Diff for /imach/src/imach.c between versions 1.7 and 1.142

version 1.7, 2001/05/02 17:50:24 version 1.142, 2014/01/26 03:57:36
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.142  2014/01/26 03:57:36  brouard
   individuals from different ages are interviewed on their health status    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   Health expectancies are computed from the transistions observed between  
   waves and are computed for each degree of severity of disability (number    Revision 1.141  2014/01/26 02:42:01  brouard
   of life states). More degrees you consider, more time is necessary to    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.140  2011/09/02 10:37:54  brouard
   the probabibility to be observed in state j at the second wave conditional    Summary: times.h is ok with mingw32 now.
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.139  2010/06/14 07:50:17  brouard
   is a covariate. If you want to have a more complex model than "constant and    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   age", you should modify the program where the markup    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.137  2010/04/29 18:11:38  brouard
   individual missed an interview, the information is not rounded or lost, but    (Module): Checking covariates for more complex models
   taken into account using an interpolation or extrapolation.    than V1+V2. A lot of change to be done. Unstable.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    Revision 1.136  2010/04/26 20:30:53  brouard
   x. The delay 'h' can be split into an exact number (nh*stepm) of    (Module): merging some libgsl code. Fixing computation
   unobserved intermediate  states. This elementary transition (by month or    of likelione (using inter/intrapolation if mle = 0) in order to
   quarter trimester, semester or year) is model as a multinomial logistic.    get same likelihood as if mle=1.
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Some cleaning of code and comments added.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.135  2009/10/29 15:33:14  brouard
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.134  2009/10/29 13:18:53  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.133  2009/07/06 10:21:25  brouard
   from the European Union.    just nforces
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.132  2009/07/06 08:22:05  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Many tings
   **********************************************************************/  
      Revision 1.131  2009/06/20 16:22:47  brouard
 #include <math.h>    Some dimensions resccaled
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.130  2009/05/26 06:44:34  brouard
 #include <unistd.h>    (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 #define MAXLINE 256    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.129  2007/08/31 13:49:27  lievre
 #define windows    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 #define NINTERVMAX 8    imach-114 because nhstepm was no more computed in the age
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    loop. Now we define nhstepma in the age loop.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): In order to speed up (in case of numerous covariates) we
 #define NCOVMAX 8 /* Maximum number of covariates */    compute health expectancies (without variances) in a first step
 #define MAXN 20000    and then all the health expectancies with variances or standard
 #define YEARM 12. /* Number of months per year */    deviation (needs data from the Hessian matrices) which slows the
 #define AGESUP 130    computation.
 #define AGEBASE 40    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   
 int nvar;    Revision 1.126  2006/04/28 17:23:28  brouard
 static int cptcov;    (Module): Yes the sum of survivors was wrong since
 int cptcovn, cptcovage=0, cptcoveff=0;    imach-114 because nhstepm was no more computed in the age
 int npar=NPARMAX;    loop. Now we define nhstepma in the age loop.
 int nlstate=2; /* Number of live states */    Version 0.98h
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 int *wav; /* Number of waves for this individuual 0 is possible */    Forecasting file added.
 int maxwav; /* Maxim number of waves */  
 int mle, weightopt;    Revision 1.124  2006/03/22 17:13:53  lievre
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Parameters are printed with %lf instead of %f (more numbers after the comma).
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    The log-likelihood is printed in the log file
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.123  2006/03/20 10:52:43  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    * imach.c (Module): <title> changed, corresponds to .htm file
 FILE *ficgp, *fichtm;    name. <head> headers where missing.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    * imach.c (Module): Weights can have a decimal point as for
  FILE  *ficresvij;    English (a comma might work with a correct LC_NUMERIC environment,
   char fileresv[FILENAMELENGTH];    otherwise the weight is truncated).
  FILE  *ficresvpl;    Modification of warning when the covariates values are not 0 or
   char fileresvpl[FILENAMELENGTH];    1.
     Version 0.98g
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.122  2006/03/20 09:45:41  brouard
 #define FTOL 1.0e-10    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define NRANSI    otherwise the weight is truncated).
 #define ITMAX 200    Modification of warning when the covariates values are not 0 or
     1.
 #define TOL 2.0e-4    Version 0.98g
   
 #define CGOLD 0.3819660    Revision 1.121  2006/03/16 17:45:01  lievre
 #define ZEPS 1.0e-10    * imach.c (Module): Comments concerning covariates added
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     * imach.c (Module): refinements in the computation of lli if
 #define GOLD 1.618034    status=-2 in order to have more reliable computation if stepm is
 #define GLIMIT 100.0    not 1 month. Version 0.98f
 #define TINY 1.0e-20  
     Revision 1.120  2006/03/16 15:10:38  lievre
 static double maxarg1,maxarg2;    (Module): refinements in the computation of lli if
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    status=-2 in order to have more reliable computation if stepm is
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    not 1 month. Version 0.98f
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.119  2006/03/15 17:42:26  brouard
 #define rint(a) floor(a+0.5)    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.118  2006/03/14 18:20:07  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 int imx;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int stepm;    (Module): Function pstamp added
 /* Stepm, step in month: minimum step interpolation*/    (Module): Version 0.98d
   
 int m,nb;    Revision 1.117  2006/03/14 17:16:22  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): varevsij Comments added explaining the second
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    table of variances if popbased=1 .
 double **pmmij;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 double *weight;    (Module): Version 0.98d
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.116  2006/03/06 10:29:27  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    Revision 1.114  2006/02/26 12:57:58  brouard
 {    (Module): Some improvements in processing parameter
    char *s;                             /* pointer */    filename with strsep.
    int  l1, l2;                         /* length counters */  
     Revision 1.113  2006/02/24 14:20:24  brouard
    l1 = strlen( path );                 /* length of path */    (Module): Memory leaks checks with valgrind and:
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    datafile was not closed, some imatrix were not freed and on matrix
    s = strrchr( path, '\\' );           /* find last / */    allocation too.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.112  2006/01/30 09:55:26  brouard
       extern char       *getwd( );    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.111  2006/01/25 20:38:18  brouard
 #else    (Module): Lots of cleaning and bugs added (Gompertz)
       extern char       *getcwd( );    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.110  2006/01/25 00:51:50  brouard
          return( GLOCK_ERROR_GETCWD );    (Module): Lots of cleaning and bugs added (Gompertz)
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.109  2006/01/24 19:37:15  brouard
    } else {                             /* strip direcotry from path */    (Module): Comments (lines starting with a #) are allowed in data.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.108  2006/01/19 18:05:42  lievre
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Gnuplot problem appeared...
       strcpy( name, s );                /* save file name */    To be fixed
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.107  2006/01/19 16:20:37  brouard
    }    Test existence of gnuplot in imach path
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.106  2006/01/19 13:24:36  brouard
    return( 0 );                         /* we're done */    Some cleaning and links added in html output
 }  
     Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 /******************************************/  
     Revision 1.104  2005/09/30 16:11:43  lievre
 void replace(char *s, char*t)    (Module): sump fixed, loop imx fixed, and simplifications.
 {    (Module): If the status is missing at the last wave but we know
   int i;    that the person is alive, then we can code his/her status as -2
   int lg=20;    (instead of missing=-1 in earlier versions) and his/her
   i=0;    contributions to the likelihood is 1 - Prob of dying from last
   lg=strlen(t);    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   for(i=0; i<= lg; i++) {    the healthy state at last known wave). Version is 0.98
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.103  2005/09/30 15:54:49  lievre
   }    (Module): sump fixed, loop imx fixed, and simplifications.
 }  
     Revision 1.102  2004/09/15 17:31:30  brouard
 int nbocc(char *s, char occ)    Add the possibility to read data file including tab characters.
 {  
   int i,j=0;    Revision 1.101  2004/09/15 10:38:38  brouard
   int lg=20;    Fix on curr_time
   i=0;  
   lg=strlen(s);    Revision 1.100  2004/07/12 18:29:06  brouard
   for(i=0; i<= lg; i++) {    Add version for Mac OS X. Just define UNIX in Makefile
   if  (s[i] == occ ) j++;  
   }    Revision 1.99  2004/06/05 08:57:40  brouard
   return j;    *** empty log message ***
 }  
     Revision 1.98  2004/05/16 15:05:56  brouard
 void cutv(char *u,char *v, char*t, char occ)    New version 0.97 . First attempt to estimate force of mortality
 {    directly from the data i.e. without the need of knowing the health
   int i,lg,j,p=0;    state at each age, but using a Gompertz model: log u =a + b*age .
   i=0;    This is the basic analysis of mortality and should be done before any
   for(j=0; j<=strlen(t)-1; j++) {    other analysis, in order to test if the mortality estimated from the
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    cross-longitudinal survey is different from the mortality estimated
   }    from other sources like vital statistic data.
   
   lg=strlen(t);    The same imach parameter file can be used but the option for mle should be -3.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Agnès, who wrote this part of the code, tried to keep most of the
   }    former routines in order to include the new code within the former code.
      u[p]='\0';  
     The output is very simple: only an estimate of the intercept and of
    for(j=0; j<= lg; j++) {    the slope with 95% confident intervals.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Current limitations:
 }    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.
 /********************** nrerror ********************/    B) There is no computation of Life Expectancy nor Life Table.
   
 void nrerror(char error_text[])    Revision 1.97  2004/02/20 13:25:42  lievre
 {    Version 0.96d. Population forecasting command line is (temporarily)
   fprintf(stderr,"ERREUR ...\n");    suppressed.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.96  2003/07/15 15:38:55  brouard
 }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 /*********************** vector *******************/    rewritten within the same printf. Workaround: many printfs.
 double *vector(int nl, int nh)  
 {    Revision 1.95  2003/07/08 07:54:34  brouard
   double *v;    * imach.c (Repository):
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Repository): Using imachwizard code to output a more meaningful covariance
   if (!v) nrerror("allocation failure in vector");    matrix (cov(a12,c31) instead of numbers.
   return v-nl+NR_END;  
 }    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.93  2003/06/25 16:33:55  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   free((FREE_ARG)(v+nl-NR_END));    exist so I changed back to asctime which exists.
 }    (Module): Version 0.96b
   
 /************************ivector *******************************/    Revision 1.92  2003/06/25 16:30:45  brouard
 int *ivector(long nl,long nh)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.91  2003/06/25 15:30:29  brouard
   if (!v) nrerror("allocation failure in ivector");    * imach.c (Repository): Duplicated warning errors corrected.
   return v-nl+NR_END;    (Repository): Elapsed time after each iteration is now output. It
 }    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 /******************free ivector **************************/    concerning matrix of covariance. It has extension -cov.htm.
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.90  2003/06/24 12:34:15  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.89  2003/06/24 12:30:52  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    of the covariance matrix to be input.
   int **m;  
      Revision 1.88  2003/06/23 17:54:56  brouard
   /* allocate pointers to rows */    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.87  2003/06/18 12:26:01  brouard
   m += NR_END;    Version 0.96
   m -= nrl;  
      Revision 1.86  2003/06/17 20:04:08  brouard
      (Module): Change position of html and gnuplot routines and added
   /* allocate rows and set pointers to them */    routine fileappend.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.85  2003/06/17 13:12:43  brouard
   m[nrl] += NR_END;    * imach.c (Repository): Check when date of death was earlier that
   m[nrl] -= ncl;    current date of interview. It may happen when the death was just
      prior to the death. In this case, dh was negative and likelihood
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    was wrong (infinity). We still send an "Error" but patch by
      assuming that the date of death was just one stepm after the
   /* return pointer to array of pointers to rows */    interview.
   return m;    (Repository): Because some people have very long ID (first column)
 }    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 /****************** free_imatrix *************************/    truncation)
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Repository): No more line truncation errors.
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.84  2003/06/13 21:44:43  brouard
      /* free an int matrix allocated by imatrix() */    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    many times. Probs is memory consuming and must be used with
   free((FREE_ARG) (m+nrl-NR_END));    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /******************* matrix *******************************/    Revision 1.83  2003/06/10 13:39:11  lievre
 double **matrix(long nrl, long nrh, long ncl, long nch)    *** empty log message ***
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.82  2003/06/05 15:57:20  brouard
   double **m;    Add log in  imach.c and  fullversion number is now printed.
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  */
   if (!m) nrerror("allocation failure 1 in matrix()");  /*
   m += NR_END;     Interpolated Markov Chain
   m -= nrl;  
     Short summary of the programme:
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    This program computes Healthy Life Expectancies from
   m[nrl] += NR_END;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m[nrl] -= ncl;    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    case of a health survey which is our main interest) -2- at least a
   return m;    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 /*************************free matrix ************************/    model. More health states you consider, more time is necessary to reach the
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Maximum Likelihood of the parameters involved in the model.  The
 {    simplest model is the multinomial logistic model where pij is the
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    probability to be observed in state j at the second wave
   free((FREE_ARG)(m+nrl-NR_END));    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
     'age' is age and 'sex' is a covariate. If you want to have a more
 /******************* ma3x *******************************/    complex model than "constant and age", you should modify the program
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    where the markup *Covariates have to be included here again* invites
 {    you to do it.  More covariates you add, slower the
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    convergence.
   double ***m;  
     The advantage of this computer programme, compared to a simple
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    multinomial logistic model, is clear when the delay between waves is not
   if (!m) nrerror("allocation failure 1 in matrix()");    identical for each individual. Also, if a individual missed an
   m += NR_END;    intermediate interview, the information is lost, but taken into
   m -= nrl;    account using an interpolation or extrapolation.  
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    hPijx is the probability to be observed in state i at age x+h
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    conditional to the observed state i at age x. The delay 'h' can be
   m[nrl] += NR_END;    split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl] -= ncl;    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    hPijx.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Also this programme outputs the covariance matrix of the parameters but also
   m[nrl][ncl] -= nll;    of the life expectancies. It also computes the period (stable) prevalence. 
   for (j=ncl+1; j<=nch; j++)    
     m[nrl][j]=m[nrl][j-1]+nlay;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
   for (i=nrl+1; i<=nrh; i++) {    This software have been partly granted by Euro-REVES, a concerted action
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    from the European Union.
     for (j=ncl+1; j<=nch; j++)    It is copyrighted identically to a GNU software product, ie programme and
       m[i][j]=m[i][j-1]+nlay;    software can be distributed freely for non commercial use. Latest version
   }    can be accessed at http://euroreves.ined.fr/imach .
   return m;  
 }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 /*************************free ma3x ************************/    
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    **********************************************************************/
 {  /*
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    main
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    read parameterfile
   free((FREE_ARG)(m+nrl-NR_END));    read datafile
 }    concatwav
     freqsummary
 /***************** f1dim *************************/    if (mle >= 1)
 extern int ncom;      mlikeli
 extern double *pcom,*xicom;    print results files
 extern double (*nrfunc)(double []);    if mle==1 
         computes hessian
 double f1dim(double x)    read end of parameter file: agemin, agemax, bage, fage, estepm
 {        begin-prev-date,...
   int j;    open gnuplot file
   double f;    open html file
   double *xt;    period (stable) prevalence
       for age prevalim()
   xt=vector(1,ncom);    h Pij x
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    variance of p varprob
   f=(*nrfunc)(xt);    forecasting if prevfcast==1 prevforecast call prevalence()
   free_vector(xt,1,ncom);    health expectancies
   return f;    Variance-covariance of DFLE
 }    prevalence()
      movingaverage()
 /*****************brent *************************/    varevsij() 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if popbased==1 varevsij(,popbased)
 {    total life expectancies
   int iter;    Variance of period (stable) prevalence
   double a,b,d,etemp;   end
   double fu,fv,fw,fx;  */
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  
     
