Diff for /imach/src/imach.c between versions 1.19 and 1.141

version 1.19, 2002/02/20 17:19:10 version 1.141, 2014/01/26 02:42:01
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.141  2014/01/26 02:42:01  brouard
   individuals from different ages are interviewed on their health status    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.140  2011/09/02 10:37:54  brouard
   Health expectancies are computed from the transistions observed between    Summary: times.h is ok with mingw32 now.
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.139  2010/06/14 07:50:17  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   The simplest model is the multinomial logistic model where pij is    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   the probabibility to be observed in state j at the second wave conditional  
   to be observed in state i at the first wave. Therefore the model is:    Revision 1.138  2010/04/30 18:19:40  brouard
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    *** empty log message ***
   is a covariate. If you want to have a more complex model than "constant and  
   age", you should modify the program where the markup    Revision 1.137  2010/04/29 18:11:38  brouard
     *Covariates have to be included here again* invites you to do it.    (Module): Checking covariates for more complex models
   More covariates you add, less is the speed of the convergence.    than V1+V2. A lot of change to be done. Unstable.
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.136  2010/04/26 20:30:53  brouard
   delay between waves is not identical for each individual, or if some    (Module): merging some libgsl code. Fixing computation
   individual missed an interview, the information is not rounded or lost, but    of likelione (using inter/intrapolation if mle = 0) in order to
   taken into account using an interpolation or extrapolation.    get same likelihood as if mle=1.
   hPijx is the probability to be    Some cleaning of code and comments added.
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.135  2009/10/29 15:33:14  brouard
   unobserved intermediate  states. This elementary transition (by month or    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.134  2009/10/29 13:18:53  brouard
   and the contribution of each individual to the likelihood is simply hPijx.    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.133  2009/07/06 10:21:25  brouard
   of the life expectancies. It also computes the prevalence limits.    just nforces
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.132  2009/07/06 08:22:05  brouard
            Institut national d'études démographiques, Paris.    Many tings
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.131  2009/06/20 16:22:47  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Some dimensions resccaled
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.130  2009/05/26 06:44:34  brouard
   **********************************************************************/    (Module): Max Covariate is now set to 20 instead of 8. A
      lot of cleaning with variables initialized to 0. Trying to make
 #include <math.h>    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.129  2007/08/31 13:49:27  lievre
 #include <unistd.h>    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
 #define MAXLINE 256    Revision 1.128  2006/06/30 13:02:05  brouard
 #define FILENAMELENGTH 80    (Module): Clarifications on computing e.j
 /*#define DEBUG*/  
 #define windows    Revision 1.127  2006/04/28 18:11:50  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Yes the sum of survivors was wrong since
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): In order to speed up (in case of numerous covariates) we
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
 #define NINTERVMAX 8    deviation (needs data from the Hessian matrices) which slows the
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    computation.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    In the future we should be able to stop the program is only health
 #define NCOVMAX 8 /* Maximum number of covariates */    expectancies and graph are needed without standard deviations.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.126  2006/04/28 17:23:28  brouard
 #define AGESUP 130    (Module): Yes the sum of survivors was wrong since
 #define AGEBASE 40    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
     Version 0.98h
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.125  2006/04/04 15:20:31  lievre
 int npar=NPARMAX;    Errors in calculation of health expectancies. Age was not initialized.
 int nlstate=2; /* Number of live states */    Forecasting file added.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.124  2006/03/22 17:13:53  lievre
 int popbased=0;    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.123  2006/03/20 10:52:43  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    * imach.c (Module): <title> changed, corresponds to .htm file
 int mle, weightopt;    name. <head> headers where missing.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    * imach.c (Module): Weights can have a decimal point as for
 double jmean; /* Mean space between 2 waves */    English (a comma might work with a correct LC_NUMERIC environment,
 double **oldm, **newm, **savm; /* Working pointers to matrices */    otherwise the weight is truncated).
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Modification of warning when the covariates values are not 0 or
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    1.
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    Version 0.98g
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.122  2006/03/20 09:45:41  brouard
  FILE  *ficresvij;    (Module): Weights can have a decimal point as for
   char fileresv[FILENAMELENGTH];    English (a comma might work with a correct LC_NUMERIC environment,
  FILE  *ficresvpl;    otherwise the weight is truncated).
   char fileresvpl[FILENAMELENGTH];    Modification of warning when the covariates values are not 0 or
     1.
 #define NR_END 1    Version 0.98g
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
 #define NRANSI  
 #define ITMAX 200    * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 #define TOL 2.0e-4    not 1 month. Version 0.98f
   
 #define CGOLD 0.3819660    Revision 1.120  2006/03/16 15:10:38  lievre
 #define ZEPS 1.0e-10    (Module): refinements in the computation of lli if
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.119  2006/03/15 17:42:26  brouard
 #define TINY 1.0e-20    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.118  2006/03/14 18:20:07  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): varevsij Comments added explaining the second
      table of variances if popbased=1 .
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define rint(a) floor(a+0.5)    (Module): Function pstamp added
     (Module): Version 0.98d
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.117  2006/03/14 17:16:22  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 1.116  2006/03/06 10:29:27  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Variance-covariance wrong links and
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    varian-covariance of ej. is needed (Saito).
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 double *weight;  
 int **s; /* Status */    Revision 1.114  2006/02/26 12:57:58  brouard
 double *agedc, **covar, idx;    (Module): Some improvements in processing parameter
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    filename with strsep.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.113  2006/02/24 14:20:24  brouard
 double ftolhess; /* Tolerance for computing hessian */    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 /**************** split *************************/    allocation too.
 static  int split( char *path, char *dirc, char *name )  
 {    Revision 1.112  2006/01/30 09:55:26  brouard
    char *s;                             /* pointer */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    int  l1, l2;                         /* length counters */  
     Revision 1.111  2006/01/25 20:38:18  brouard
    l1 = strlen( path );                 /* length of path */    (Module): Lots of cleaning and bugs added (Gompertz)
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Comments can be added in data file. Missing date values
    s = strrchr( path, '\\' );           /* find last / */    can be a simple dot '.'.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.110  2006/01/25 00:51:50  brouard
       extern char       *getwd( );    (Module): Lots of cleaning and bugs added (Gompertz)
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.109  2006/01/24 19:37:15  brouard
 #else    (Module): Comments (lines starting with a #) are allowed in data.
       extern char       *getcwd( );  
     Revision 1.108  2006/01/19 18:05:42  lievre
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Gnuplot problem appeared...
 #endif    To be fixed
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.107  2006/01/19 16:20:37  brouard
       strcpy( name, path );             /* we've got it */    Test existence of gnuplot in imach path
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.106  2006/01/19 13:24:36  brouard
       l2 = strlen( s );                 /* length of filename */    Some cleaning and links added in html output
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.105  2006/01/05 20:23:19  lievre
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    *** empty log message ***
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.104  2005/09/30 16:11:43  lievre
    l1 = strlen( dirc );                 /* length of directory */    (Module): sump fixed, loop imx fixed, and simplifications.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): If the status is missing at the last wave but we know
    return( 0 );                         /* we're done */    that the person is alive, then we can code his/her status as -2
 }    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /******************************************/    the healthy state at last known wave). Version is 0.98
   
