
           for(i=1; i<=nlstate;i++)     * curvature will be obtained if estepm is as small as stepm. */
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);    /* For example we decided to compute the life expectancy with the smallest unit */
           fprintf(ficrespij,"\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           for (h=0; h<=nhstepm; h++){       nhstepm is the number of hstepm from age to agelim 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       nstepm is the number of stepm from age to agelin. 
             for(i=1; i<=nlstate;i++)       Look at hpijx to understand the reason of that which relies in memory size
               for(j=1; j<=nlstate+ndeath;j++)       and note for a fixed period like estepm months */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             fprintf(ficrespij,"\n");       survival function given by stepm (the optimization length). Unfortunately it
           }       means that if the survival funtion is printed only each two years of age and if
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           fprintf(ficrespij,"\n");       results. So we changed our mind and took the option of the best precision.
         }    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
     /* If stepm=6 months */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
   fclose(ficrespij);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /*---------- Forecasting ------------------*/    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   strcpy(fileresf,"f");    
   strcat(fileresf,fileres);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
  if ((nbocc(strfprevfore,'/')==1) && (nbocc(strlprevfore,'/')==1)){  
      boolprev=0;    for (age=bage; age<=fage; age ++){ 
      cutv(stra,strb,strfprevfore,'/');      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      cutv(stra,strb,strlprevfore,'/');      /* if (stepm >= YEARM) hstepm=1;*/
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    }  
          /* If stepm=6 months */
    else if ((nbocc(strfprevfore,'/')==0) &&(nbocc(strlprevfore,'/')==0)){      /* Computed by stepm unit matrices, product of hstepma matrices, stored
      boolprev=1;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
      fprev=atoi(strfprevfore); lprev=atoi(strlprevfore);      
    }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     else {  
       printf("Error in statement lprevalence or fprevalence\n");      /* Computing  Variances of health expectancies */
       goto end;      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     }         decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore,mint,anint,boolprev,dateprev1,dateprev2);        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   free_matrix(mint,1,maxwav,1,n);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   free_matrix(anint,1,maxwav,1,n);        }
   free_matrix(agev,1,maxwav,1,imx);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   /* Mobile average */        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   if (mobilav==1) {            for(h=0; h<=nhstepm-1; h++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       for (i=1; i<=nlstate;i++)            }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          }
           mobaverage[(int)agedeb][i][cptcod]=0.;        }
           
     for (agedeb=bage+4; agedeb<=fage; agedeb++){        for(ij=1; ij<= nlstate*nlstate; ij++)
       for (i=1; i<=nlstate;i++){          for(h=0; h<=nhstepm-1; h++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      }/* End theta */
           }      
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      
         }      for(h=0; h<=nhstepm-1; h++)
       }        for(j=1; j<=nlstate*nlstate;j++)
     }            for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
       
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
   agelim=AGESUP;          varhe[ij][ji][(int)age] =0.;
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   if (popforecast==1) {       for(h=0;h<=nhstepm-1;h++){
     if((ficpop=fopen(popfile,"r"))==NULL)    {        for(k=0;k<=nhstepm-1;k++){
       printf("Problem with population file : %s\n",popfile);goto end;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     popage=ivector(0,AGESUP);          for(ij=1;ij<=nlstate*nlstate;ij++)
     popeffectif=vector(0,AGESUP);            for(ji=1;ji<=nlstate*nlstate;ji++)
     popcount=vector(0,AGESUP);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
     i=1;        }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)  
       {      /* Computing expectancies */
         i=i+1;      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       }      for(i=1; i<=nlstate;i++)
     imx=i;        for(j=1; j<=nlstate;j++)
            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   }            
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
       k=k+1;  
       fprintf(ficresf,"\n#****** ");      fprintf(ficresstdeij,"%3.0f",age );
       for(j=1;j<=cptcoveff;j++) {      for(i=1; i<=nlstate;i++){
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        eip=0.;
       }        vip=0.;
       fprintf(ficresf,"******\n");        for(j=1; j<=nlstate;j++){
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");          eip += eij[i][j][(int)age];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
       if (popforecast==1)  fprintf(ficresf," [Population]");            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]) );
       for (agedeb=fage; agedeb>=bage; agedeb--){        }
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
        if (mobilav==1) {      }
         for(j=1; j<=nlstate;j++)      fprintf(ficresstdeij,"\n");
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);  
         }      fprintf(ficrescveij,"%3.0f",age );
         else {      for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++){
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);          cptj= (j-1)*nlstate+i;
         }            for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");              cptj2= (j2-1)*nlstate+i2;
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);              if(cptj2 <= cptj)
       }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                  }
       for (cpt=1; cpt<=nforecast;cpt++) {        }
         fprintf(ficresf,"\n");      fprintf(ficrescveij,"\n");
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    }
         nhstepm = nhstepm/hstepm;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         oldm=oldms;savm=savms;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                    printf("\n");
         for (h=0; h<=nhstepm; h++){    fprintf(ficlog,"\n");
          