   a=(ax < cx ? ax : cx);  #include <math.h>
   b=(ax > cx ? ax : cx);  #include <stdio.h>
   x=w=v=bx;  #include <stdlib.h>
   fw=fv=fx=(*f)(x);  #include <string.h>
   for (iter=1;iter<=ITMAX;iter++) {  #include <unistd.h>
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #include <limits.h>
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #include <sys/types.h>
     printf(".");fflush(stdout);  #include <sys/stat.h>
 #ifdef DEBUG  #include <errno.h>
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  extern int errno;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  #ifdef LINUX
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #include <time.h>
       *xmin=x;  #include "timeval.h"
       return fx;  #else
     }  #include <sys/time.h>
     ftemp=fu;  #endif
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  #ifdef GSL
       q=(x-v)*(fx-fw);  #include <gsl/gsl_errno.h>
       p=(x-v)*q-(x-w)*r;  #include <gsl/gsl_multimin.h>
       q=2.0*(q-r);  #endif
       if (q > 0.0) p = -p;  
       q=fabs(q);  /* #include <libintl.h> */
       etemp=e;  /* #define _(String) gettext (String) */
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  #define GNUPLOTPROGRAM "gnuplot"
         d=p/q;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         u=x+d;  #define FILENAMELENGTH 132
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
     }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  #define NINTERVMAX 8
     if (fu <= fx) {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       if (u >= x) a=x; else b=x;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       SHFT(v,w,x,u)  #define NCOVMAX 20 /* Maximum number of covariates */
         SHFT(fv,fw,fx,fu)  #define MAXN 20000
         } else {  #define YEARM 12. /* Number of months per year */
           if (u < x) a=u; else b=u;  #define AGESUP 130
           if (fu <= fw || w == x) {  #define AGEBASE 40
             v=w;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
             w=u;  #ifdef UNIX
             fv=fw;  #define DIRSEPARATOR '/'
             fw=fu;  #define CHARSEPARATOR "/"
           } else if (fu <= fv || v == x || v == w) {  #define ODIRSEPARATOR '\\'
             v=u;  #else
             fv=fu;  #define DIRSEPARATOR '\\'
           }  #define CHARSEPARATOR "\\"
         }  #define ODIRSEPARATOR '/'
   }  #endif
   nrerror("Too many iterations in brent");  
   *xmin=x;  /* $Id$ */
   return fx;  /* $State$ */
 }  
   char version[]="Imach version 0.98nR, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 /****************** mnbrak ***********************/  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
             double (*func)(double))  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar=0, nforce=0; /* Number of variables, number of forces */
   double ulim,u,r,q, dum;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   double fu;  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
   *fa=(*func)(*ax);  int ndeath=1; /* Number of dead states */
   *fb=(*func)(*bx);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   if (*fb > *fa) {  int popbased=0;
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  int *wav; /* Number of waves for this individuual 0 is possible */
       }  int maxwav=0; /* Maxim number of waves */
   *cx=(*bx)+GOLD*(*bx-*ax);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   *fc=(*func)(*cx);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   while (*fb > *fc) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     r=(*bx-*ax)*(*fb-*fc);                     to the likelihood and the sum of weights (done by funcone)*/
     q=(*bx-*cx)*(*fb-*fa);  int mle=1, weightopt=0;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     if ((*bx-u)*(u-*cx) > 0.0) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       fu=(*func)(u);  double jmean=1; /* Mean space between 2 waves */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
       fu=(*func)(u);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       if (fu < *fc) {  /*FILE *fic ; */ /* Used in readdata only */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
           SHFT(*fb,*fc,fu,(*func)(u))  FILE *ficlog, *ficrespow;
           }  int globpr=0; /* Global variable for printing or not */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double fretone; /* Only one call to likelihood */
       u=ulim;  long ipmx=0; /* Number of contributions */
       fu=(*func)(u);  double sw; /* Sum of weights */
     } else {  char filerespow[FILENAMELENGTH];
       u=(*cx)+GOLD*(*cx-*bx);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       fu=(*func)(u);  FILE *ficresilk;
     }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     SHFT(*ax,*bx,*cx,u)  FILE *ficresprobmorprev;
       SHFT(*fa,*fb,*fc,fu)  FILE *fichtm, *fichtmcov; /* Html File */
       }  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
 /*************** linmin ************************/  char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
 int ncom;  char filerescve[FILENAMELENGTH];
 double *pcom,*xicom;  FILE  *ficresvij;
 double (*nrfunc)(double []);  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
   double brent(double ax, double bx, double cx,  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
                double (*f)(double), double tol, double *xmin);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double f1dim(double x);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  char command[FILENAMELENGTH];
               double *fc, double (*func)(double));  int  outcmd=0;
   int j;  
   double xx,xmin,bx,ax;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   double fx,fb,fa;  
    char filelog[FILENAMELENGTH]; /* Log file */
   ncom=n;  char filerest[FILENAMELENGTH];
   pcom=vector(1,n);  char fileregp[FILENAMELENGTH];
   xicom=vector(1,n);  char popfile[FILENAMELENGTH];
   nrfunc=func;  
   for (j=1;j<=n;j++) {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     pcom[j]=p[j];  
     xicom[j]=xi[j];  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   }  struct timezone tzp;
   ax=0.0;  extern int gettimeofday();
   xx=1.0;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  long time_value;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  extern long time();
 #ifdef DEBUG  char strcurr[80], strfor[80];
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  char *endptr;
   for (j=1;j<=n;j++) {  long lval;
     xi[j] *= xmin;  double dval;
     p[j] += xi[j];  
   }  #define NR_END 1
   free_vector(xicom,1,n);  #define FREE_ARG char*
   free_vector(pcom,1,n);  #define FTOL 1.0e-10
 }  
   #define NRANSI 
 /*************** powell ************************/  #define ITMAX 200 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  #define TOL 2.0e-4 
 {  
   void linmin(double p[], double xi[], int n, double *fret,  #define CGOLD 0.3819660 
               double (*func)(double []));  #define ZEPS 1.0e-10 
   int i,ibig,j;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  #define GOLD 1.618034 
   double *xits;  #define GLIMIT 100.0 
   pt=vector(1,n);  #define TINY 1.0e-20 
   ptt=vector(1,n);  
   xit=vector(1,n);  static double maxarg1,maxarg2;
   xits=vector(1,n);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   *fret=(*func)(p);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for (j=1;j<=n;j++) pt[j]=p[j];    
   for (*iter=1;;++(*iter)) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     fp=(*fret);  #define rint(a) floor(a+0.5)
     ibig=0;  
     del=0.0;  static double sqrarg;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     for (i=1;i<=n;i++)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       printf(" %d %.12f",i, p[i]);  int agegomp= AGEGOMP;
     printf("\n");  
     for (i=1;i<=n;i++) {  int imx; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int stepm=1;
       fptt=(*fret);  /* Stepm, step in month: minimum step interpolation*/
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  int estepm;
 #endif  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  int m,nb;
       if (fabs(fptt-(*fret)) > del) {  long *num;
         del=fabs(fptt-(*fret));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         ibig=i;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       }  double **pmmij, ***probs;
 #ifdef DEBUG  double *ageexmed,*agecens;
       printf("%d %.12e",i,(*fret));  double dateintmean=0;
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  double *weight;
         printf(" x(%d)=%.12e",j,xit[j]);  int **s; /* Status */
       }  double *agedc;
       for(j=1;j<=n;j++)  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
         printf(" p=%.12e",p[j]);                    * covar=matrix(0,NCOVMAX,1,n); 
       printf("\n");                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
 #endif  double  idx; 
     }  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  int **codtab; /**< codtab=imatrix(1,100,1,10); */
 #ifdef DEBUG  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       int k[2],l;  double *lsurv, *lpop, *tpop;
       k[0]=1;  
       k[1]=-1;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       printf("Max: %.12e",(*func)(p));  double ftolhess; /* Tolerance for computing hessian */
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /**************** split *************************/
       printf("\n");  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       for(l=0;l<=1;l++) {  {
         for (j=1;j<=n;j++) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];       the name of the file (name), its extension only (ext) and its first part of the name (finame)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    */ 
         }    char  *ss;                            /* pointer */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    int   l1, l2;                         /* length counters */
       }  
 #endif    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       free_vector(xit,1,n);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       free_vector(xits,1,n);      strcpy( name, path );               /* we got the fullname name because no directory */
       free_vector(ptt,1,n);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       free_vector(pt,1,n);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       return;      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     for (j=1;j<=n;j++) {        return( GLOCK_ERROR_GETCWD );
       ptt[j]=2.0*p[j]-pt[j];      }
       xit[j]=p[j]-pt[j];      /* got dirc from getcwd*/
       pt[j]=p[j];      printf(" DIRC = %s \n",dirc);
     }    } else {                              /* strip direcotry from path */
     fptt=(*func)(ptt);      ss++;                               /* after this, the filename */
     if (fptt < fp) {      l2 = strlen( ss );                  /* length of filename */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       if (t < 0.0) {      strcpy( name, ss );         /* save file name */
         linmin(p,xit,n,fret,func);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         for (j=1;j<=n;j++) {      dirc[l1-l2] = 0;                    /* add zero */
           xi[j][ibig]=xi[j][n];      printf(" DIRC2 = %s \n",dirc);
           xi[j][n]=xit[j];    }
         }    /* We add a separator at the end of dirc if not exists */
 #ifdef DEBUG    l1 = strlen( dirc );                  /* length of directory */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    if( dirc[l1-1] != DIRSEPARATOR ){
         for(j=1;j<=n;j++)      dirc[l1] =  DIRSEPARATOR;
           printf(" %.12e",xit[j]);      dirc[l1+1] = 0; 
         printf("\n");      printf(" DIRC3 = %s \n",dirc);
 #endif    }
       }    ss = strrchr( name, '.' );            /* find last / */
     }    if (ss >0){
   }      ss++;
 }      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 /**** Prevalence limit ****************/      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      finame[l1-l2]= 0;
 {    }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */    return( 0 );                          /* we're done */
   }
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  /******************************************/
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  void replace_back_to_slash(char *s, char*t)
   double agefin, delaymax=50 ; /* Max number of years to converge */  {
     int i;
   for (ii=1;ii<=nlstate+ndeath;ii++)    int lg=0;
     for (j=1;j<=nlstate+ndeath;j++){    i=0;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    lg=strlen(t);
     }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
    cov[1]=1.;      if (t[i]== '\\') s[i]='/';
      }
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  char *trimbb(char *out, char *in)
     /* Covariates have to be included here again */  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
      cov[2]=agefin;    char *s;
      s=out;
       for (k=1; k<=cptcovn;k++) {    while (*in != '\0'){
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        in++;
       }      }
       for (k=1; k<=cptcovage;k++)      *out++ = *in++;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    }
       for (k=1; k<=cptcovprod;k++)    *out='\0';
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    return s;
   }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
   char *cutv(char *blocc, char *alocc, char *in, char occ)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  {
     /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
     savm=oldm;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     oldm=newm;    */
     maxmax=0.;    char *s, *t;
     for(j=1;j<=nlstate;j++){    t=in;s=in;
       min=1.;    while (*in != '\0'){
       max=0.;      while( *in == occ){
       for(i=1; i<=nlstate; i++) {        *blocc++ = *in++;
         sumnew=0;        s=in;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      }
         prlim[i][j]= newm[i][j]/(1-sumnew);      *blocc++ = *in++;
         max=FMAX(max,prlim[i][j]);    }
         min=FMIN(min,prlim[i][j]);    if (s == t) /* occ not found */
       }      *(blocc-(in-s))='\0';
       maxmin=max-min;    else
       maxmax=FMAX(maxmax,maxmin);      *(blocc-(in-s)-1)='\0';
     }    in=s;
     if(maxmax < ftolpl){    while ( *in != '\0'){
       return prlim;      *alocc++ = *in++;
     }    }
   }  
 }    *alocc='\0';
     return s;
 /*************** transition probabilities **********/  }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  int nbocc(char *s, char occ)
 {  {
   double s1, s2;    int i,j=0;
   /*double t34;*/    int lg=20;
   int i,j,j1, nc, ii, jj;    i=0;
     lg=strlen(s);
     for(i=1; i<= nlstate; i++){    for(i=0; i<= lg; i++) {
     for(j=1; j<i;j++){    if  (s[i] == occ ) j++;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    }
         /*s2 += param[i][j][nc]*cov[nc];*/    return j;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /* void cutv(char *u,char *v, char*t, char occ) */
       ps[i][j]=s2;  /* { */
       /*printf("s1=%.17e, s2=%.17e\n",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') */
     for(j=i+1; j<=nlstate+ndeath;j++){  /*      gives u="abcdef2ghi" and v="j" *\/ */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*   int i,lg,j,p=0; */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*   i=0; */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /*   lg=strlen(t); */
       }  /*   for(j=0; j<=lg-1; j++) { */
       ps[i][j]=s2;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     }  /*   } */
   }  
   for(i=1; i<= nlstate; i++){  /*   for(j=0; j<p; j++) { */
      s1=0;  /*     (u[j] = t[j]); */
     for(j=1; j<i; j++)  /*   } */
       s1+=exp(ps[i][j]);  /*      u[p]='\0'; */
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);  /*    for(j=0; j<= lg; j++) { */
     ps[i][i]=1./(s1+1.);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     for(j=1; j<i; j++)  /*   } */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* } */
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /********************** nrerror ********************/
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  void nrerror(char error_text[])
   {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    fprintf(stderr,"ERREUR ...\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){    fprintf(stderr,"%s\n",error_text);
       ps[ii][jj]=0;    exit(EXIT_FAILURE);
       ps[ii][ii]=1;  }
     }  /*********************** vector *******************/
   }  double *vector(int nl, int nh)
   {
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double *v;
     for(jj=1; jj<= nlstate+ndeath; jj++){    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      printf("%lf ",ps[ii][jj]);    if (!v) nrerror("allocation failure in vector");
    }    return v-nl+NR_END;
     printf("\n ");  }
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /************************ free vector ******************/
 /*  void free_vector(double*v, int nl, int nh)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  {
   goto end;*/    free((FREE_ARG)(v+nl-NR_END));
     return ps;  }
 }  
   /************************ivector *******************************/
 /**************** Product of 2 matrices ******************/  int *ivector(long nl,long nh)
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    int *v;
 {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    if (!v) nrerror("allocation failure in ivector");
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    return v-nl+NR_END;
   /* in, b, out are matrice of pointers which should have been initialized  }
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  /******************free ivector **************************/
   long i, j, k;  void free_ivector(int *v, long nl, long nh)
   for(i=nrl; i<= nrh; i++)  {
     for(k=ncolol; k<=ncoloh; k++)    free((FREE_ARG)(v+nl-NR_END));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  }
         out[i][k] +=in[i][j]*b[j][k];  
   /************************lvector *******************************/
   return out;  long *lvector(long nl,long nh)
 }  {
     long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 /************* Higher Matrix Product ***************/    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  }
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /******************free lvector **************************/
      duration (i.e. until  void free_lvector(long *v, long nl, long nh)
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    free((FREE_ARG)(v+nl-NR_END));
      (typically every 2 years instead of every month which is too big).  }
      Model is determined by parameters x and covariates have to be  
      included manually here.  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
      */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
   int i, j, d, h, k;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double **out, cov[NCOVMAX];    int **m; 
   double **newm;    
     /* allocate pointers to rows */ 
   /* Hstepm could be zero and should return the unit matrix */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for (i=1;i<=nlstate+ndeath;i++)    if (!m) nrerror("allocation failure 1 in matrix()"); 
     for (j=1;j<=nlstate+ndeath;j++){    m += NR_END; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    m -= nrl; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    
     }    
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* allocate rows and set pointers to them */ 
   for(h=1; h <=nhstepm; h++){    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for(d=1; d <=hstepm; d++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       newm=savm;    m[nrl] += NR_END; 
       /* Covariates have to be included here again */    m[nrl] -= ncl; 
       cov[1]=1.;    
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    
 for (k=1; k<=cptcovage;k++)    /* return pointer to array of pointers to rows */ 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return m; 
    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]]];  
   /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        int **m;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        long nch,ncl,nrh,nrl; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,       /* free an int matrix allocated by imatrix() */ 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  { 
       savm=oldm;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       oldm=newm;    free((FREE_ARG) (m+nrl-NR_END)); 
     }  } 
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  /******************* matrix *******************************/
         po[i][j][h]=newm[i][j];  double **matrix(long nrl, long nrh, long ncl, long nch)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       }    double **m;
   } /* end h */  
   return po;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
     m -= nrl;
 /*************** log-likelihood *************/  
 double func( double *x)    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int i, ii, j, k, mi, d, kk;    m[nrl] += NR_END;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    m[nrl] -= ncl;
   double **out;  
   double sw; /* Sum of weights */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double lli; /* Individual log likelihood */    return m;
   long ipmx;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   /*extern weight */     */
   /* We are differentiating ll according to initial status */  }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /*************************free matrix ************************/
 printf(" %d\n",s[4][i]);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   */  {
   cov[1]=1.;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   for(k=1; k<=nlstate; k++) ll[k]=0.;  }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /******************* ma3x *******************************/
        for(mi=1; mi<= wav[i]-1; mi++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       for (ii=1;ii<=nlstate+ndeath;ii++)  {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
             for(d=0; d<dh[mi][i]; d++){    double ***m;
               newm=savm;  
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
               for (kk=1; kk<=cptcovage;kk++) {    if (!m) nrerror("allocation failure 1 in matrix()");
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    m += NR_END;
                  /*printf("%d %d",kk,Tage[kk]);*/    m -= nrl;
               }  
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
               /*cov[3]=pow(cov[2],2)/1000.;*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    m[nrl] -= ncl;
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
           savm=oldm;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           oldm=newm;  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       } /* end mult */    m[nrl][ncl] += NR_END;
        m[nrl][ncl] -= nll;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    for (j=ncl+1; j<=nch; j++) 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      m[nrl][j]=m[nrl][j-1]+nlay;
       ipmx +=1;    
       sw += weight[i];    for (i=nrl+1; i<=nrh; i++) {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     } /* end of wave */      for (j=ncl+1; j<=nch; j++) 
   } /* end of individual */        m[i][j]=m[i][j-1]+nlay;
     }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    return m; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   return -l;    */
 }  }
   