 void replace(char *s, char*t)    Revision 1.103  2005/09/30 15:54:49  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   int i;  
   int lg=20;    Revision 1.102  2004/09/15 17:31:30  brouard
   i=0;    Add the possibility to read data file including tab characters.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.101  2004/09/15 10:38:38  brouard
     (s[i] = t[i]);    Fix on curr_time
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.100  2004/07/12 18:29:06  brouard
 }    Add version for Mac OS X. Just define UNIX in Makefile
   
 int nbocc(char *s, char occ)    Revision 1.99  2004/06/05 08:57:40  brouard
 {    *** empty log message ***
   int i,j=0;  
   int lg=20;    Revision 1.98  2004/05/16 15:05:56  brouard
   i=0;    New version 0.97 . First attempt to estimate force of mortality
   lg=strlen(s);    directly from the data i.e. without the need of knowing the health
   for(i=0; i<= lg; i++) {    state at each age, but using a Gompertz model: log u =a + b*age .
   if  (s[i] == occ ) j++;    This is the basic analysis of mortality and should be done before any
   }    other analysis, in order to test if the mortality estimated from the
   return j;    cross-longitudinal survey is different from the mortality estimated
 }    from other sources like vital statistic data.
   
 void cutv(char *u,char *v, char*t, char occ)    The same imach parameter file can be used but the option for mle should be -3.
 {  
   int i,lg,j,p=0;    Agnès, who wrote this part of the code, tried to keep most of the
   i=0;    former routines in order to include the new code within the former code.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    The output is very simple: only an estimate of the intercept and of
   }    the slope with 95% confident intervals.
   
   lg=strlen(t);    Current limitations:
   for(j=0; j<p; j++) {    A) Even if you enter covariates, i.e. with the
     (u[j] = t[j]);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   }    B) There is no computation of Life Expectancy nor Life Table.
      u[p]='\0';  
     Revision 1.97  2004/02/20 13:25:42  lievre
    for(j=0; j<= lg; j++) {    Version 0.96d. Population forecasting command line is (temporarily)
     if (j>=(p+1))(v[j-p-1] = t[j]);    suppressed.
   }  
 }    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 /********************** nrerror ********************/    rewritten within the same printf. Workaround: many printfs.
   
 void nrerror(char error_text[])    Revision 1.95  2003/07/08 07:54:34  brouard
 {    * imach.c (Repository):
   fprintf(stderr,"ERREUR ...\n");    (Repository): Using imachwizard code to output a more meaningful covariance
   fprintf(stderr,"%s\n",error_text);    matrix (cov(a12,c31) instead of numbers.
   exit(1);  
 }    Revision 1.94  2003/06/27 13:00:02  brouard
 /*********************** vector *******************/    Just cleaning
 double *vector(int nl, int nh)  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   double *v;    (Module): On windows (cygwin) function asctime_r doesn't
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    exist so I changed back to asctime which exists.
   if (!v) nrerror("allocation failure in vector");    (Module): Version 0.96b
   return v-nl+NR_END;  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /************************ free vector ******************/    exist so I changed back to asctime which exists.
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Repository): Duplicated warning errors corrected.
 }    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 /************************ivector *******************************/    is stamped in powell.  We created a new html file for the graphs
 int *ivector(long nl,long nh)    concerning matrix of covariance. It has extension -cov.htm.
 {  
   int *v;    Revision 1.90  2003/06/24 12:34:15  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): Some bugs corrected for windows. Also, when
   if (!v) nrerror("allocation failure in ivector");    mle=-1 a template is output in file "or"mypar.txt with the design
   return v-nl+NR_END;    of the covariance matrix to be input.
 }  
     Revision 1.89  2003/06/24 12:30:52  brouard
 /******************free ivector **************************/    (Module): Some bugs corrected for windows. Also, when
 void free_ivector(int *v, long nl, long nh)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.88  2003/06/23 17:54:56  brouard
     * 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.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.87  2003/06/18 12:26:01  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Version 0.96
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.86  2003/06/17 20:04:08  brouard
   int **m;    (Module): Change position of html and gnuplot routines and added
      routine fileappend.
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.85  2003/06/17 13:12:43  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    * imach.c (Repository): Check when date of death was earlier that
   m += NR_END;    current date of interview. It may happen when the death was just
   m -= nrl;    prior to the death. In this case, dh was negative and likelihood
      was wrong (infinity). We still send an "Error" but patch by
      assuming that the date of death was just one stepm after the
   /* allocate rows and set pointers to them */    interview.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Repository): Because some people have very long ID (first column)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    we changed int to long in num[] and we added a new lvector for
   m[nrl] += NR_END;    memory allocation. But we also truncated to 8 characters (left
   m[nrl] -= ncl;    truncation)
      (Repository): No more line truncation errors.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Revision 1.84  2003/06/13 21:44:43  brouard
   /* return pointer to array of pointers to rows */    * imach.c (Repository): Replace "freqsummary" at a correct
   return m;    place. It differs from routine "prevalence" which may be called
 }    many times. Probs is memory consuming and must be used with
     parcimony.
 /****************** free_imatrix *************************/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.83  2003/06/10 13:39:11  lievre
       long nch,ncl,nrh,nrl;    *** empty log message ***
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.82  2003/06/05 15:57:20  brouard
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Add log in  imach.c and  fullversion number is now printed.
   free((FREE_ARG) (m+nrl-NR_END));  
 }  */
   /*
 /******************* matrix *******************************/     Interpolated Markov Chain
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Short summary of the programme:
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    
   double **m;    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    first survey ("cross") where individuals from different ages are
   if (!m) nrerror("allocation failure 1 in matrix()");    interviewed on their health status or degree of disability (in the
   m += NR_END;    case of a health survey which is our main interest) -2- at least a
   m -= nrl;    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    computed from the time spent in each health state according to a
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    model. More health states you consider, more time is necessary to reach the
   m[nrl] += NR_END;    Maximum Likelihood of the parameters involved in the model.  The
   m[nrl] -= ncl;    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    conditional to be observed in state i at the first wave. Therefore
   return m;    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
     complex model than "constant and age", you should modify the program
 /*************************free matrix ************************/    where the markup *Covariates have to be included here again* invites
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    you to do it.  More covariates you add, slower the
 {    convergence.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    The advantage of this computer programme, compared to a simple
 }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 /******************* ma3x *******************************/    intermediate interview, the information is lost, but taken into
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    account using an interpolation or extrapolation.  
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    hPijx is the probability to be observed in state i at age x+h
   double ***m;    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    states. This elementary transition (by month, quarter,
   if (!m) nrerror("allocation failure 1 in matrix()");    semester or year) is modelled as a multinomial logistic.  The hPx
   m += NR_END;    matrix is simply the matrix product of nh*stepm elementary matrices
   m -= nrl;    and the contribution of each individual to the likelihood is simply
     hPijx.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Also this programme outputs the covariance matrix of the parameters but also
   m[nrl] += NR_END;    of the life expectancies. It also computes the period (stable) prevalence. 
   m[nrl] -= ncl;    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    from the European Union.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    It is copyrighted identically to a GNU software product, ie programme and
   m[nrl][ncl] += NR_END;    software can be distributed freely for non commercial use. Latest version
   m[nrl][ncl] -= nll;    can be accessed at http://euroreves.ined.fr/imach .
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    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
   for (i=nrl+1; i<=nrh; i++) {    
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    **********************************************************************/
     for (j=ncl+1; j<=nch; j++)  /*
       m[i][j]=m[i][j-1]+nlay;    main
   }    read parameterfile
   return m;    read datafile
 }    concatwav
     freqsummary
 /*************************free ma3x ************************/    if (mle >= 1)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)      mlikeli
 {    print results files
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if mle==1 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));       computes hessian
   free((FREE_ARG)(m+nrl-NR_END));    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 /***************** f1dim *************************/    open html file
 extern int ncom;    period (stable) prevalence
 extern double *pcom,*xicom;     for age prevalim()
 extern double (*nrfunc)(double []);    h Pij x
      variance of p varprob
 double f1dim(double x)    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
   int j;    Variance-covariance of DFLE
   double f;    prevalence()
   double *xt;     movingaverage()
      varevsij() 
   xt=vector(1,ncom);    if popbased==1 varevsij(,popbased)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    total life expectancies
   f=(*nrfunc)(xt);    Variance of period (stable) prevalence
   free_vector(xt,1,ncom);   end
   return f;  */
 }  
   