          if (h*hstepm/YEARM*stepm==cpt)    free_vector(xm,1,npar);
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);    free_vector(xp,1,npar);
              free_matrix(dnewm,1,nlstate*nlstate,1,npar);
              free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
          for(j=1; j<=nlstate+ndeath;j++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
            kk1=0.;kk2=0;  }
            for(i=1; i<=nlstate;i++) {          
              if (mobilav==1)  /************ Variance ******************/
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];  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[])
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];  {
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    /* Variance of health expectancies */
             }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
            if (h*hstepm/YEARM*stepm==cpt) {    /* double **newm;*/
              fprintf(ficresf," %.3f", kk1);    double **dnewm,**doldm;
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    double **dnewmp,**doldmp;
            }    int i, j, nhstepm, hstepm, h, nstepm ;
           }    int k, cptcode;
         }    double *xp;
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **gp, **gm;  /* for var eij */
            double ***gradg, ***trgradg; /*for var eij */
       }    double **gradgp, **trgradgp; /* for var p point j */
       }    double *gpp, *gmp; /* for var p point j */
     }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   }    double ***p3mat;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double age,agelim, hf;
   if (popforecast==1) {    double ***mobaverage;
     free_ivector(popage,0,AGESUP);    int theta;
     free_vector(popeffectif,0,AGESUP);    char digit[4];
     free_vector(popcount,0,AGESUP);    char digitp[25];
   }  
   free_imatrix(s,1,maxwav+1,1,n);    char fileresprobmorprev[FILENAMELENGTH];
   free_vector(weight,1,n);  
   fclose(ficresf);    if(popbased==1){
   /*---------- Health expectancies and variances ------------*/      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
   strcpy(filerest,"t");      else strcpy(digitp,"-populbased-nomobil-");
   strcat(filerest,fileres);    }
   if((ficrest=fopen(filerest,"w"))==NULL) {    else 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      strcpy(digitp,"-stablbased-");
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   strcpy(filerese,"e");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcat(filerese,fileres);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    }
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
  strcpy(fileresv,"v");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   strcat(fileresv,fileres);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    strcat(fileresprobmorprev,fileres);
   }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   k=0;    }
   for(cptcov=1;cptcov<=i1;cptcov++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   
       k=k+1;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficrest,"\n#****** ");    pstamp(ficresprobmorprev);
       for(j=1;j<=cptcoveff;j++)    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(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficrest,"******\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       fprintf(ficreseij,"\n#****** ");      for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }  
       fprintf(ficreseij,"******\n");    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
       fprintf(ficresvij,"\n#****** ");    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
       for(j=1;j<=cptcoveff;j++)    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       fprintf(ficresvij,"******\n");  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    pstamp(ficresvij);
       oldm=oldms;savm=savms;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      if(popbased==1)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      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);
       oldm=oldms;savm=savms;    else
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
          fprintf(ficresvij,"# Age");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    for(i=1; i<=nlstate;i++)
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      for(j=1; j<=nlstate;j++)
       fprintf(ficrest,"\n");        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
            fprintf(ficresvij,"\n");
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;    xp=vector(1,npar);
       epj=vector(1,nlstate+1);    dnewm=matrix(1,nlstate,1,npar);
       for(age=bage; age <=fage ;age++){    doldm=matrix(1,nlstate,1,nlstate);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         if (popbased==1) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         }    gpp=vector(nlstate+1,nlstate+ndeath);
            gmp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficrest," %.0f",age);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    if(estepm < stepm){