   /*************************free ma3x ************************/
 /*********** Maximum Likelihood Estimation ***************/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int i,j, iter;    free((FREE_ARG)(m+nrl-NR_END));
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /*************** function subdirf ***********/
   for (i=1;i<=npar;i++)  char *subdirf(char fileres[])
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    /* Caution optionfilefiname is hidden */
   printf("Powell\n");    strcpy(tmpout,optionfilefiname);
   powell(p,xi,npar,ftol,&iter,&fret,func);    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    return tmpout;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  }
   
 }  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
 /**** Computes Hessian and covariance matrix ***/  {
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    
 {    /* Caution optionfilefiname is hidden */
   double  **a,**y,*x,pd;    strcpy(tmpout,optionfilefiname);
   double **hess;    strcat(tmpout,"/");
   int i, j,jk;    strcat(tmpout,preop);
   int *indx;    strcat(tmpout,fileres);
     return tmpout;
   double hessii(double p[], double delta, int theta, double delti[]);  }
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /*************** function subdirf3 ***********/
   void ludcmp(double **a, int npar, int *indx, double *d) ;  char *subdirf3(char fileres[], char *preop, char *preop2)
   {
     
   hess=matrix(1,npar,1,npar);    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   printf("\nCalculation of the hessian matrix. Wait...\n");    strcat(tmpout,"/");
   for (i=1;i<=npar;i++){    strcat(tmpout,preop);
     printf("%d",i);fflush(stdout);    strcat(tmpout,preop2);
     hess[i][i]=hessii(p,ftolhess,i,delti);    strcat(tmpout,fileres);
     /*printf(" %f ",p[i]);*/    return tmpout;
   }  }
   
   for (i=1;i<=npar;i++) {  /***************** f1dim *************************/
     for (j=1;j<=npar;j++)  {  extern int ncom; 
       if (j>i) {  extern double *pcom,*xicom;
         printf(".%d%d",i,j);fflush(stdout);  extern double (*nrfunc)(double []); 
         hess[i][j]=hessij(p,delti,i,j);   
         hess[j][i]=hess[i][j];  double f1dim(double x) 
       }  { 
     }    int j; 
   }    double f;
   printf("\n");    double *xt; 
    
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    xt=vector(1,ncom); 
      for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   a=matrix(1,npar,1,npar);    f=(*nrfunc)(xt); 
   y=matrix(1,npar,1,npar);    free_vector(xt,1,ncom); 
   x=vector(1,npar);    return f; 
   indx=ivector(1,npar);  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*****************brent *************************/
   ludcmp(a,npar,indx,&pd);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
   for (j=1;j<=npar;j++) {    int iter; 
     for (i=1;i<=npar;i++) x[i]=0;    double a,b,d,etemp;
     x[j]=1;    double fu,fv,fw,fx;
     lubksb(a,npar,indx,x);    double ftemp;
     for (i=1;i<=npar;i++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       matcov[i][j]=x[i];    double e=0.0; 
     }   
   }    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
   printf("\n#Hessian matrix#\n");    x=w=v=bx; 
   for (i=1;i<=npar;i++) {    fw=fv=fx=(*f)(x); 
     for (j=1;j<=npar;j++) {    for (iter=1;iter<=ITMAX;iter++) { 
       printf("%.3e ",hess[i][j]);      xm=0.5*(a+b); 
     }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     printf("\n");      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   /* Recompute Inverse */  #ifdef DEBUG
   for (i=1;i<=npar;i++)      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      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);
   ludcmp(a,npar,indx,&pd);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
   /*  printf("\n#Hessian matrix recomputed#\n");      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
   for (j=1;j<=npar;j++) {        return fx; 
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      ftemp=fu;
     lubksb(a,npar,indx,x);      if (fabs(e) > tol1) { 
     for (i=1;i<=npar;i++){        r=(x-w)*(fx-fv); 
       y[i][j]=x[i];        q=(x-v)*(fx-fw); 
       printf("%.3e ",y[i][j]);        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     printf("\n");        if (q > 0.0) p = -p; 
   }        q=fabs(q); 
   */        etemp=e; 
         e=d; 
   free_matrix(a,1,npar,1,npar);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   free_matrix(y,1,npar,1,npar);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   free_vector(x,1,npar);        else { 
   free_ivector(indx,1,npar);          d=p/q; 
   free_matrix(hess,1,npar,1,npar);          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 }        } 
       } else { 
 /*************** hessian matrix ****************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 double hessii( double x[], double delta, int theta, double delti[])      } 
 {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   int i;      fu=(*f)(u); 
   int l=1, lmax=20;      if (fu <= fx) { 
   double k1,k2;        if (u >= x) a=x; else b=x; 
   double p2[NPARMAX+1];        SHFT(v,w,x,u) 
   double res;          SHFT(fv,fw,fx,fu) 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          } else { 
   double fx;            if (u < x) a=u; else b=u; 
   int k=0,kmax=10;            if (fu <= fw || w == x) { 
   double l1;              v=w; 
               w=u; 
   fx=func(x);              fv=fw; 
   for (i=1;i<=npar;i++) p2[i]=x[i];              fw=fu; 
   for(l=0 ; l <=lmax; l++){            } else if (fu <= fv || v == x || v == w) { 
     l1=pow(10,l);              v=u; 
     delts=delt;              fv=fu; 
     for(k=1 ; k <kmax; k=k+1){            } 
       delt = delta*(l1*k);          } 
       p2[theta]=x[theta] +delt;    } 
       k1=func(p2)-fx;    nrerror("Too many iterations in brent"); 
       p2[theta]=x[theta]-delt;    *xmin=x; 
       k2=func(p2)-fx;    return fx; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */  } 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
        /****************** mnbrak ***********************/
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 #endif              double (*func)(double)) 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  { 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    double ulim,u,r,q, dum;
         k=kmax;    double fu; 
       }   
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    *fa=(*func)(*ax); 
         k=kmax; l=lmax*10.;    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      SHFT(dum,*ax,*bx,dum) 
         delts=delt;        SHFT(dum,*fb,*fa,dum) 
       }        } 
     }    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
   delti[theta]=delts;    while (*fb > *fc) { 
   return res;      r=(*bx-*ax)*(*fb-*fc); 
        q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 double hessij( double x[], double delti[], int thetai,int thetaj)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 {      if ((*bx-u)*(u-*cx) > 0.0) { 
   int i;        fu=(*func)(u); 
   int l=1, l1, lmax=20;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double k1,k2,k3,k4,res,fx;        fu=(*func)(u); 
   double p2[NPARMAX+1];        if (fu < *fc) { 
   int k;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
   fx=func(x);            } 
   for (k=1; k<=2; k++) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for (i=1;i<=npar;i++) p2[i]=x[i];        u=ulim; 
     p2[thetai]=x[thetai]+delti[thetai]/k;        fu=(*func)(u); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } else { 
     k1=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) 
     k2=func(p2)-fx;        SHFT(*fa,*fb,*fc,fu) 
          } 
     p2[thetai]=x[thetai]-delti[thetai]/k;  } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  /*************** linmin ************************/
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  int ncom; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  double *pcom,*xicom;
     k4=func(p2)-fx;  double (*nrfunc)(double []); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */   
 #ifdef DEBUG  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  { 
 #endif    double brent(double ax, double bx, double cx, 
   }                 double (*f)(double), double tol, double *xmin); 
   return res;    double f1dim(double x); 
 }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
 /************** Inverse of matrix **************/    int j; 
 void ludcmp(double **a, int n, int *indx, double *d)    double xx,xmin,bx,ax; 
 {    double fx,fb,fa;
   int i,imax,j,k;   
   double big,dum,sum,temp;    ncom=n; 
   double *vv;    pcom=vector(1,n); 
      xicom=vector(1,n); 
   vv=vector(1,n);    nrfunc=func; 
   *d=1.0;    for (j=1;j<=n;j++) { 
   for (i=1;i<=n;i++) {      pcom[j]=p[j]; 
     big=0.0;      xicom[j]=xi[j]; 
     for (j=1;j<=n;j++)    } 
       if ((temp=fabs(a[i][j])) > big) big=temp;    ax=0.0; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    xx=1.0; 
     vv[i]=1.0/big;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (j=1;j<=n;j++) {  #ifdef DEBUG
     for (i=1;i<j;i++) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       sum=a[i][j];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  #endif
       a[i][j]=sum;    for (j=1;j<=n;j++) { 
     }      xi[j] *= xmin; 
     big=0.0;      p[j] += xi[j]; 
     for (i=j;i<=n;i++) {    } 
       sum=a[i][j];    free_vector(xicom,1,n); 
       for (k=1;k<j;k++)    free_vector(pcom,1,n); 
         sum -= a[i][k]*a[k][j];  } 
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  char *asc_diff_time(long time_sec, char ascdiff[])
         big=dum;  {
         imax=i;    long sec_left, days, hours, minutes;
       }    days = (time_sec) / (60*60*24);
     }    sec_left = (time_sec) % (60*60*24);
     if (j != imax) {    hours = (sec_left) / (60*60) ;
       for (k=1;k<=n;k++) {    sec_left = (sec_left) %(60*60);
         dum=a[imax][k];    minutes = (sec_left) /60;
         a[imax][k]=a[j][k];    sec_left = (sec_left) % (60);
         a[j][k]=dum;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       }    return ascdiff;
       *d = -(*d);  }
       vv[imax]=vv[j];  
     }  /*************** powell ************************/
     indx[j]=imax;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     if (a[j][j] == 0.0) a[j][j]=TINY;              double (*func)(double [])) 
     if (j != n) {  { 
       dum=1.0/(a[j][j]);    void linmin(double p[], double xi[], int n, double *fret, 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;                double (*func)(double [])); 
     }    int i,ibig,j; 
   }    double del,t,*pt,*ptt,*xit;
   free_vector(vv,1,n);  /* Doesn't work */    double fp,fptt;
 ;    double *xits;
 }    int niterf, itmp;
   