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)   
 {  #include <math.h>
   int iter;  #include <stdio.h>
   double a,b,d,etemp;  #include <stdlib.h>
   double fu,fv,fw,fx;  #include <string.h>
   double ftemp;  #include <unistd.h>
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  #include <limits.h>
    #include <sys/types.h>
   a=(ax < cx ? ax : cx);  #include <sys/stat.h>
   b=(ax > cx ? ax : cx);  #include <errno.h>
   x=w=v=bx;  extern int errno;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  #ifdef LINUX
     xm=0.5*(a+b);  #include <time.h>
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #include "timeval.h"
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #else
     printf(".");fflush(stdout);  #include <sys/time.h>
 #ifdef DEBUG  #endif
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #ifdef GSL
 #endif  #include <gsl/gsl_errno.h>
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #include <gsl/gsl_multimin.h>
       *xmin=x;  #endif
       return fx;  
     }  /* #include <libintl.h> */
     ftemp=fu;  /* #define _(String) gettext (String) */
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  #define GNUPLOTPROGRAM "gnuplot"
       q=2.0*(q-r);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       if (q > 0.0) p = -p;  #define FILENAMELENGTH 132
       q=fabs(q);  
       etemp=e;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       e=d;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
       else {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
         d=p/q;  
         u=x+d;  #define NINTERVMAX 8
         if (u-a < tol2 || b-u < tol2)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
           d=SIGN(tol1,xm-x);  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       }  #define NCOVMAX 20 /* Maximum number of covariates */
     } else {  #define MAXN 20000
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define YEARM 12. /* Number of months per year */
     }  #define AGESUP 130
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define AGEBASE 40
     fu=(*f)(u);  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
     if (fu <= fx) {  #ifdef UNIX
       if (u >= x) a=x; else b=x;  #define DIRSEPARATOR '/'
       SHFT(v,w,x,u)  #define CHARSEPARATOR "/"
         SHFT(fv,fw,fx,fu)  #define ODIRSEPARATOR '\\'
         } else {  #else
           if (u < x) a=u; else b=u;  #define DIRSEPARATOR '\\'
           if (fu <= fw || w == x) {  #define CHARSEPARATOR "\\"
             v=w;  #define ODIRSEPARATOR '/'
             w=u;  #endif
             fv=fw;  
             fw=fu;  /* $Id$ */
           } else if (fu <= fv || v == x || v == w) {  /* $State$ */
             v=u;  
             fv=fu;  char version[]="Imach version 0.98n, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Sicentific Research 25293121)";
           }  char fullversion[]="$Revision$ $Date$"; 
         }  char strstart[80];
   }  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   nrerror("Too many iterations in brent");  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   *xmin=x;  int nvar=0, nforce=0; /* Number of variables, number of forces */
   return fx;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /****************** mnbrak ***********************/  int ndeath=1; /* Number of dead states */
   int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  int popbased=0;
             double (*func)(double))  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   double ulim,u,r,q, dum;  int maxwav=0; /* Maxim number of waves */
   double fu;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
    int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   *fa=(*func)(*ax);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   *fb=(*func)(*bx);                     to the likelihood and the sum of weights (done by funcone)*/
   if (*fb > *fa) {  int mle=1, weightopt=0;
     SHFT(dum,*ax,*bx,dum)  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       SHFT(dum,*fb,*fa,dum)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   *cx=(*bx)+GOLD*(*bx-*ax);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   *fc=(*func)(*cx);  double jmean=1; /* Mean space between 2 waves */
   while (*fb > *fc) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
     r=(*bx-*ax)*(*fb-*fc);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     q=(*bx-*cx)*(*fb-*fa);  /*FILE *fic ; */ /* Used in readdata only */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  FILE *ficlog, *ficrespow;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int globpr=0; /* Global variable for printing or not */
     if ((*bx-u)*(u-*cx) > 0.0) {  double fretone; /* Only one call to likelihood */
       fu=(*func)(u);  long ipmx=0; /* Number of contributions */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double sw; /* Sum of weights */
       fu=(*func)(u);  char filerespow[FILENAMELENGTH];
       if (fu < *fc) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  FILE *ficresilk;
           SHFT(*fb,*fc,fu,(*func)(u))  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
           }  FILE *ficresprobmorprev;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  FILE *fichtm, *fichtmcov; /* Html File */
       u=ulim;  FILE *ficreseij;
       fu=(*func)(u);  char filerese[FILENAMELENGTH];
     } else {  FILE *ficresstdeij;
       u=(*cx)+GOLD*(*cx-*bx);  char fileresstde[FILENAMELENGTH];
       fu=(*func)(u);  FILE *ficrescveij;
     }  char filerescve[FILENAMELENGTH];
     SHFT(*ax,*bx,*cx,u)  FILE  *ficresvij;
       SHFT(*fa,*fb,*fc,fu)  char fileresv[FILENAMELENGTH];
       }  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /*************** linmin ************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 int ncom;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 double *pcom,*xicom;  char command[FILENAMELENGTH];
 double (*nrfunc)(double []);  int  outcmd=0;
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 {  
   double brent(double ax, double bx, double cx,  char filelog[FILENAMELENGTH]; /* Log file */
                double (*f)(double), double tol, double *xmin);  char filerest[FILENAMELENGTH];
   double f1dim(double x);  char fileregp[FILENAMELENGTH];
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  char popfile[FILENAMELENGTH];
               double *fc, double (*func)(double));  
   int j;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
    struct timezone tzp;
   ncom=n;  extern int gettimeofday();
   pcom=vector(1,n);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   xicom=vector(1,n);  long time_value;
   nrfunc=func;  extern long time();
   for (j=1;j<=n;j++) {  char strcurr[80], strfor[80];
     pcom[j]=p[j];  
     xicom[j]=xi[j];  char *endptr;
   }  long lval;
   ax=0.0;  double dval;
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define NR_END 1
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define FREE_ARG char*
 #ifdef DEBUG  #define FTOL 1.0e-10
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  #define NRANSI 
   for (j=1;j<=n;j++) {  #define ITMAX 200 
     xi[j] *= xmin;  
     p[j] += xi[j];  #define TOL 2.0e-4 
   }  
   free_vector(xicom,1,n);  #define CGOLD 0.3819660 
   free_vector(pcom,1,n);  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /*************** powell ************************/  #define GOLD 1.618034 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define GLIMIT 100.0 
             double (*func)(double []))  #define TINY 1.0e-20 
 {  
   void linmin(double p[], double xi[], int n, double *fret,  static double maxarg1,maxarg2;
               double (*func)(double []));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   int i,ibig,j;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double del,t,*pt,*ptt,*xit;    
   double fp,fptt;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   double *xits;  #define rint(a) floor(a+0.5)
   pt=vector(1,n);  
   ptt=vector(1,n);  static double sqrarg;
   xit=vector(1,n);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   xits=vector(1,n);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   *fret=(*func)(p);  int agegomp= AGEGOMP;
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  int imx; 
     fp=(*fret);  int stepm=1;
     ibig=0;  /* Stepm, step in month: minimum step interpolation*/
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int estepm;
     for (i=1;i<=n;i++)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  int m,nb;
     for (i=1;i<=n;i++) {  long *num;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       fptt=(*fret);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #ifdef DEBUG  double **pmmij, ***probs;
       printf("fret=%lf \n",*fret);  double *ageexmed,*agecens;
 #endif  double dateintmean=0;
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  double *weight;
       if (fabs(fptt-(*fret)) > del) {  int **s; /* Status */
         del=fabs(fptt-(*fret));  double *agedc;
         ibig=i;  double  **covar; /**< covar[i,j], value of jth covariate for individual i,
       }                    * covar=matrix(0,NCOVMAX,1,n); 
 #ifdef DEBUG                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       printf("%d %.12e",i,(*fret));  double  idx; 
       for (j=1;j<=n;j++) {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int **codtab; /**< codtab=imatrix(1,100,1,10); */
         printf(" x(%d)=%.12e",j,xit[j]);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       }  double *lsurv, *lpop, *tpop;
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       printf("\n");  double ftolhess; /* Tolerance for computing hessian */
 #endif  
     }  /**************** split *************************/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 #ifdef DEBUG  {
       int k[2],l;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       k[0]=1;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       k[1]=-1;    */ 
       printf("Max: %.12e",(*func)(p));    char  *ss;                            /* pointer */
       for (j=1;j<=n;j++)    int   l1, l2;                         /* length counters */
         printf(" %.12e",p[j]);  
       printf("\n");    l1 = strlen(path );                   /* length of path */
       for(l=0;l<=1;l++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         for (j=1;j<=n;j++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      strcpy( name, path );               /* we got the fullname name because no directory */
         }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       }      /* get current working directory */
 #endif      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
       free_vector(xit,1,n);      }
       free_vector(xits,1,n);      /* got dirc from getcwd*/
       free_vector(ptt,1,n);      printf(" DIRC = %s \n",dirc);
       free_vector(pt,1,n);    } else {                              /* strip direcotry from path */
       return;      ss++;                               /* after this, the filename */
     }      l2 = strlen( ss );                  /* length of filename */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (j=1;j<=n;j++) {      strcpy( name, ss );         /* save file name */
       ptt[j]=2.0*p[j]-pt[j];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       xit[j]=p[j]-pt[j];      dirc[l1-l2] = 0;                    /* add zero */
       pt[j]=p[j];      printf(" DIRC2 = %s \n",dirc);
     }    }
     fptt=(*func)(ptt);    /* We add a separator at the end of dirc if not exists */
     if (fptt < fp) {    l1 = strlen( dirc );                  /* length of directory */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    if( dirc[l1-1] != DIRSEPARATOR ){
       if (t < 0.0) {      dirc[l1] =  DIRSEPARATOR;
         linmin(p,xit,n,fret,func);      dirc[l1+1] = 0; 
         for (j=1;j<=n;j++) {      printf(" DIRC3 = %s \n",dirc);
           xi[j][ibig]=xi[j][n];    }
           xi[j][n]=xit[j];    ss = strrchr( name, '.' );            /* find last / */
         }    if (ss >0){
 #ifdef DEBUG      ss++;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      strcpy(ext,ss);                     /* save extension */
         for(j=1;j<=n;j++)      l1= strlen( name);
           printf(" %.12e",xit[j]);      l2= strlen(ss)+1;
         printf("\n");      strncpy( finame, name, l1-l2);
 #endif      finame[l1-l2]= 0;
       }    }
     }  
   }    return( 0 );                          /* we're done */
 }  }
   