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      printf ("Problem %d lower than %d\n",estepm, stepm);
           }    }
           epj[nlstate+1] +=epj[j];    else  hstepm=estepm;   
         }    /* For example we decided to compute the life expectancy with the smallest unit */
         for(i=1, vepp=0.;i <=nlstate;i++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           for(j=1;j <=nlstate;j++)       nhstepm is the number of hstepm from age to agelim 
             vepp += vareij[i][j][(int)age];       nstepm is the number of stepm from age to agelin. 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));       Look at function hpijx to understand why (it is linked to memory size questions) */
         for(j=1;j <=nlstate;j++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));       survival function given by stepm (the optimization length). Unfortunately it
         }       means that if the survival funtion is printed every two years of age and if
         fprintf(ficrest,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       }       results. So we changed our mind and took the option of the best precision.
     }    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            agelim = AGESUP;
            for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  fclose(ficreseij);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fclose(ficresvij);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   fclose(ficrest);      gp=matrix(0,nhstepm,1,nlstate);
   fclose(ficpar);      gm=matrix(0,nhstepm,1,nlstate);
   free_vector(epj,1,nlstate+1);  
   /*  scanf("%d ",i); */  
       for(theta=1; theta <=npar; theta++){
   /*------- Variance limit prevalence------*/          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
 strcpy(fileresvpl,"vpl");        }
   strcat(fileresvpl,fileres);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);        if (popbased==1) {
   }          if(mobilav ==0){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
  k=0;          }else{ /* mobilav */ 
  for(cptcov=1;cptcov<=i1;cptcov++){            for(i=1; i<=nlstate;i++)
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              prlim[i][i]=mobaverage[(int)age][i][ij];
      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]]);        for(j=1; j<= nlstate; j++){
      fprintf(ficresvpl,"******\n");          for(h=0; h<=nhstepm; h++){
                  for(i=1, gp[h][j]=0.;i<=nlstate;i++)
      varpl=matrix(1,nlstate,(int) bage, (int) fage);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
      oldm=oldms;savm=savms;          }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }
    }        /* This for computing probability of death (h=1 means
  }           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   fclose(ficresvpl);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /*---------- End : free ----------------*/          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        /* end probability of death */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);   
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        if (popbased==1) {
            if(mobilav ==0){
   free_matrix(matcov,1,npar,1,npar);            for(i=1; i<=nlstate;i++)
   free_vector(delti,1,npar);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   printf("End of Imach\n");          }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        }
    
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   /*printf("Total time was %d uSec.\n", total_usecs);*/          for(h=0; h<=nhstepm; h++){
   /*------ End -----------*/            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
  end:        }
 #ifdef windows        /* This for computing probability of death (h=1 means
  chdir(pathcd);           computed over hstepm matrices product = hstepm*stepm months) 
 #endif           as a weighted average of prlim.
          */
  system("..\\gp37mgw\\wgnuplot graph.plt");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
 #ifdef windows           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   while (z[0] != 'q') {        }    
     chdir(pathcd);        /* end probability of death */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);        for(j=1; j<= nlstate; j++) /* vareij */
     if (z[0] == 'c') system("./imach");          for(h=0; h<=nhstepm; h++){
     else if (z[0] == 'e') {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       chdir(path);          }
       system(optionfilehtm);  
     }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     else if (z[0] == 'q') exit(0);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   }        }
 #endif  
 }      } /* 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 <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.18  
changed lines
  Added in v.1.143


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