 void lubksb(double **a, int n, int *indx, double b[])    pt=vector(1,n); 
 {    ptt=vector(1,n); 
   int i,ii=0,ip,j;    xit=vector(1,n); 
   double sum;    xits=vector(1,n); 
      *fret=(*func)(p); 
   for (i=1;i<=n;i++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
     ip=indx[i];    for (*iter=1;;++(*iter)) { 
     sum=b[ip];      fp=(*fret); 
     b[ip]=b[i];      ibig=0; 
     if (ii)      del=0.0; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      last_time=curr_time;
     else if (sum) ii=i;      (void) gettimeofday(&curr_time,&tzp);
     b[i]=sum;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
   for (i=n;i>=1;i--) {  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     sum=b[i];     for (i=1;i<=n;i++) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        printf(" %d %.12f",i, p[i]);
     b[i]=sum/a[i][i];        fprintf(ficlog," %d %.12lf",i, p[i]);
   }        fprintf(ficrespow," %.12lf", p[i]);
 }      }
       printf("\n");
 /************ Frequencies ********************/      fprintf(ficlog,"\n");
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)      fprintf(ficrespow,"\n");fflush(ficrespow);
 {  /* Some frequencies */      if(*iter <=3){
          tm = *localtime(&curr_time.tv_sec);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        strcpy(strcurr,asctime(&tm));
   double ***freq; /* Frequencies */  /*       asctime_r(&tm,strcurr); */
   double *pp;        forecast_time=curr_time; 
   double pos;        itmp = strlen(strcurr);
   FILE *ficresp;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   char fileresp[FILENAMELENGTH];          strcurr[itmp-1]='\0';
         printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   pp=vector(1,nlstate);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   strcpy(fileresp,"p");          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   strcat(fileresp,fileres);          tmf = *localtime(&forecast_time.tv_sec);
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*      asctime_r(&tmf,strfor); */
     printf("Problem with prevalence resultfile: %s\n", fileresp);          strcpy(strfor,asctime(&tmf));
     exit(0);          itmp = strlen(strfor);
   }          if(strfor[itmp-1]=='\n')
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          strfor[itmp-1]='\0';
   j1=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);
           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);
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
       for (i=1;i<=n;i++) { 
   for(k1=1; k1<=j;k1++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
    for(i1=1; i1<=ncodemax[k1];i1++){        fptt=(*fret); 
        j1++;  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
         for (i=-1; i<=nlstate+ndeath; i++)          fprintf(ficlog,"fret=%lf \n",*fret);
          for (jk=-1; jk<=nlstate+ndeath; jk++)    #endif
            for(m=agemin; m <= agemax+3; m++)        printf("%d",i);fflush(stdout);
              freq[i][jk][m]=0;        fprintf(ficlog,"%d",i);fflush(ficlog);
                linmin(p,xit,n,fret,func); 
        for (i=1; i<=imx; i++) {        if (fabs(fptt-(*fret)) > del) { 
          bool=1;          del=fabs(fptt-(*fret)); 
          if  (cptcovn>0) {          ibig=i; 
            for (z1=1; z1<=cptcoveff; z1++)        } 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;  #ifdef DEBUG
          }        printf("%d %.12e",i,(*fret));
           if (bool==1) {        fprintf(ficlog,"%d %.12e",i,(*fret));
            for(m=firstpass; m<=lastpass-1; m++){        for (j=1;j<=n;j++) {
              if(agev[m][i]==0) agev[m][i]=agemax+1;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
              if(agev[m][i]==1) agev[m][i]=agemax+2;          printf(" x(%d)=%.12e",j,xit[j]);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        }
            }        for(j=1;j<=n;j++) {
          }          printf(" p=%.12e",p[j]);
        }          fprintf(ficlog," p=%.12e",p[j]);
         if  (cptcovn>0) {        }
          fprintf(ficresp, "\n#********** Variable ");        printf("\n");
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        fprintf(ficlog,"\n");
        }  #endif
        fprintf(ficresp, "**********\n#");      } 
        for(i=1; i<=nlstate;i++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  #ifdef DEBUG
        fprintf(ficresp, "\n");        int k[2],l;
                k[0]=1;
   for(i=(int)agemin; i <= (int)agemax+3; i++){        k[1]=-1;
     if(i==(int)agemax+3)        printf("Max: %.12e",(*func)(p));
       printf("Total");        fprintf(ficlog,"Max: %.12e",(*func)(p));
     else        for (j=1;j<=n;j++) {
       printf("Age %d", i);          printf(" %.12e",p[j]);
     for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog," %.12e",p[j]);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
         pp[jk] += freq[jk][m][i];        printf("\n");
     }        fprintf(ficlog,"\n");
     for(jk=1; jk <=nlstate ; jk++){        for(l=0;l<=1;l++) {
       for(m=-1, pos=0; m <=0 ; m++)          for (j=1;j<=n;j++) {
         pos += freq[jk][m][i];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       if(pp[jk]>=1.e-10)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       else          }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(jk=1; jk <=nlstate ; jk++){        }
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)  #endif
         pp[jk] += freq[jk][m][i];  
     }  
     for(jk=1,pos=0; jk <=nlstate ; jk++)        free_vector(xit,1,n); 
       pos += pp[jk];        free_vector(xits,1,n); 
     for(jk=1; jk <=nlstate ; jk++){        free_vector(ptt,1,n); 
       if(pos>=1.e-5)        free_vector(pt,1,n); 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        return; 
       else      } 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       if( i <= (int) agemax){      for (j=1;j<=n;j++) { 
         if(pos>=1.e-5)        ptt[j]=2.0*p[j]-pt[j]; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        xit[j]=p[j]-pt[j]; 
       else        pt[j]=p[j]; 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      } 
       }      fptt=(*func)(ptt); 
     }      if (fptt < fp) { 
     for(jk=-1; jk <=nlstate+ndeath; jk++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       for(m=-1; m <=nlstate+ndeath; m++)        if (t < 0.0) { 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          linmin(p,xit,n,fret,func); 
     if(i <= (int) agemax)          for (j=1;j<=n;j++) { 
       fprintf(ficresp,"\n");            xi[j][ibig]=xi[j][n]; 
     printf("\n");            xi[j][n]=xit[j]; 
     }          }
     }  #ifdef DEBUG
  }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fclose(ficresp);          for(j=1;j<=n;j++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            printf(" %.12e",xit[j]);
   free_vector(pp,1,nlstate);            fprintf(ficlog," %.12e",xit[j]);
           }
 }  /* End of Freq */          printf("\n");
           fprintf(ficlog,"\n");
 /************* Waves Concatenation ***************/  #endif
         }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      } 
 {    } 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  } 
      Death is a valid wave (if date is known).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  /**** Prevalence limit (stable or period prevalence)  ****************/
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
      */  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   int i, mi, m;       matrix by transitions matrix until convergence is reached */
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
 float sum=0.;    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   for(i=1; i<=imx; i++){    double **matprod2();
     mi=0;    double **out, cov[NCOVMAX+1], **pmij();
     m=firstpass;    double **newm;
     while(s[m][i] <= nlstate){    double agefin, delaymax=50 ; /* Max number of years to converge */
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    for (ii=1;ii<=nlstate+ndeath;ii++)
       if(m >=lastpass)      for (j=1;j<=nlstate+ndeath;j++){
         break;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else      }
         m++;  
     }/* end while */     cov[1]=1.;
     if (s[m][i] > nlstate){   
       mi++;     /* Death is another wave */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /* if(mi==0)  never been interviewed correctly before death */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
          /* Only death is a correct wave */      newm=savm;
       mw[mi][i]=m;      /* Covariates have to be included here again */
     }      cov[2]=agefin;
       