 /**** Prevalence limit ****************/  
   /******************************************/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  void replace_back_to_slash(char *s, char*t)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  {
      matrix by transitions matrix until convergence is reached */    int i;
     int lg=0;
   int i, ii,j,k;    i=0;
   double min, max, maxmin, maxmax,sumnew=0.;    lg=strlen(t);
   double **matprod2();    for(i=0; i<= lg; i++) {
   double **out, cov[NCOVMAX], **pmij();      (s[i] = t[i]);
   double **newm;      if (t[i]== '\\') s[i]='/';
   double agefin, delaymax=50 ; /* Max number of years to converge */    }
   }
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  char *trimbb(char *out, char *in)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     }    char *s;
     s=out;
    cov[1]=1.;    while (*in != '\0'){
        while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        in++;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      }
     newm=savm;      *out++ = *in++;
     /* Covariates have to be included here again */    }
      cov[2]=agefin;    *out='\0';
      return s;
       for (k=1; k<=cptcovn;k++) {  }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  char *cutv(char *blocc, char *alocc, char *in, char occ)
       }  {
       for (k=1; k<=cptcovage;k++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       for (k=1; k<=cptcovprod;k++)       gives blocc="abcdef2ghi" and alocc="j".
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    char *s, *t;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    t=in;s=in;
     while (*in != '\0'){
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      while( *in == occ){
         *blocc++ = *in++;
     savm=oldm;        s=in;
     oldm=newm;      }
     maxmax=0.;      *blocc++ = *in++;
     for(j=1;j<=nlstate;j++){    }
       min=1.;    if (s == t) /* occ not found */
       max=0.;      *(blocc-(in-s))='\0';
       for(i=1; i<=nlstate; i++) {    else
         sumnew=0;      *(blocc-(in-s)-1)='\0';
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    in=s;
         prlim[i][j]= newm[i][j]/(1-sumnew);    while ( *in != '\0'){
         max=FMAX(max,prlim[i][j]);      *alocc++ = *in++;
         min=FMIN(min,prlim[i][j]);    }
       }  
       maxmin=max-min;    *alocc='\0';
       maxmax=FMAX(maxmax,maxmin);    return s;
     }  }
     if(maxmax < ftolpl){  
       return prlim;  int nbocc(char *s, char occ)
     }  {
   }    int i,j=0;
 }    int lg=20;
     i=0;
 /*************** transition probabilities ***************/    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    if  (s[i] == occ ) j++;
 {    }
   double s1, s2;    return j;
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   /* void cutv(char *u,char *v, char*t, char occ) */
     for(i=1; i<= nlstate; i++){  /* { */
     for(j=1; j<i;j++){  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
         /*s2 += param[i][j][nc]*cov[nc];*/  /*      gives u="abcdef2ghi" and v="j" *\/ */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*   int i,lg,j,p=0; */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /*   i=0; */
       }  /*   lg=strlen(t); */
       ps[i][j]=s2;  /*   for(j=0; j<=lg-1; j++) { */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     }  /*   } */
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*   for(j=0; j<p; j++) { */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*     (u[j] = t[j]); */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /*   } */
       }  /*      u[p]='\0'; */
       ps[i][j]=(s2);  
     }  /*    for(j=0; j<= lg; j++) { */
   }  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     /*ps[3][2]=1;*/  /*   } */
   /* } */
   for(i=1; i<= nlstate; i++){  
      s1=0;  /********************** nrerror ********************/
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  void nrerror(char error_text[])
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       s1+=exp(ps[i][j]);    fprintf(stderr,"ERREUR ...\n");
     ps[i][i]=1./(s1+1.);    fprintf(stderr,"%s\n",error_text);
     for(j=1; j<i; j++)    exit(EXIT_FAILURE);
       ps[i][j]= exp(ps[i][j])*ps[i][i];  }
     for(j=i+1; j<=nlstate+ndeath; j++)  /*********************** vector *******************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double *vector(int nl, int nh)
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  {
   } /* end i */    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    if (!v) nrerror("allocation failure in vector");
     for(jj=1; jj<= nlstate+ndeath; jj++){    return v-nl+NR_END;
       ps[ii][jj]=0;  }
       ps[ii][ii]=1;  
     }  /************************ free vector ******************/
   }  void free_vector(double*v, int nl, int nh)
   {
     free((FREE_ARG)(v+nl-NR_END));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /************************ivector *******************************/
    }  int *ivector(long nl,long nh)
     printf("\n ");  {
     }    int *v;
     printf("\n ");printf("%lf ",cov[2]);*/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /*    if (!v) nrerror("allocation failure in ivector");
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    return v-nl+NR_END;
   goto end;*/  }
     return ps;  
 }  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
 /**************** Product of 2 matrices ******************/  {
     free((FREE_ARG)(v+nl-NR_END));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /************************lvector *******************************/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  long *lvector(long nl,long nh)
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    long *v;
      a pointer to pointers identical to out */    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   long i, j, k;    if (!v) nrerror("allocation failure in ivector");
   for(i=nrl; i<= nrh; i++)    return v-nl+NR_END;
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
   return out;  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
   
 /************* Higher Matrix Product ***************/  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 {  { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
      duration (i.e. until    int **m; 
      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    /* allocate pointers to rows */ 
      (typically every 2 years instead of every month which is too big).    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      Model is determined by parameters x and covariates have to be    if (!m) nrerror("allocation failure 1 in matrix()"); 
      included manually here.    m += NR_END; 
     m -= nrl; 
      */    
     
   int i, j, d, h, k;    /* allocate rows and set pointers to them */ 
   double **out, cov[NCOVMAX];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double **newm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   /* Hstepm could be zero and should return the unit matrix */    m[nrl] -= ncl; 
   for (i=1;i<=nlstate+ndeath;i++)    
     for (j=1;j<=nlstate+ndeath;j++){    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    
       po[i][j][0]=(i==j ? 1.0 : 0.0);    /* return pointer to array of pointers to rows */ 
     }    return m; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  } 
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  /****************** free_imatrix *************************/
       newm=savm;  void free_imatrix(m,nrl,nrh,ncl,nch)
       /* Covariates have to be included here again */        int **m;
       cov[1]=1.;        long nch,ncl,nrh,nrl; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;       /* free an int matrix allocated by imatrix() */ 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  { 
       for (k=1; k<=cptcovage;k++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG) (m+nrl-NR_END)); 
       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]]];  
   /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  {
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double **m;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       oldm=newm;    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     for(i=1; i<=nlstate+ndeath; i++)    m -= nrl;
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
          */    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
   } /* end h */  
   return po;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
 /*************** log-likelihood *************/  }
 double func( double *x)  
 {  /*************************free matrix ************************/
   int i, ii, j, k, mi, d, kk;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double sw; /* Sum of weights */    free((FREE_ARG)(m+nrl-NR_END));
   double lli; /* Individual log likelihood */  }
   long ipmx;  
   /*extern weight */  /******************* ma3x *******************************/
   /* We are differentiating ll according to initial status */  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  {
   /*for(i=1;i<imx;i++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     printf(" %d\n",s[4][i]);    double ***m;
   */  
   cov[1]=1.;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
   for(k=1; k<=nlstate; k++) ll[k]=0.;    m += NR_END;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    m -= nrl;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (ii=1;ii<=nlstate+ndeath;ii++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    m[nrl] += NR_END;
       for(d=0; d<dh[mi][i]; d++){    m[nrl] -= ncl;
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
            m[nrl][ncl] += NR_END;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    m[nrl][ncl] -= nll;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    for (j=ncl+1; j<=nch; j++) 
         savm=oldm;      m[nrl][j]=m[nrl][j-1]+nlay;
         oldm=newm;    
            for (i=nrl+1; i<=nrh; i++) {
              m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       } /* end mult */      for (j=ncl+1; j<=nch; j++) 
              m[i][j]=m[i][j-1]+nlay;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    return m; 
       ipmx +=1;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       sw += weight[i];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    */
     } /* end of wave */  }
   } /* end of individual */  
   /*************************free ma3x ************************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  {
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   return -l;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
   
 /*********** Maximum Likelihood Estimation ***************/  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    /* Caution optionfilefiname is hidden */
   int i,j, iter;    strcpy(tmpout,optionfilefiname);
   double **xi,*delti;    strcat(tmpout,"/"); /* Add to the right */
   double fret;    strcat(tmpout,fileres);
   xi=matrix(1,npar,1,npar);    return tmpout;
   for (i=1;i<=npar;i++)  }
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  /*************** function subdirf2 ***********/
   printf("Powell\n");  char *subdirf2(char fileres[], char *preop)
   powell(p,xi,npar,ftol,&iter,&fret,func);  {
     