     wav[i]=mi;      for (k=1; k<=cptcovn;k++) {
     if(mi==0)        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   }      }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for(i=1; i<=imx; i++){      for (k=1; k<=cptcovprod;k++)
     for(mi=1; mi<wav[i];mi++){        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if (stepm <=0)      
         dh[mi][i]=1;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       else{      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         if (s[mw[mi+1][i]][i] > nlstate) {      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           if(j=0) j=1;  /* Survives at least one month after exam */      
         }      savm=oldm;
         else{      oldm=newm;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      maxmax=0.;
           k=k+1;      for(j=1;j<=nlstate;j++){
           if (j >= jmax) jmax=j;        min=1.;
           else if (j <= jmin)jmin=j;        max=0.;
           sum=sum+j;        for(i=1; i<=nlstate; i++) {
         }          sumnew=0;
         jk= j/stepm;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         jl= j -jk*stepm;          prlim[i][j]= newm[i][j]/(1-sumnew);
         ju= j -(jk+1)*stepm;          max=FMAX(max,prlim[i][j]);
         if(jl <= -ju)          min=FMIN(min,prlim[i][j]);
           dh[mi][i]=jk;        }
         else        maxmin=max-min;
           dh[mi][i]=jk+1;        maxmax=FMAX(maxmax,maxmin);
         if(dh[mi][i]==0)      }
           dh[mi][i]=1; /* At least one step */      if(maxmax < ftolpl){
       }        return prlim;
     }      }
   }    }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);  }
 }  
 /*********** Tricode ****************************/  /*************** transition probabilities ***************/ 
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   int Ndum[20],ij=1, k, j, i;  {
   int cptcode=0;    /* According to parameters values stored in x and the covariate's values stored in cov,
   cptcoveff=0;       computes the probability to be observed in state j being in state i by appying the
         model to the ncovmodel covariates (including constant and age).
   for (k=0; k<19; k++) Ndum[k]=0;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   for (k=1; k<=7; k++) ncodemax[k]=0;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     for (i=1; i<=imx; i++) {       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       ij=(int)(covar[Tvar[j]][i]);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       Ndum[ij]++;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       if (ij > cptcode) cptcode=ij;       Outputs ps[i][j] the probability to be observed in j being in j according to
     }       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     */
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/    double s1, lnpijopii;
     for (i=0; i<=cptcode; i++) {    /*double t34;*/
       if(Ndum[i]!=0) ncodemax[j]++;    int i,j,j1, nc, ii, jj;
     }  
     ij=1;      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
     for (i=1; i<=ncodemax[j]; i++) {          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       for (k=0; k<=19; k++) {            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         if (Ndum[k] != 0) {            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           nbcode[Tvar[j]][ij]=k;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/          }
           ij++;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         if (ij > ncodemax[j]) break;        }
       }          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];*/
  for (i=1; i<=10; i++) {            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       ij=Tvar[i];  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       Ndum[ij]++;          }
     }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
  ij=1;        }
  for (i=1; i<=cptcovn; i++) {      }
    if((Ndum[i]!=0) && (i<=ncov)){      
      Tvaraff[i]=ij;      for(i=1; i<= nlstate; i++){
    ij++;        s1=0;
    }        for(j=1; j<i; j++){
  }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
            /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        }
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];        for(j=i+1; j<=nlstate+ndeath; j++){
    /*printf("j=%d %d\n",j,Tvar[j]);*/          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
  }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
          }
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     scanf("%d",i);*/        ps[i][i]=1./(s1+1.);
 }        /* Computing other pijs */
         for(j=1; j<i; j++)
 /*********** Health Expectancies ****************/          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          ps[i][j]= exp(ps[i][j])*ps[i][i];
 {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   /* Health expectancies */      } /* end i */
   int i, j, nhstepm, hstepm, h;      
   double age, agelim,hf;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   double ***p3mat;        for(jj=1; jj<= nlstate+ndeath; jj++){
            ps[ii][jj]=0;
   fprintf(ficreseij,"# Health expectancies\n");          ps[ii][ii]=1;
   fprintf(ficreseij,"# Age");        }
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   hstepm=1*YEARM; /*  Every j years of age (in month) */  /*         printf("ddd %lf ",ps[ii][jj]); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  /*       } */
   /*       printf("\n "); */
   agelim=AGESUP;  /*        } */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /*        printf("\n ");printf("%lf ",cov[2]); */
     /* nhstepm age range expressed in number of stepm */         /*
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     /* Typically if 20 years = 20*12/6=40 stepm */        goto end;*/
     if (stepm >= YEARM) hstepm=1;      return ps;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  /**************** Product of 2 matrices ******************/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     for(i=1; i<=nlstate;i++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for(j=1; j<=nlstate;j++)    /* in, b, out are matrice of pointers which should have been initialized 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){       before: only the contents of out is modified. The function returns
           eij[i][j][(int)age] +=p3mat[i][j][h];       a pointer to pointers identical to out */
         }    long i, j, k;
        for(i=nrl; i<= nrh; i++)
     hf=1;      for(k=ncolol; k<=ncoloh; k++)
     if (stepm >= YEARM) hf=stepm/YEARM;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     fprintf(ficreseij,"%.0f",age );          out[i][k] +=in[i][j]*b[j][k];
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    return out;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  }
       }  
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /************* Higher Matrix Product ***************/
   }  
 }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
 /************ Variance ******************/    /* Computes the transition matrix starting at age 'age' over 
 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)       'nhstepm*hstepm*stepm' months (i.e. until
 {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   /* Variance of health expectancies */       nhstepm*hstepm matrices. 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   double **newm;       (typically every 2 years instead of every month which is too big 
   double **dnewm,**doldm;       for the memory).
   int i, j, nhstepm, hstepm, h;       Model is determined by parameters x and covariates have to be 
   int k, cptcode;       included manually here. 
    double *xp;  
   double **gp, **gm;       */
   double ***gradg, ***trgradg;  
   double ***p3mat;    int i, j, d, h, k;
   double age,agelim;    double **out, cov[NCOVMAX+1];
   int theta;    double **newm;
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /* Hstepm could be zero and should return the unit matrix */
   fprintf(ficresvij,"# Age");    for (i=1;i<=nlstate+ndeath;i++)
   for(i=1; i<=nlstate;i++)      for (j=1;j<=nlstate+ndeath;j++){
     for(j=1; j<=nlstate;j++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   fprintf(ficresvij,"\n");      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   xp=vector(1,npar);    for(h=1; h <=nhstepm; h++){
   dnewm=matrix(1,nlstate,1,npar);      for(d=1; d <=hstepm; d++){
   doldm=matrix(1,nlstate,1,nlstate);        newm=savm;
          /* Covariates have to be included here again */
   hstepm=1*YEARM; /* Every year of age */        cov[1]=1.;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   agelim = AGESUP;        for (k=1; k<=cptcovn;k++) 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for (k=1; k<=cptcovage;k++)
     if (stepm >= YEARM) hstepm=1;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for (k=1; k<=cptcovprod;k++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);        /*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(theta=1; theta <=npar; theta++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       for(i=1; i<=npar; i++){ /* Computes gradient */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        savm=oldm;
       }        oldm=newm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1; j<= nlstate; j++){        for(j=1;j<=nlstate+ndeath;j++) {
         for(h=0; h<=nhstepm; h++){          po[i][j][h]=newm[i][j];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        }
         }      /*printf("h=%d ",h);*/
       }    } /* end h */
      /*     printf("\n H=%d \n",h); */
       for(i=1; i<=npar; i++) /* Computes gradient */    return po;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(j=1; j<= nlstate; j++){  /*************** log-likelihood *************/
         for(h=0; h<=nhstepm; h++){  double func( double *x)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    int i, ii, j, k, mi, d, kk;
         }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       }    double **out;
       for(j=1; j<= nlstate; j++)    double sw; /* Sum of weights */
         for(h=0; h<=nhstepm; h++){    double lli; /* Individual log likelihood */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int s1, s2;
         }    double bbh, survp;
     } /* End theta */    long ipmx;
     /*extern weight */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(h=0; h<=nhstepm; h++)    /*for(i=1;i<imx;i++) 
       for(j=1; j<=nlstate;j++)      printf(" %d\n",s[4][i]);
         for(theta=1; theta <=npar; theta++)    */
           trgradg[h][j][theta]=gradg[h][theta][j];    cov[1]=1.;
   
     for(i=1;i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    if(mle==1){
     for(h=0;h<=nhstepm;h++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(k=0;k<=nhstepm;k++){        /* Computes the values of the ncovmodel covariates of the model
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
         for(i=1;i<=nlstate;i++)           to be observed in j being in i according to the model.
           for(j=1;j<=nlstate;j++)         */
             vareij[i][j][(int)age] += doldm[i][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     }           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     h=1;           has been calculated etc */
     if (stepm >= YEARM) h=stepm/YEARM;        for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficresvij,"%.0f ",age );          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<=nlstate;j++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     fprintf(ficresvij,"\n");          for(d=0; d<dh[mi][i]; d++){
     free_matrix(gp,0,nhstepm,1,nlstate);            newm=savm;
     free_matrix(gm,0,nhstepm,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
   } /* End age */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(xp,1,npar);            savm=oldm;
   free_matrix(doldm,1,nlstate,1,npar);            oldm=newm;
   free_matrix(dnewm,1,nlstate,1,nlstate);          } /* end mult */
         
 }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
 /************ Variance of prevlim ******************/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 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)           * (in months) between two waves is not a multiple of stepm, we rounded to 
 {           * the nearest (and in case of equal distance, to the lowest) interval but now
   /* Variance of prevalence limit */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double **newm;           * probability in order to take into account the bias as a fraction of the way
   double **dnewm,**doldm;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   int i, j, nhstepm, hstepm;           * -stepm/2 to stepm/2 .
   int k, cptcode;           * For stepm=1 the results are the same as for previous versions of Imach.
   double *xp;           * For stepm > 1 the results are less biased than in previous versions. 
   double *gp, *gm;           */
   double **gradg, **trgradg;          s1=s[mw[mi][i]][i];
   double age,agelim;          s2=s[mw[mi+1][i]][i];
   int theta;          bbh=(double)bh[mi][i]/(double)stepm; 
              /* bias bh is positive if real duration
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");           * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficresvpl,"# Age");           */
   for(i=1; i<=nlstate;i++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       fprintf(ficresvpl," %1d-%1d",i,i);          if( s2 > nlstate){ 
   fprintf(ficresvpl,"\n");            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
   xp=vector(1,npar);               die between last step unit time and current  step unit time, 
   dnewm=matrix(1,nlstate,1,npar);               which is also equal to probability to die before dh 
   doldm=matrix(1,nlstate,1,nlstate);               minus probability to die before dh-stepm . 
                 In version up to 0.92 likelihood was computed
   hstepm=1*YEARM; /* Every year of age */          as if date of death was unknown. Death was treated as any other
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          health state: the date of the interview describes the actual state
   agelim = AGESUP;          and not the date of a change in health state. The former idea was
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          to consider that at each interview the state was recorded
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          (healthy, disable or death) and IMaCh was corrected; but when we
     if (stepm >= YEARM) hstepm=1;          introduced the exact date of death then we should have modified
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          the contribution of an exact death to the likelihood. This new
     gradg=matrix(1,npar,1,nlstate);          contribution is smaller and very dependent of the step unit
     gp=vector(1,nlstate);          stepm. It is no more the probability to die between last interview
     gm=vector(1,nlstate);          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
     for(theta=1; theta <=npar; theta++){          probability to die within a month. Thanks to Chris
       for(i=1; i<=npar; i++){ /* Computes gradient */          Jackson for correcting this bug.  Former versions increased
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          mortality artificially. The bad side is that we add another loop
       }          which slows down the processing. The difference can be up to 10%
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lower mortality.
       for(i=1;i<=nlstate;i++)            */
         gp[i] = prlim[i][i];            lli=log(out[s1][s2] - savm[s1][s2]);
      
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          } else if  (s2==-2) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (j=1,survp=0. ; j<=nlstate; j++) 
       for(i=1;i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         gm[i] = prlim[i][i];            /*survp += out[s1][j]; */
             lli= log(survp);
       for(i=1;i<=nlstate;i++)          }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          
     } /* End theta */          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
     trgradg =matrix(1,nlstate,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
     for(j=1; j<=nlstate;j++)          } 
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];          else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
     for(i=1;i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       varpl[i][(int)age] =0.;            lli= log(survp); 
     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++)          else{
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            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 */
     fprintf(ficresvpl,"%.0f ",age );          } 
     for(i=1; i<=nlstate;i++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          /*if(lli ==000.0)*/
     fprintf(ficresvpl,"\n");          /*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); */
     free_vector(gp,1,nlstate);          ipmx +=1;
     free_vector(gm,1,nlstate);          sw += weight[i];
     free_matrix(gradg,1,npar,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_matrix(trgradg,1,nlstate,1,npar);        } /* end of wave */
   } /* End age */      } /* end of individual */
     }  else if(mle==2){
   free_vector(xp,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(doldm,1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 }            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(d=0; d<=dh[mi][i]; d++){
 /**************** Main Program *****************/            newm=savm;
 /***********************************************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /*int main(int argc, char *argv[])*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 int main()            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;            savm=oldm;
   double agedeb, agefin,hf;            oldm=newm;
   double agemin=1.e20, agemax=-1.e20;          } /* end mult */
         