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    /* Caution optionfilefiname is hidden */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 }    strcat(tmpout,preop);
     strcat(tmpout,fileres);
 /**** Computes Hessian and covariance matrix ***/    return tmpout;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  /*************** function subdirf3 ***********/
   double **hess;  char *subdirf3(char fileres[], char *preop, char *preop2)
   int i, j,jk;  {
   int *indx;    
     /* Caution optionfilefiname is hidden */
   double hessii(double p[], double delta, int theta, double delti[]);    strcpy(tmpout,optionfilefiname);
   double hessij(double p[], double delti[], int i, int j);    strcat(tmpout,"/");
   void lubksb(double **a, int npar, int *indx, double b[]) ;    strcat(tmpout,preop);
   void ludcmp(double **a, int npar, int *indx, double *d) ;    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
   hess=matrix(1,npar,1,npar);    return tmpout;
   }
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  /***************** f1dim *************************/
     printf("%d",i);fflush(stdout);  extern int ncom; 
     hess[i][i]=hessii(p,ftolhess,i,delti);  extern double *pcom,*xicom;
     /*printf(" %f ",p[i]);*/  extern double (*nrfunc)(double []); 
     /*printf(" %lf ",hess[i][i]);*/   
   }  double f1dim(double x) 
    { 
   for (i=1;i<=npar;i++) {    int j; 
     for (j=1;j<=npar;j++)  {    double f;
       if (j>i) {    double *xt; 
         printf(".%d%d",i,j);fflush(stdout);   
         hess[i][j]=hessij(p,delti,i,j);    xt=vector(1,ncom); 
         hess[j][i]=hess[i][j];        for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         /*printf(" %lf ",hess[i][j]);*/    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
     }    return f; 
   }  } 
   printf("\n");  
   /*****************brent *************************/
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
    { 
   a=matrix(1,npar,1,npar);    int iter; 
   y=matrix(1,npar,1,npar);    double a,b,d,etemp;
   x=vector(1,npar);    double fu,fv,fw,fx;
   indx=ivector(1,npar);    double ftemp;
   for (i=1;i<=npar;i++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    double e=0.0; 
   ludcmp(a,npar,indx,&pd);   
     a=(ax < cx ? ax : cx); 
   for (j=1;j<=npar;j++) {    b=(ax > cx ? ax : cx); 
     for (i=1;i<=npar;i++) x[i]=0;    x=w=v=bx; 
     x[j]=1;    fw=fv=fx=(*f)(x); 
     lubksb(a,npar,indx,x);    for (iter=1;iter<=ITMAX;iter++) { 
     for (i=1;i<=npar;i++){      xm=0.5*(a+b); 
       matcov[i][j]=x[i];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   printf("\n#Hessian matrix#\n");  #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++) {      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);
       printf("%.3e ",hess[i][j]);      /*          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");      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   }        *xmin=x; 
         return fx; 
   /* Recompute Inverse */      } 
   for (i=1;i<=npar;i++)      ftemp=fu;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      if (fabs(e) > tol1) { 
   ludcmp(a,npar,indx,&pd);        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
   /*  printf("\n#Hessian matrix recomputed#\n");        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   for (j=1;j<=npar;j++) {        if (q > 0.0) p = -p; 
     for (i=1;i<=npar;i++) x[i]=0;        q=fabs(q); 
     x[j]=1;        etemp=e; 
     lubksb(a,npar,indx,x);        e=d; 
     for (i=1;i<=npar;i++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       y[i][j]=x[i];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       printf("%.3e ",y[i][j]);        else { 
     }          d=p/q; 
     printf("\n");          u=x+d; 
   }          if (u-a < tol2 || b-u < tol2) 
   */            d=SIGN(tol1,xm-x); 
         } 
   free_matrix(a,1,npar,1,npar);      } else { 
   free_matrix(y,1,npar,1,npar);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   free_vector(x,1,npar);      } 
   free_ivector(indx,1,npar);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   free_matrix(hess,1,npar,1,npar);      fu=(*f)(u); 
       if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 }        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
 /*************** hessian matrix ****************/          } else { 
 double hessii( double x[], double delta, int theta, double delti[])            if (u < x) a=u; else b=u; 
 {            if (fu <= fw || w == x) { 
   int i;              v=w; 
   int l=1, lmax=20;              w=u; 
   double k1,k2;              fv=fw; 
   double p2[NPARMAX+1];              fw=fu; 
   double res;            } else if (fu <= fv || v == x || v == w) { 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;              v=u; 
   double fx;              fv=fu; 
   int k=0,kmax=10;            } 
   double l1;          } 
     } 
   fx=func(x);    nrerror("Too many iterations in brent"); 
   for (i=1;i<=npar;i++) p2[i]=x[i];    *xmin=x; 
   for(l=0 ; l <=lmax; l++){    return fx; 
     l1=pow(10,l);  } 
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  /****************** mnbrak ***********************/
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       k1=func(p2)-fx;              double (*func)(double)) 
       p2[theta]=x[theta]-delt;  { 
       k2=func(p2)-fx;    double ulim,u,r,q, dum;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double fu; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */   
          *fa=(*func)(*ax); 
 #ifdef DEBUG    *fb=(*func)(*bx); 
       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);    if (*fb > *fa) { 
 #endif      SHFT(dum,*ax,*bx,dum) 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        SHFT(dum,*fb,*fa,dum) 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        } 
         k=kmax;    *cx=(*bx)+GOLD*(*bx-*ax); 
       }    *fc=(*func)(*cx); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    while (*fb > *fc) { 
         k=kmax; l=lmax*10.;      r=(*bx-*ax)*(*fb-*fc); 
       }      q=(*bx-*cx)*(*fb-*fa); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         delts=delt;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     }      if ((*bx-u)*(u-*cx) > 0.0) { 
   }        fu=(*func)(u); 
   delti[theta]=delts;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   return res;        fu=(*func)(u); 
          if (fu < *fc) { 
 }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 double hessij( double x[], double delti[], int thetai,int thetaj)            } 
 {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   int i;        u=ulim; 
   int l=1, l1, lmax=20;        fu=(*func)(u); 
   double k1,k2,k3,k4,res,fx;      } else { 
   double p2[NPARMAX+1];        u=(*cx)+GOLD*(*cx-*bx); 
   int k;        fu=(*func)(u); 
       } 
   fx=func(x);      SHFT(*ax,*bx,*cx,u) 
   for (k=1; k<=2; k++) {        SHFT(*fa,*fb,*fc,fu) 
     for (i=1;i<=npar;i++) p2[i]=x[i];        } 
     p2[thetai]=x[thetai]+delti[thetai]/k;  } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;  /*************** linmin ************************/
    
     p2[thetai]=x[thetai]+delti[thetai]/k;  int ncom; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  double *pcom,*xicom;
     k2=func(p2)-fx;  double (*nrfunc)(double []); 
     