   double fret;          s1=s[mw[mi][i]][i];
   double **xi,tmp,delta;          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   double dum; /* Dummy variable */          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 */
   double ***p3mat;          ipmx +=1;
   int *indx;          sw += weight[i];
   char line[MAXLINE], linepar[MAXLINE];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char title[MAXLINE];        } /* end of wave */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      } /* end of individual */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    }  else if(mle==3){  /* exponential inter-extrapolation */
   char filerest[FILENAMELENGTH];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   char fileregp[FILENAMELENGTH];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        for(mi=1; mi<= wav[i]-1; mi++){
   int firstobs=1, lastobs=10;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int sdeb, sfin; /* Status at beginning and end */            for (j=1;j<=nlstate+ndeath;j++){
   int c,  h , cpt,l;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int ju,jl, mi;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   int hstepm, nhstepm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double bage, fage, age, agelim, agebase;            for (kk=1; kk<=cptcovage;kk++) {
   double ftolpl=FTOL;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **prlim;            }
   double *severity;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***param; /* Matrix of parameters */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double  *p;            savm=oldm;
   double **matcov; /* Matrix of covariance */            oldm=newm;
   double ***delti3; /* Scale */          } /* end mult */
   double *delti; /* Scale */        
   double ***eij, ***vareij;          s1=s[mw[mi][i]][i];
   double **varpl; /* Variances of prevalence limits by age */          s2=s[mw[mi+1][i]][i];
   double *epj, vepp;          bbh=(double)bh[mi][i]/(double)stepm; 
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";          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 */
   char *alph[]={"a","a","b","c","d","e"}, str[4];          ipmx +=1;
           sw += weight[i];
   char z[1]="c", occ;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 #include <sys/time.h>        } /* end of wave */
 #include <time.h>      } /* end of individual */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   /* long total_usecs;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   struct timeval start_time, end_time;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\nIMACH, Version 0.64a");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\nEnter the parameter file name: ");            }
           for(d=0; d<dh[mi][i]; d++){
 #ifdef windows            newm=savm;
   scanf("%s",pathtot);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   getcwd(pathcd, size);            for (kk=1; kk<=cptcovage;kk++) {
   /*cygwin_split_path(pathtot,path,optionfile);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            }
   /* cutv(path,optionfile,pathtot,'\\');*/          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 split(pathtot, path,optionfile);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   chdir(path);            savm=oldm;
   replace(pathc,path);            oldm=newm;
 #endif          } /* end mult */
 #ifdef unix        
   scanf("%s",optionfile);          s1=s[mw[mi][i]][i];
 #endif          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
 /*-------- arguments in the command line --------*/            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
   strcpy(fileres,"r");            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   strcat(fileres, optionfile);          }
           ipmx +=1;
   /*---------arguments file --------*/          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  /*      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]); */
     printf("Problem with optionfile %s\n",optionfile);        } /* end of wave */
     goto end;      } /* end of individual */
   }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(filereso,"o");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(filereso,fileres);        for(mi=1; mi<= wav[i]-1; mi++){
   if((ficparo=fopen(filereso,"w"))==NULL) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            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);
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){          for(d=0; d<dh[mi][i]; d++){
     ungetc(c,ficpar);            newm=savm;
     fgets(line, MAXLINE, ficpar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     puts(line);            for (kk=1; kk<=cptcovage;kk++) {
     fputs(line,ficparo);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   ungetc(c,ficpar);          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   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);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   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);            savm=oldm;
   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);            oldm=newm;
           } /* end mult */
   covar=matrix(0,NCOVMAX,1,n);            
   if (strlen(model)<=1) cptcovn=0;          s1=s[mw[mi][i]][i];
   else {          s2=s[mw[mi+1][i]][i];
     j=0;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     j=nbocc(model,'+');          ipmx +=1;
     cptcovn=j+1;          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]);*/
   ncovmodel=2+cptcovn;        } /* end of wave */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      } /* end of individual */
      } /* End of if */
   /* Read guess parameters */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* Reads comments: lines beginning with '#' */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   while((c=getc(ficpar))=='#' && c!= EOF){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     ungetc(c,ficpar);    return -l;
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /*************** log-likelihood *************/
   }  double funcone( double *x)
   ungetc(c,ficpar);  {
      /* Same as likeli but slower because of a lot of printf and if */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    int i, ii, j, k, mi, d, kk;
     for(i=1; i <=nlstate; i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(j=1; j <=nlstate+ndeath-1; j++){    double **out;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double lli; /* Individual log likelihood */
       fprintf(ficparo,"%1d%1d",i1,j1);    double llt;
       printf("%1d%1d",i,j);    int s1, s2;
       for(k=1; k<=ncovmodel;k++){    double bbh, survp;
         fscanf(ficpar," %lf",&param[i][j][k]);    /*extern weight */
         printf(" %lf",param[i][j][k]);    /* We are differentiating ll according to initial status */
         fprintf(ficparo," %lf",param[i][j][k]);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
       fscanf(ficpar,"\n");      printf(" %d\n",s[4][i]);
       printf("\n");    */
       fprintf(ficparo,"\n");    cov[1]=1.;
     }  
      for(k=1; k<=nlstate; k++) ll[k]=0.;
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
   p=param[1][1];    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* Reads comments: lines beginning with '#' */      for(mi=1; mi<= wav[i]-1; mi++){
   while((c=getc(ficpar))=='#' && c!= EOF){        for (ii=1;ii<=nlstate+ndeath;ii++)
     ungetc(c,ficpar);          for (j=1;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     puts(line);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fputs(line,ficparo);          }
   }        for(d=0; d<dh[mi][i]; d++){
   ungetc(c,ficpar);          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for (kk=1; kk<=cptcovage;kk++) {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i <=nlstate; i++){          }
     for(j=1; j <=nlstate+ndeath-1; j++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fscanf(ficpar,"%1d%1d",&i1,&j1);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       printf("%1d%1d",i,j);          savm=oldm;
       fprintf(ficparo,"%1d%1d",i1,j1);          oldm=newm;
       for(k=1; k<=ncovmodel;k++){        } /* end mult */
         fscanf(ficpar,"%le",&delti3[i][j][k]);        
         printf(" %le",delti3[i][j][k]);        s1=s[mw[mi][i]][i];
         fprintf(ficparo," %le",delti3[i][j][k]);        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
       fscanf(ficpar,"\n");        /* bias is positive if real duration
       printf("\n");         * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficparo,"\n");         */
     }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   }          lli=log(out[s1][s2] - savm[s1][s2]);
   delti=delti3[1][1];        } else if  (s2==-2) {
            for (j=1,survp=0. ; j<=nlstate; j++) 
   /* Reads comments: lines beginning with '#' */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   while((c=getc(ficpar))=='#' && c!= EOF){          lli= log(survp);
     ungetc(c,ficpar);        }else if (mle==1){
     fgets(line, MAXLINE, ficpar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     puts(line);        } else if(mle==2){
     fputs(line,ficparo);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   }        } else if(mle==3){  /* exponential inter-extrapolation */
   ungetc(c,ficpar);          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          } else if (mle==4){  /* mle=4 no inter-extrapolation */
   matcov=matrix(1,npar,1,npar);          lli=log(out[s1][s2]); /* Original formula */
   for(i=1; i <=npar; i++){        } else{  /* mle=0 back to 1 */
     fscanf(ficpar,"%s",&str);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     printf("%s",str);          /*lli=log(out[s1][s2]); */ /* Original formula */
     fprintf(ficparo,"%s",str);        } /* End of if */
     for(j=1; j <=i; j++){        ipmx +=1;
       fscanf(ficpar," %le",&matcov[i][j]);        sw += weight[i];
       printf(" %.5le",matcov[i][j]);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficparo," %.5le",matcov[i][j]);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     }        if(globpr){
     fscanf(ficpar,"\n");          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     printf("\n");   %11.6f %11.6f %11.6f ", \
     fprintf(ficparo,"\n");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   for(i=1; i <=npar; i++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     for(j=i+1;j<=npar;j++)            llt +=ll[k]*gipmx/gsw;
       matcov[i][j]=matcov[j][i];            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
              }
   printf("\n");          fprintf(ficresilk," %10.6f\n", -llt);
         }
       } /* end of wave */
     /*-------- data file ----------*/    } /* end of individual */
     if((ficres =fopen(fileres,"w"))==NULL) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       printf("Problem with resultfile: %s\n", fileres);goto end;    /* 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 */
     fprintf(ficres,"#%s\n",version);    if(globpr==0){ /* First time we count the contributions and weights */
          gipmx=ipmx;
     if((fic=fopen(datafile,"r"))==NULL)    {      gsw=sw;
       printf("Problem with datafile: %s\n", datafile);goto end;    }
     }    return -l;
   }
     n= lastobs;  
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);  /*************** function likelione ***********/
     num=ivector(1,n);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     moisnais=vector(1,n);  {
     annais=vector(1,n);    /* This routine should help understanding what is done with 
     moisdc=vector(1,n);       the selection of individuals/waves and
     andc=vector(1,n);       to check the exact contribution to the likelihood.
     agedc=vector(1,n);       Plotting could be done.
     cod=ivector(1,n);     */
     weight=vector(1,n);    int k;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  
     mint=matrix(1,maxwav,1,n);    if(*globpri !=0){ /* Just counts and sums, no printings */
     anint=matrix(1,maxwav,1,n);      strcpy(fileresilk,"ilk"); 
     s=imatrix(1,maxwav+1,1,n);      strcat(fileresilk,fileres);
     adl=imatrix(1,maxwav+1,1,n);          if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     tab=ivector(1,NCOVMAX);        printf("Problem with resultfile: %s\n", fileresilk);
     ncodemax=ivector(1,8);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
     i=1;      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");
     while (fgets(line, MAXLINE, fic) != NULL)    {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       if ((i >= firstobs) && (i <=lastobs)) {      /*  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++) 
         for (j=maxwav;j>=1;j--){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           strcpy(line,stra);    }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
              fclose(ficresilk);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      fflush(fichtm); 
     } 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    return;
         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--){  /*********** Maximum Likelihood Estimation ***************/
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         num[i]=atol(stra);  {
     int i,j, iter;
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    double **xi;
     double fret;
         i=i+1;    double fretone; /* Only one call to likelihood */
       }    /*  char filerespow[FILENAMELENGTH];*/
     }    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
     /*scanf("%d",i);*/      for (j=1;j<=npar;j++)
   imx=i-1; /* Number of individuals */        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   /* Calculation of the number of parameter from char model*/    strcpy(filerespow,"pow"); 
   Tvar=ivector(1,15);    strcat(filerespow,fileres);
   Tprod=ivector(1,15);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   Tvaraff=ivector(1,15);      printf("Problem with resultfile: %s\n", filerespow);
   Tvard=imatrix(1,15,1,2);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   Tage=ivector(1,15);          }
        fprintf(ficrespow,"# Powell\n# iter -2*LL");
   if (strlen(model) >1){    for (i=1;i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;      for(j=1;j<=nlstate+ndeath;j++)
     j=nbocc(model,'+');        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     j1=nbocc(model,'*');    fprintf(ficrespow,"\n");
     cptcovn=j+1;  
     cptcovprod=j1;    powell(p,xi,npar,ftol,&iter,&fret,func);
      
     strcpy(modelsav,model);    free_matrix(xi,1,npar,1,npar);
    if (j==0) {    fclose(ficrespow);
       if (j1==0){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         cutv(stra,strb,modelsav,'V');    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         Tvar[1]=atoi(strb);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
       else if (j1==1) {  }
         cutv(stra,strb,modelsav,'*');  
         Tage[1]=1; cptcovage++;  /**** Computes Hessian and covariance matrix ***/
         if (strcmp(stra,"age")==0) {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           cptcovprod--;  {
           cutv(strd,strc,strb,'V');    double  **a,**y,*x,pd;
           Tvar[1]=atoi(strc);    double **hess;
         }    int i, j,jk;
         else if (strcmp(strb,"age")==0) {    int *indx;
           cptcovprod--;  
           cutv(strd,strc,stra,'V');    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           Tvar[1]=atoi(strc);    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[]) ;
         else {    void ludcmp(double **a, int npar, int *indx, double *d) ;
           cutv(strd,strc,strb,'V');    double gompertz(double p[]);
           cutv(stre,strd,stra,'V');    hess=matrix(1,npar,1,npar);
           Tvar[1]=ncov+1;  
           for (k=1; k<=lastobs;k++)    printf("\nCalculation of the hessian matrix. Wait...\n");
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         }    for (i=1;i<=npar;i++){
         /*printf("%s %s %s\n", stra,strb,modelsav);      printf("%d",i);fflush(stdout);
 printf("%d ",Tvar[1]);      fprintf(ficlog,"%d",i);fflush(ficlog);
 scanf("%d",i);*/     
       }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     }      
    else {      /*  printf(" %f ",p[i]);
       for(i=j; i>=1;i--){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         cutv(stra,strb,modelsav,'+');    }
         /*printf("%s %s %s\n", stra,strb,modelsav);    
           scanf("%d",i);*/    for (i=1;i<=npar;i++) {
         if (strchr(strb,'*')) {      for (j=1;j<=npar;j++)  {
           cutv(strd,strc,strb,'*');        if (j>i) { 
           if (strcmp(strc,"age")==0) {          printf(".%d%d",i,j);fflush(stdout);
             cptcovprod--;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
             cutv(strb,stre,strd,'V');          hess[i][j]=hessij(p,delti,i,j,func,npar);
             Tvar[i+1]=atoi(stre);          
             cptcovage++;          hess[j][i]=hess[i][j];    
             Tage[cptcovage]=i+1;          /*printf(" %lf ",hess[i][j]);*/
             printf("stre=%s ", stre);        }
           }      }
           else if (strcmp(strd,"age")==0) {    }
             cptcovprod--;    printf("\n");
             cutv(strb,stre,strc,'V');    fprintf(ficlog,"\n");
             Tvar[i+1]=atoi(stre);  
             cptcovage++;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
             Tage[cptcovage]=i+1;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           }    
           else {    a=matrix(1,npar,1,npar);
             cutv(strb,stre,strc,'V');    y=matrix(1,npar,1,npar);
             Tvar[i+1]=ncov+k1;    x=vector(1,npar);
             cutv(strb,strc,strd,'V');    indx=ivector(1,npar);
             Tprod[k1]=i+1;    for (i=1;i<=npar;i++)
             Tvard[k1][1]=atoi(strc);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
             Tvard[k1][2]=atoi(stre);    ludcmp(a,npar,indx,&pd);
             Tvar[cptcovn+k2]=Tvard[k1][1];  
             Tvar[cptcovn+k2+1]=Tvard[k1][2];    for (j=1;j<=npar;j++) {
             for (k=1; k<=lastobs;k++)      for (i=1;i<=npar;i++) x[i]=0;
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      x[j]=1;
             k1++;      lubksb(a,npar,indx,x);
             k2=k2+2;      for (i=1;i<=npar;i++){ 
           }        matcov[i][j]=x[i];
         }      }
         else {    }
           cutv(strd,strc,strb,'V');  
           /* printf("%s %s %s", strd,strc,strb);*/    printf("\n#Hessian matrix#\n");
           Tvar[i+1]=atoi(strc);    fprintf(ficlog,"\n#Hessian matrix#\n");
         }    for (i=1;i<=npar;i++) { 
         strcpy(modelsav,stra);        for (j=1;j<=npar;j++) { 
       }        printf("%.3e ",hess[i][j]);
       cutv(strd,strc,stra,'V');        fprintf(ficlog,"%.3e ",hess[i][j]);
       Tvar[1]=atoi(strc);      }
     }      printf("\n");
   }      fprintf(ficlog,"\n");
   /* for (i=1; i<=5; i++)    }
      printf("i=%d %d ",i,Tvar[i]);*/  
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/    /* Recompute Inverse */
  /*printf("cptcovprod=%d ", cptcovprod);*/    for (i=1;i<=npar;i++)
   /*  scanf("%d ",i);*/      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fclose(fic);    ludcmp(a,npar,indx,&pd);
   