     p2[thetai]=x[thetai]-delti[thetai]/k;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  { 
     k3=func(p2)-fx;    double brent(double ax, double bx, double cx, 
                   double (*f)(double), double tol, double *xmin); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    double f1dim(double x); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     k4=func(p2)-fx;                double *fc, double (*func)(double)); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    int j; 
 #ifdef DEBUG    double xx,xmin,bx,ax; 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    double fx,fb,fa;
 #endif   
   }    ncom=n; 
   return res;    pcom=vector(1,n); 
 }    xicom=vector(1,n); 
     nrfunc=func; 
 /************** Inverse of matrix **************/    for (j=1;j<=n;j++) { 
 void ludcmp(double **a, int n, int *indx, double *d)      pcom[j]=p[j]; 
 {      xicom[j]=xi[j]; 
   int i,imax,j,k;    } 
   double big,dum,sum,temp;    ax=0.0; 
   double *vv;    xx=1.0; 
      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   vv=vector(1,n);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   *d=1.0;  #ifdef DEBUG
   for (i=1;i<=n;i++) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     big=0.0;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (j=1;j<=n;j++)  #endif
       if ((temp=fabs(a[i][j])) > big) big=temp;    for (j=1;j<=n;j++) { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      xi[j] *= xmin; 
     vv[i]=1.0/big;      p[j] += xi[j]; 
   }    } 
   for (j=1;j<=n;j++) {    free_vector(xicom,1,n); 
     for (i=1;i<j;i++) {    free_vector(pcom,1,n); 
       sum=a[i][j];  } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  char *asc_diff_time(long time_sec, char ascdiff[])
     }  {
     big=0.0;    long sec_left, days, hours, minutes;
     for (i=j;i<=n;i++) {    days = (time_sec) / (60*60*24);
       sum=a[i][j];    sec_left = (time_sec) % (60*60*24);
       for (k=1;k<j;k++)    hours = (sec_left) / (60*60) ;
         sum -= a[i][k]*a[k][j];    sec_left = (sec_left) %(60*60);
       a[i][j]=sum;    minutes = (sec_left) /60;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    sec_left = (sec_left) % (60);
         big=dum;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
         imax=i;    return ascdiff;
       }  }
     }  
     if (j != imax) {  /*************** powell ************************/
       for (k=1;k<=n;k++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         dum=a[imax][k];              double (*func)(double [])) 
         a[imax][k]=a[j][k];  { 
         a[j][k]=dum;    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
       *d = -(*d);    int i,ibig,j; 
       vv[imax]=vv[j];    double del,t,*pt,*ptt,*xit;
     }    double fp,fptt;
     indx[j]=imax;    double *xits;
     if (a[j][j] == 0.0) a[j][j]=TINY;    int niterf, itmp;
     if (j != n) {  
       dum=1.0/(a[j][j]);    pt=vector(1,n); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    ptt=vector(1,n); 
     }    xit=vector(1,n); 
   }    xits=vector(1,n); 
   free_vector(vv,1,n);  /* Doesn't work */    *fret=(*func)(p); 
 ;    for (j=1;j<=n;j++) pt[j]=p[j]; 
 }    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 void lubksb(double **a, int n, int *indx, double b[])      ibig=0; 
 {      del=0.0; 
   int i,ii=0,ip,j;      last_time=curr_time;
   double sum;      (void) gettimeofday(&curr_time,&tzp);
        printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   for (i=1;i<=n;i++) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
     ip=indx[i];  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     sum=b[ip];     for (i=1;i<=n;i++) {
     b[ip]=b[i];        printf(" %d %.12f",i, p[i]);
     if (ii)        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        fprintf(ficrespow," %.12lf", p[i]);
     else if (sum) ii=i;      }
     b[i]=sum;      printf("\n");
   }      fprintf(ficlog,"\n");
   for (i=n;i>=1;i--) {      fprintf(ficrespow,"\n");fflush(ficrespow);
     sum=b[i];      if(*iter <=3){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        tm = *localtime(&curr_time.tv_sec);
     b[i]=sum/a[i][i];        strcpy(strcurr,asctime(&tm));
   }  /*       asctime_r(&tm,strcurr); */
 }        forecast_time=curr_time; 
         itmp = strlen(strcurr);
 /************ Frequencies ********************/        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)          strcurr[itmp-1]='\0';
 {  /* Some frequencies */        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
          fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for(niterf=10;niterf<=30;niterf+=10){
   double ***freq; /* Frequencies */          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   double *pp;          tmf = *localtime(&forecast_time.tv_sec);
   double pos, k2, dateintsum=0,k2cpt=0;  /*      asctime_r(&tmf,strfor); */
   FILE *ficresp;          strcpy(strfor,asctime(&tmf));
   char fileresp[FILENAMELENGTH];          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   pp=vector(1,nlstate);          strfor[itmp-1]='\0';
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          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);
   strcpy(fileresp,"p");          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);
   strcat(fileresp,fileres);        }
   if((ficresp=fopen(fileresp,"w"))==NULL) {      }
     printf("Problem with prevalence resultfile: %s\n", fileresp);      for (i=1;i<=n;i++) { 
     exit(0);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  #ifdef DEBUG
   j1=0;        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   j=cptcoveff;  #endif
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   for(k1=1; k1<=j;k1++){        linmin(p,xit,n,fret,func); 
    for(i1=1; i1<=ncodemax[k1];i1++){        if (fabs(fptt-(*fret)) > del) { 
        j1++;          del=fabs(fptt-(*fret)); 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          ibig=i; 
          scanf("%d", i);*/        } 
         for (i=-1; i<=nlstate+ndeath; i++)    #ifdef DEBUG
          for (jk=-1; jk<=nlstate+ndeath; jk++)          printf("%d %.12e",i,(*fret));
            for(m=agemin; m <= agemax+3; m++)        fprintf(ficlog,"%d %.12e",i,(*fret));
              freq[i][jk][m]=0;        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         dateintsum=0;          printf(" x(%d)=%.12e",j,xit[j]);
         k2cpt=0;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
        for (i=1; i<=imx; i++) {        }
          bool=1;        for(j=1;j<=n;j++) {
          if  (cptcovn>0) {          printf(" p=%.12e",p[j]);
            for (z1=1; z1<=cptcoveff; z1++)          fprintf(ficlog," p=%.12e",p[j]);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
                bool=0;        printf("\n");
          }        fprintf(ficlog,"\n");
          if (bool==1) {  #endif
            for(m=firstpass; m<=lastpass; m++){      } 
              k2=anint[m][i]+(mint[m][i]/12.);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  #ifdef DEBUG
                if(agev[m][i]==0) agev[m][i]=agemax+1;        int k[2],l;
                if(agev[m][i]==1) agev[m][i]=agemax+2;        k[0]=1;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        k[1]=-1;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        printf("Max: %.12e",(*func)(p));
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
                  dateintsum=dateintsum+k2;        for (j=1;j<=n;j++) {
                  k2cpt++;          printf(" %.12e",p[j]);
                }          fprintf(ficlog," %.12e",p[j]);
         }
              }        printf("\n");
            }        fprintf(ficlog,"\n");
          }        for(l=0;l<=1;l++) {
        }          for (j=1;j<=n;j++) {
         if  (cptcovn>0) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
          fprintf(ficresp, "\n#********** Variable ");            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
        fprintf(ficresp, "**********\n#");          }
         }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        for(i=1; i<=nlstate;i++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        }
        fprintf(ficresp, "\n");  #endif
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){  
     if(i==(int)agemax+3)        free_vector(xit,1,n); 
       printf("Total");        free_vector(xits,1,n); 
     else        free_vector(ptt,1,n); 
       printf("Age %d", i);        free_vector(pt,1,n); 
     for(jk=1; jk <=nlstate ; jk++){        return; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      } 
         pp[jk] += freq[jk][m][i];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { 
     for(jk=1; jk <=nlstate ; jk++){        ptt[j]=2.0*p[j]-pt[j]; 
       for(m=-1, pos=0; m <=0 ; m++)        xit[j]=p[j]-pt[j]; 
         pos += freq[jk][m][i];        pt[j]=p[j]; 
       if(pp[jk]>=1.e-10)      } 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      fptt=(*func)(ptt); 
       else      if (fptt < fp) { 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     }        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
      for(jk=1; jk <=nlstate ; jk++){          for (j=1;j<=n;j++) { 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            xi[j][ibig]=xi[j][n]; 
         pp[jk] += freq[jk][m][i];            xi[j][n]=xit[j]; 
      }          }
   #ifdef DEBUG
     for(jk=1,pos=0; jk <=nlstate ; jk++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       pos += pp[jk];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(jk=1; jk <=nlstate ; jk++){          for(j=1;j<=n;j++){
       if(pos>=1.e-5)            printf(" %.12e",xit[j]);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            fprintf(ficlog," %.12e",xit[j]);
       else          }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          printf("\n");
       if( i <= (int) agemax){          fprintf(ficlog,"\n");
         if(pos>=1.e-5){  #endif
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        }
           probs[i][jk][j1]= pp[jk]/pos;      } 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    } 
         }  } 
       else  
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  /**** Prevalence limit (stable or period prevalence)  ****************/
       }  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(jk=-1; jk <=nlstate+ndeath; jk++)  {
       for(m=-1; m <=nlstate+ndeath; m++)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);       matrix by transitions matrix until convergence is reached */
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");    int i, ii,j,k;
     printf("\n");    double min, max, maxmin, maxmax,sumnew=0.;
     }    double **matprod2();
     }    double **out, cov[NCOVMAX+1], **pmij();
  }    double **newm;
   dateintmean=dateintsum/k2cpt;    double agefin, delaymax=50 ; /* Max number of years to converge */
    