     /*  if(mle==1){*/    /*  printf("\n#Hessian matrix recomputed#\n");
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
     /*-calculation of age at interview from date of interview and age at death -*/      x[j]=1;
     agev=matrix(1,maxwav,1,imx);      lubksb(a,npar,indx,x);
          for (i=1;i<=npar;i++){ 
     for (i=1; i<=imx; i++)  {        y[i][j]=x[i];
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        printf("%.3e ",y[i][j]);
       for(m=1; (m<= maxwav); m++){        fprintf(ficlog,"%.3e ",y[i][j]);
         if(s[m][i] >0){      }
           if (s[m][i] == nlstate+1) {      printf("\n");
             if(agedc[i]>0)      fprintf(ficlog,"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)    }
               agev[m][i]=agedc[i];    */
             else{  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    free_matrix(a,1,npar,1,npar);
               agev[m][i]=-1;    free_matrix(y,1,npar,1,npar);
             }    free_vector(x,1,npar);
           }    free_ivector(indx,1,npar);
           else if(s[m][i] !=9){ /* Should no more exist */    free_matrix(hess,1,npar,1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;  }
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];  /*************** hessian matrix ****************/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
             }  {
             else if(agev[m][i] >agemax){    int i;
               agemax=agev[m][i];    int l=1, lmax=20;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    double k1,k2;
             }    double p2[MAXPARM+1]; /* identical to x */
             /*agev[m][i]=anint[m][i]-annais[i];*/    double res;
             /*   agev[m][i] = age[i]+2*m;*/    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           }    double fx;
           else { /* =9 */    int k=0,kmax=10;
             agev[m][i]=1;    double l1;
             s[m][i]=-1;  
           }    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
         else /*= 0 Unknown */    for(l=0 ; l <=lmax; l++){
           agev[m][i]=1;      l1=pow(10,l);
       }      delts=delt;
          for(k=1 ; k <kmax; k=k+1){
     }        delt = delta*(l1*k);
     for (i=1; i<=imx; i++)  {        p2[theta]=x[theta] +delt;
       for(m=1; (m<= maxwav); m++){        k1=func(p2)-fx;
         if (s[m][i] > (nlstate+ndeath)) {        p2[theta]=x[theta]-delt;
           printf("Error: Wrong value in nlstate or ndeath\n");          k2=func(p2)-fx;
           goto end;        /*res= (k1-2.0*fx+k2)/delt/delt; */
         }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       }        
     }  #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);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        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
     free_vector(severity,1,maxwav);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     free_imatrix(outcome,1,maxwav+1,1,n);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     free_vector(moisnais,1,n);          k=kmax;
     free_vector(annais,1,n);        }
     free_matrix(mint,1,maxwav,1,n);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_matrix(anint,1,maxwav,1,n);          k=kmax; l=lmax*10.;
     free_vector(moisdc,1,n);        }
     free_vector(andc,1,n);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
            }
     wav=ivector(1,imx);      }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    delti[theta]=delts;
        return res; 
     /* Concatenates waves */    
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  }
   
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       Tcode=ivector(1,100);  {
       nbcode=imatrix(1,nvar,1,8);    int i;
       ncodemax[1]=1;    int l=1, l1, lmax=20;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double k1,k2,k3,k4,res,fx;
          double p2[MAXPARM+1];
    codtab=imatrix(1,100,1,10);    int k;
    h=0;  
    m=pow(2,cptcoveff);    fx=func(x);
      for (k=1; k<=2; k++) {
    for(k=1;k<=cptcoveff; k++){      for (i=1;i<=npar;i++) p2[i]=x[i];
      for(i=1; i <=(m/pow(2,k));i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
        for(j=1; j <= ncodemax[k]; j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      k1=func(p2)-fx;
            h++;    
            if (h>m) h=1;codtab[h][k]=j;      p2[thetai]=x[thetai]+delti[thetai]/k;
          }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        }      k2=func(p2)-fx;
      }    
    }      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
    /*for(i=1; i <=m ;i++){    
      for(k=1; k <=cptcovn; k++){      p2[thetai]=x[thetai]-delti[thetai]/k;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      }      k4=func(p2)-fx;
      printf("\n");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    }  #ifdef DEBUG
    scanf("%d",i);*/      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
          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);
    /* Calculates basic frequencies. Computes observed prevalence at single age  #endif
        and prints on file fileres'p'. */    }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    return res;
   }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /************** Inverse of matrix **************/
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void ludcmp(double **a, int n, int *indx, double *d) 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  { 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int i,imax,j,k; 
        double big,dum,sum,temp; 
     /* For Powell, parameters are in a vector p[] starting at p[1]    double *vv; 
        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) */    vv=vector(1,n); 
     *d=1.0; 
     if(mle==1){    for (i=1;i<=n;i++) { 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      big=0.0; 
     }      for (j=1;j<=n;j++) 
            if ((temp=fabs(a[i][j])) > big) big=temp; 
     /*--------- results files --------------*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      vv[i]=1.0/big; 
        } 
    jk=1;    for (j=1;j<=n;j++) { 
    fprintf(ficres,"# Parameters\n");      for (i=1;i<j;i++) { 
    printf("# Parameters\n");        sum=a[i][j]; 
    for(i=1,jk=1; i <=nlstate; i++){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      for(k=1; k <=(nlstate+ndeath); k++){        a[i][j]=sum; 
        if (k != i)      } 
          {      big=0.0; 
            printf("%d%d ",i,k);      for (i=j;i<=n;i++) { 
            fprintf(ficres,"%1d%1d ",i,k);        sum=a[i][j]; 
            for(j=1; j <=ncovmodel; j++){        for (k=1;k<j;k++) 
              printf("%f ",p[jk]);          sum -= a[i][k]*a[k][j]; 
              fprintf(ficres,"%f ",p[jk]);        a[i][j]=sum; 
              jk++;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
            }          big=dum; 
            printf("\n");          imax=i; 
            fprintf(ficres,"\n");        } 
          }      } 
      }      if (j != imax) { 
    }        for (k=1;k<=n;k++) { 
  if(mle==1){          dum=a[imax][k]; 
     /* Computing hessian and covariance matrix */          a[imax][k]=a[j][k]; 
     ftolhess=ftol; /* Usually correct */          a[j][k]=dum; 
     hesscov(matcov, p, npar, delti, ftolhess, func);        } 
  }        *d = -(*d); 
     fprintf(ficres,"# Scales\n");        vv[imax]=vv[j]; 
     printf("# Scales\n");      } 
      for(i=1,jk=1; i <=nlstate; i++){      indx[j]=imax; 
       for(j=1; j <=nlstate+ndeath; j++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
         if (j!=i) {      if (j != n) { 
           fprintf(ficres,"%1d%1d",i,j);        dum=1.0/(a[j][j]); 
           printf("%1d%1d",i,j);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           for(k=1; k<=ncovmodel;k++){      } 
             printf(" %.5e",delti[jk]);    } 
             fprintf(ficres," %.5e",delti[jk]);    free_vector(vv,1,n);  /* Doesn't work */
             jk++;  ;
           }  } 
           printf("\n");  
           fprintf(ficres,"\n");  void lubksb(double **a, int n, int *indx, double b[]) 
         }  { 
       }    int i,ii=0,ip,j; 
       }    double sum; 
       
     k=1;    for (i=1;i<=n;i++) { 
     fprintf(ficres,"# Covariance\n");      ip=indx[i]; 
     printf("# Covariance\n");      sum=b[ip]; 
     for(i=1;i<=npar;i++){      b[ip]=b[i]; 
       /*  if (k>nlstate) k=1;      if (ii) 
       i1=(i-1)/(ncovmodel*nlstate)+1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      else if (sum) ii=i; 
       printf("%s%d%d",alph[k],i1,tab[i]);*/      b[i]=sum; 
       fprintf(ficres,"%3d",i);    } 
       printf("%3d",i);    for (i=n;i>=1;i--) { 
       for(j=1; j<=i;j++){      sum=b[i]; 
         fprintf(ficres," %.5e",matcov[i][j]);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         printf(" %.5e",matcov[i][j]);      b[i]=sum/a[i][i]; 
       }    } 
       fprintf(ficres,"\n");  } 
       printf("\n");  
       k++;  void pstamp(FILE *fichier)
     }  {
        fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     while((c=getc(ficpar))=='#' && c!= EOF){  }
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  /************ Frequencies ********************/
       puts(line);  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[])
       fputs(line,ficparo);  {  /* Some frequencies */
     }    
     ungetc(c,ficpar);    int i, m, jk, k1,i1, j1, bool, z1,j;
      int first;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    double ***freq; /* Frequencies */
        double *pp, **prop;
     if (fage <= 2) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       bage = agemin;    char fileresp[FILENAMELENGTH];
       fage = agemax;    
     }    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    strcpy(fileresp,"p");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
          printf("Problem with prevalence resultfile: %s\n", fileresp);
 /*------------ gnuplot -------------*/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 chdir(pathcd);      exit(0);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    }
     printf("Problem with file graph.gp");goto end;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   }    j1=0;
 #ifdef windows    
   fprintf(ficgp,"cd \"%s\" \n",pathc);    j=cptcoveff;
 #endif    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 m=pow(2,cptcoveff);  
      first=1;
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for(k1=1; k1<=j;k1++){
    for (k1=1; k1<= m ; k1 ++) {      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
 #ifdef windows        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     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);          scanf("%d", i);*/
 #endif        for (i=-5; i<=nlstate+ndeath; i++)  
 #ifdef unix          for (jk=-5; jk<=nlstate+ndeath; jk++)  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);            for(m=iagemin; m <= iagemax+3; m++)
 #endif              freq[i][jk][m]=0;
   
 for (i=1; i<= nlstate ; i ++) {      for (i=1; i<=nlstate; i++)  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(m=iagemin; m <= iagemax+3; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          prop[i][m]=0;
 }        
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        dateintsum=0;
     for (i=1; i<= nlstate ; i ++) {        k2cpt=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (i=1; i<=imx; i++) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");          bool=1;
 }          if  (cptcovn>0) {
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            for (z1=1; z1<=cptcoveff; z1++) 
      for (i=1; i<= nlstate ; i ++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                bool=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }            if (bool==1){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            for(m=firstpass; m<=lastpass; m++){
 #ifdef unix              k2=anint[m][i]+(mint[m][i]/12.);
 fprintf(ficgp,"\nset ter gif small size 400,300");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 #endif                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
    }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                if (m<lastpass) {
   /*2 eme*/                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   for (k1=1; k1<= m ; k1 ++) {                }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);                
                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for (i=1; i<= nlstate+1 ; i ++) {                  dateintsum=dateintsum+k2;
       k=2*i;                  k2cpt++;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                }
       for (j=1; j<= nlstate+1 ; j ++) {                /*}*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
   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(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        pstamp(ficresp);
       for (j=1; j<= nlstate+1 ; j ++) {        if  (cptcovn>0) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresp, "\n#********** Variable "); 
         else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }            fprintf(ficresp, "**********\n#");
       fprintf(ficgp,"\" t\"\" w l 0,");        }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(i=1; i<=nlstate;i++) 
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresp, "\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");        
 }          for(i=iagemin; i <= iagemax+3; i++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          if(i==iagemax+3){
       else fprintf(ficgp,"\" t\"\" w l 0,");            fprintf(ficlog,"Total");
     }          }else{
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            if(first==1){
   }              first=0;
                printf("See log file for details...\n");
   /*3eme*/            }
             fprintf(ficlog,"Age %d", i);
   for (k1=1; k1<= m ; k1 ++) {          }
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(jk=1; jk <=nlstate ; jk++){
       k=2+nlstate*(cpt-1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       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);              pp[jk] += freq[jk][m][i]; 
       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);          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=-1, pos=0; m <=0 ; m++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              pos += freq[jk][m][i];
     }            if(pp[jk]>=1.e-10){
   }              if(first==1){
                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /* CV preval stat */              }
   for (k1=1; k1<= m ; k1 ++) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for (cpt=1; cpt<nlstate ; cpt ++) {            }else{
       k=3;              if(first==1)
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for (i=1; i< nlstate ; i ++)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficgp,"+$%d",k+i+1);            }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          }
        
       l=3+(nlstate+ndeath)*cpt;          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for (i=1; i< nlstate ; i ++) {              pp[jk] += freq[jk][m][i];
         l=3+(nlstate+ndeath)*cpt;          }       
         fprintf(ficgp,"+$%d",l+i+1);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       }            pos += pp[jk];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              posprop += prop[jk][i];
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
     }          for(jk=1; jk <=nlstate ; jk++){
   }            if(pos>=1.e-5){
               if(first==1)
   /* proba elementaires */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    for(i=1,jk=1; i <=nlstate; i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(k=1; k <=(nlstate+ndeath); k++){            }else{
       if (k != i) {              if(first==1)
         for(j=1; j <=ncovmodel; j++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           /*fprintf(ficgp,"%s",alph[1]);*/            }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            if( i <= iagemax){
           jk++;              if(pos>=1.e-5){
           fprintf(ficgp,"\n");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         }                /*probs[i][jk][j1]= pp[jk]/pos;*/
       }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     }              }
     }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   for(jk=1; jk <=m; jk++) {            }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          }
    i=1;          
    for(k2=1; k2<=nlstate; k2++) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
      k3=i;            for(m=-1; m <=nlstate+ndeath; m++)
      for(k=1; k<=(nlstate+ndeath); k++) {              if(freq[jk][m][i] !=0 ) {
        if (k != k2){              if(first==1)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 ij=1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(j=3; j <=ncovmodel; j++) {              }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          if(i <= iagemax)
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            fprintf(ficresp,"\n");
             ij++;          if(first==1)
           }            printf("Others in log...\n");
           else          fprintf(ficlog,"\n");
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }
         }      }
           fprintf(ficgp,")/(1");    }
            dateintmean=dateintsum/k2cpt; 
         for(k1=1; k1 <=nlstate; k1++){     
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    fclose(ficresp);
 ij=1;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
           for(j=3; j <=ncovmodel; j++){    free_vector(pp,1,nlstate);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* End of Freq */
             ij++;  }
           }  
           else  /************ Prevalence ********************/
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
           }  {  
           fprintf(ficgp,")");    /* 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).
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);       We still use firstpass and lastpass as another selection.
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    */
         i=i+ncovmodel;   
        }    int i, m, jk, k1, i1, j1, bool, z1,j;
      }    double ***freq; /* Frequencies */
    }    double *pp, **prop;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    double pos,posprop; 
   }    double  y2; /* in fractional years */
        int iagemin, iagemax;
   fclose(ficgp);  
        iagemin= (int) agemin;
 chdir(path);    iagemax= (int) agemax;
     free_matrix(agev,1,maxwav,1,imx);    /*pp=vector(1,nlstate);*/
     free_ivector(wav,1,imx);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    j1=0;
        
     free_imatrix(s,1,maxwav+1,1,n);    j=cptcoveff;
        if (cptcovn<1) {j=1;ncodemax[1]=1;}
        
     free_ivector(num,1,n);    for(k1=1; k1<=j;k1++){
     free_vector(agedc,1,n);      for(i1=1; i1<=ncodemax[k1];i1++){
     free_vector(weight,1,n);        j1++;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        
     fclose(ficparo);        for (i=1; i<=nlstate; i++)  
     fclose(ficres);          for(m=iagemin; m <= iagemax+3; m++)
     /*  }*/            prop[i][m]=0.0;
           
    /*________fin mle=1_________*/        for (i=1; i<=imx; i++) { /* Each individual */
              bool=1;
           if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
     /* No more information from the sample is required now */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   /* Reads comments: lines beginning with '#' */                bool=0;
   while((c=getc(ficpar))=='#' && c!= EOF){          } 
     ungetc(c,ficpar);          if (bool==1) { 
     fgets(line, MAXLINE, ficpar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     puts(line);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     fputs(line,ficparo);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   ungetc(c,ficpar);                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); 
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 /*--------- index.htm --------*/                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
   if((fichtm=fopen("index.htm","w"))==NULL)    {              }
     printf("Problem with index.htm \n");goto end;            } /* end selection of waves */
   }          }
         }
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n        for(i=iagemin; i <= iagemax+3; i++){  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            posprop += prop[jk][i]; 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          } 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          for(jk=1; jk <=nlstate ; jk++){     
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            if( i <=  iagemax){ 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              if(posprop>=1.e-5){ 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                probs[i][jk][j1]= prop[jk][i]/posprop;
               } else
  fprintf(fichtm," <li>Graphs</li>\n<p>");                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
             } 
  m=cptcoveff;          }/* end jk */ 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        }/* end i */ 
       } /* end i1 */
  j1=0;    } /* end k1 */
  for(k1=1; k1<=m;k1++){    
    for(i1=1; i1<=ncodemax[k1];i1++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
        j1++;    /*free_vector(pp,1,nlstate);*/
        if (cptcovn > 0) {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
          fprintf(fichtm,"<hr>************ Results for covariates");  }  /* End of prevalence */
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  /************* Waves Concatenation ***************/
          fprintf(fichtm," ************\n<hr>");  
        }  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)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  {
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        for(cpt=1; cpt<nlstate;cpt++){       Death is a valid wave (if date is known).
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       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.
     for(cpt=1; cpt<=nlstate;cpt++) {       */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>    int i, mi, m;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      }       double sum=0., jmean=0.;*/
      for(cpt=1; cpt<=nlstate;cpt++) {    int first;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    int j, k=0,jk, ju, jl;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    double sum=0.;
      }    first=0;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    jmin=1e+5;
 health expectancies in states (1) and (2): e%s%d.gif<br>    jmax=-1;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    jmean=0.;
 fprintf(fichtm,"\n</body>");    for(i=1; i<=imx; i++){
    }      mi=0;
  }      m=firstpass;
 fclose(fichtm);      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   /*--------------- Prevalence limit --------------*/          mw[++mi][i]=m;
          if(m >=lastpass)
   strcpy(filerespl,"pl");          break;
   strcat(filerespl,fileres);        else
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          m++;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      }/* end while */
   }      if (s[m][i] > nlstate){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        mi++;     /* Death is another wave */
   fprintf(ficrespl,"#Prevalence limit\n");        /* if(mi==0)  never been interviewed correctly before death */
   fprintf(ficrespl,"#Age ");           /* Only death is a correct wave */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        mw[mi][i]=m;
   fprintf(ficrespl,"\n");      }
    
   prlim=matrix(1,nlstate,1,nlstate);      wav[i]=mi;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if(mi==0){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        nbwarn++;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(first==0){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          first=1;
   k=0;        }
   agebase=agemin;        if(first==1){
   agelim=agemax;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   ftolpl=1.e-10;        }
   i1=cptcoveff;      } /* end mi==0 */
   if (cptcovn < 1){i1=1;}    } /* End individuals */
   
   for(cptcov=1;cptcov<=i1;cptcov++){    for(i=1; i<=imx; i++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(mi=1; mi<wav[i];mi++){
         k=k+1;        if (stepm <=0)
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          dh[mi][i]=1;
         fprintf(ficrespl,"\n#******");        else{
         for(j=1;j<=cptcoveff;j++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if (agedc[i] < 2*AGESUP) {
         fprintf(ficrespl,"******\n");              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                      if(j==0) j=1;  /* Survives at least one month after exam */
         for (age=agebase; age<=agelim; age++){              else if(j<0){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                nberr++;
           fprintf(ficrespl,"%.0f",age );                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           for(i=1; i<=nlstate;i++)                j=1; /* Temporary Dangerous patch */
           fprintf(ficrespl," %.5f", prlim[i][i]);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           fprintf(ficrespl,"\n");                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       }              }
     }              k=k+1;
   fclose(ficrespl);              if (j >= jmax){
   /*------------- h Pij x at various ages ------------*/                jmax=j;
                  ijmax=i;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              if (j <= jmin){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                jmin=j;
   }                ijmin=i;
   printf("Computing pij: result on file '%s' \n", filerespij);              }
                sum=sum+j;
   stepsize=(int) (stepm+YEARM-1)/YEARM;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   if (stepm<=24) stepsize=2;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
   agelim=AGESUP;          }
   hstepm=stepsize*YEARM; /* Every year of age */          else{
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
    /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){            k=k+1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            if (j >= jmax) {
       k=k+1;              jmax=j;
         fprintf(ficrespij,"\n#****** ");              ijmax=i;
         for(j=1;j<=cptcoveff;j++)            }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            else if (j <= jmin){
         fprintf(ficrespij,"******\n");              jmin=j;
                      ijmin=i;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            /*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]);*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(j<0){
           oldm=oldms;savm=savms;              nberr++;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                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(ficrespij,"# Age");              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           for(i=1; i<=nlstate;i++)            }
             for(j=1; j<=nlstate+ndeath;j++)            sum=sum+j;
               fprintf(ficrespij," %1d-%1d",i,j);          }
           fprintf(ficrespij,"\n");          jk= j/stepm;
           for (h=0; h<=nhstepm; h++){          jl= j -jk*stepm;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          ju= j -(jk+1)*stepm;
             for(i=1; i<=nlstate;i++)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
               for(j=1; j<=nlstate+ndeath;j++)            if(jl==0){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              dh[mi][i]=jk;
             fprintf(ficrespij,"\n");              bh[mi][i]=0;
           }            }else{ /* We want a negative bias in order to only have interpolation ie
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    * to avoid the price of an extra matrix product in likelihood */
           fprintf(ficrespij,"\n");              dh[mi][i]=jk+1;
         }              bh[mi][i]=ju;
     }            }
   }          }else{
             if(jl <= -ju){
   fclose(ficrespij);              dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
   /*---------- Health expectancies and variances ------------*/                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
   strcpy(filerest,"t");            }
   strcat(filerest,fileres);            else{
   if((ficrest=fopen(filerest,"w"))==NULL) {              dh[mi][i]=jk+1;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              bh[mi][i]=ju;
   }            }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   strcpy(filerese,"e");              /*  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);*/
   strcat(filerese,fileres);            }
   if((ficreseij=fopen(filerese,"w"))==NULL) {          } /* end if mle */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        }
   }      } /* end wave */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    }
     jmean=sum/k;
  strcpy(fileresv,"v");    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);
   strcat(fileresv,fileres);    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);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }  /*********** Tricode ****************************/
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  void tricode(int *Tvar, int **nbcode, int imx)
   {
   k=0;    /* Uses cptcovn+2*cptcovprod as the number of covariates */
   for(cptcov=1;cptcov<=i1;cptcov++){    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       fprintf(ficrest,"\n#****** ");    int modmaxcovj=0; /* Modality max of covariates j */
       for(j=1;j<=cptcoveff;j++)    cptcoveff=0; 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   
       fprintf(ficrest,"******\n");    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
       fprintf(ficreseij,"******\n");                                 modality of this covariate Vj*/ 
         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(ficresvij,"\n#****** ");                                        modality of the nth covariate of individual i. */
       for(j=1;j<=cptcoveff;j++)        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       fprintf(ficresvij,"******\n");        if (ij > modmaxcovj) modmaxcovj=ij; 
         /* getting the maximum value of the modality of the covariate
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
       oldm=oldms;savm=savms;           female is 1, then modmaxcovj=1.*/
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       oldm=oldms;savm=savms;      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        if( Ndum[i] != 0 )
                ncodemax[j]++; 
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        /* Number of modalities of the j th covariate. In fact
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);           ncodemax[j]=2 (dichotom. variables only) but it could be more for
       fprintf(ficrest,"\n");           historical reasons */
              } /* Ndum[-1] number of undefined modalities */
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       epj=vector(1,nlstate+1);      ij=1; 
       for(age=bage; age <=fage ;age++){      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
         fprintf(ficrest," %.0f",age);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                                       k is a modality. If we have model=V1+V1*sex 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           }            ij++;
           epj[nlstate+1] +=epj[j];          }
         }          if (ij > ncodemax[j]) break; 
         for(i=1, vepp=0.;i <=nlstate;i++)        }  /* end of loop on */
           for(j=1;j <=nlstate;j++)      } /* end of loop on modality */ 
             vepp += vareij[i][j][(int)age];    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    
         for(j=1;j <=nlstate;j++){    for (k=0; k< maxncov; k++) Ndum[k]=0;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    
         }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
         fprintf(ficrest,"\n");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     }     Ndum[ij]++;
   }   }
          
  fclose(ficreseij);   ij=1;
  fclose(ficresvij);   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   fclose(ficrest);     if((Ndum[i]!=0) && (i<=ncovcol)){
   fclose(ficpar);       Tvaraff[ij]=i; /*For printing */
   free_vector(epj,1,nlstate+1);       ij++;
   /*  scanf("%d ",i); */     }
    }
   /*------- Variance limit prevalence------*/     ij--;
    cptcoveff=ij; /*Number of simple covariates*/
 strcpy(fileresvpl,"vpl");  }
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  /*********** Health Expectancies ****************/
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  {
     /* Health expectancies, no variances */
  k=0;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
  for(cptcov=1;cptcov<=i1;cptcov++){    int nhstepma, nstepma; /* Decreasing with age */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double age, agelim, hf;
      k=k+1;    double ***p3mat;
      fprintf(ficresvpl,"\n#****** ");    double eip;
      for(j=1;j<=cptcoveff;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    pstamp(ficreseij);
      fprintf(ficresvpl,"******\n");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
          fprintf(ficreseij,"# Age");
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    for(i=1; i<=nlstate;i++){
      oldm=oldms;savm=savms;      for(j=1; j<=nlstate;j++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficreseij," e%1d%1d ",i,j);
    }      }
  }      fprintf(ficreseij," e%1d. ",i);
     }
   fclose(ficresvpl);    fprintf(ficreseij,"\n");
   
   /*---------- End : free ----------------*/    
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    else  hstepm=estepm;   
      /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);     * if stepm=24 months pijx are given only every 2 years and by summing them
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);     * progression in between and thus overestimating or underestimating according
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);     * to the curvature of the survival function. If, for the same date, we 
       * estimate the model with stepm=1 month, we can keep estepm to 24 months
   free_matrix(matcov,1,npar,1,npar);     * to compare the new estimate of Life expectancy with the same linear 
   free_vector(delti,1,npar);     * hypothesis. A more precise result, taking into account a more precise
       * curvature will be obtained if estepm is as small as stepm. */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
     /* For example we decided to compute the life expectancy with the smallest unit */
   printf("End of Imach\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   /* 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);*/       Look at hpijx to understand the reason of that which relies in memory size
   /*printf("Total time was %d uSec.\n", total_usecs);*/       and note for a fixed period like estepm months */
   /*------ End -----------*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
  end:       means that if the survival funtion is printed only each two years of age and if
 #ifdef windows       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  chdir(pathcd);       results. So we changed our mind and took the option of the best precision.
 #endif    */
  system("wgnuplot graph.plt");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
 #ifdef windows    agelim=AGESUP;
   while (z[0] != 'q') {    /* If stepm=6 months */
     chdir(pathcd);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     printf("\nType e to edit output files, c to start again, and q for exiting: ");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     scanf("%s",z);      
     if (z[0] == 'c') system("./imach");  /* nhstepm age range expressed in number of stepm */
     else if (z[0] == 'e') {    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       chdir(path);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       system("index.htm");    /* if (stepm >= YEARM) hstepm=1;*/
     }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     else if (z[0] == 'q') exit(0);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }  
 #endif    for (age=bage; age<=fage; age ++){ 
 }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           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;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   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[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        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 */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       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];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           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]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     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;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 3 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 3 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 1,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 2,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 2,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 3",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 1,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 1");
         else fprintf(ficgp,"\" t\"\" w l lt 1,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=cptcovn; k>=1;k--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
             Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
             Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
             k1++;
             k2=k2+2;
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutv(strd,strc,strb,'V');
           Tvar[k]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             codtab[h][k]=j;
             codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.7  
changed lines
  Added in v.1.142


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