   fclose(ficresp);    for (ii=1;ii<=nlstate+ndeath;ii++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (j=1;j<=nlstate+ndeath;j++){
   free_vector(pp,1,nlstate);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   /* End of Freq */  
 }     cov[1]=1.;
    
 /************ Prevalence ********************/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {  /* Some frequencies */      newm=savm;
        /* Covariates have to be included here again */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      cov[2]=agefin;
   double ***freq; /* Frequencies */      
   double *pp;      for (k=1; k<=cptcovn;k++) {
   double pos, k2;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   pp=vector(1,nlstate);      }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        for (k=1; k<=cptcovprod;k++)
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   j1=0;      
        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   j=cptcoveff;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
        out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
  for(k1=1; k1<=j;k1++){      
     for(i1=1; i1<=ncodemax[k1];i1++){      savm=oldm;
       j1++;      oldm=newm;
        maxmax=0.;
       for (i=-1; i<=nlstate+ndeath; i++)        for(j=1;j<=nlstate;j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)          min=1.;
           for(m=agemin; m <= agemax+3; m++)        max=0.;
             freq[i][jk][m]=0;        for(i=1; i<=nlstate; i++) {
                sumnew=0;
       for (i=1; i<=imx; i++) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         bool=1;          prlim[i][j]= newm[i][j]/(1-sumnew);
         if  (cptcovn>0) {          max=FMAX(max,prlim[i][j]);
           for (z1=1; z1<=cptcoveff; z1++)          min=FMIN(min,prlim[i][j]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;        maxmin=max-min;
         }        maxmax=FMAX(maxmax,maxmin);
         if (bool==1) {      }
           for(m=firstpass; m<=lastpass; m++){      if(maxmax < ftolpl){
             k2=anint[m][i]+(mint[m][i]/12.);        return prlim;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      }
               if(agev[m][i]==0) agev[m][i]=agemax+1;    }
               if(agev[m][i]==1) agev[m][i]=agemax+2;  }
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-1/12.)] += weight[i];  
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];    /*************** transition probabilities ***************/ 
             }  
           }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         }  {
       }    /* According to parameters values stored in x and the covariate's values stored in cov,
             computes the probability to be observed in state j being in state i by appying the
         for(i=(int)agemin; i <= (int)agemax+3; i++){       model to the ncovmodel covariates (including constant and age).
           for(jk=1; jk <=nlstate ; jk++){       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
               pp[jk] += freq[jk][m][i];       ncth covariate in the global vector x is given by the formula:
           }       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           for(jk=1; jk <=nlstate ; jk++){       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
             for(m=-1, pos=0; m <=0 ; m++)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
             pos += freq[jk][m][i];       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         }       Outputs ps[i][j] the probability to be observed in j being in j according to
               the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
          for(jk=1; jk <=nlstate ; jk++){    */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double s1, lnpijopii;
              pp[jk] += freq[jk][m][i];    /*double t34;*/
          }    int i,j,j1, nc, ii, jj;
            
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
          for(jk=1; jk <=nlstate ; jk++){                    for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
            if( i <= (int) agemax){            /*lnpijopii += param[i][j][nc]*cov[nc];*/
              if(pos>=1.e-5){            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                probs[i][jk][j1]= pp[jk]/pos;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
              }          }
            }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
          }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                  }
         }        for(j=i+1; j<=nlstate+ndeath;j++){
     }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
              lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
    /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          }
   free_vector(pp,1,nlstate);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
          }
 }  /* End of Freq */      }
       
 /************* Waves Concatenation ***************/      for(i=1; i<= nlstate; i++){
         s1=0;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        for(j=1; j<i; j++){
 {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
      Death is a valid wave (if date is known).        }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for(j=i+1; j<=nlstate+ndeath; j++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
      and mw[mi+1][i]. dh depends on stepm.          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
      */        }
         /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   int i, mi, m;        ps[i][i]=1./(s1+1.);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        /* Computing other pijs */
      double sum=0., jmean=0.;*/        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
   int j, k=0,jk, ju, jl;        for(j=i+1; j<=nlstate+ndeath; j++)
   double sum=0.;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   jmin=1e+5;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   jmax=-1;      } /* end i */
   jmean=0.;      
   for(i=1; i<=imx; i++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     mi=0;        for(jj=1; jj<= nlstate+ndeath; jj++){
     m=firstpass;          ps[ii][jj]=0;
     while(s[m][i] <= nlstate){          ps[ii][ii]=1;
       if(s[m][i]>=1)        }
         mw[++mi][i]=m;      }
       if(m >=lastpass)      
         break;  
       else  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         m++;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     }/* end while */  /*         printf("ddd %lf ",ps[ii][jj]); */
     if (s[m][i] > nlstate){  /*       } */
       mi++;     /* Death is another wave */  /*       printf("\n "); */
       /* if(mi==0)  never been interviewed correctly before death */  /*        } */
          /* Only death is a correct wave */  /*        printf("\n ");printf("%lf ",cov[2]); */
       mw[mi][i]=m;         /*
     }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
     wav[i]=mi;      return ps;
     if(mi==0)  }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }  /**************** Product of 2 matrices ******************/
   
   for(i=1; i<=imx; i++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for(mi=1; mi<wav[i];mi++){  {
       if (stepm <=0)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         dh[mi][i]=1;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       else{    /* in, b, out are matrice of pointers which should have been initialized 
         if (s[mw[mi+1][i]][i] > nlstate) {       before: only the contents of out is modified. The function returns
           if (agedc[i] < 2*AGESUP) {       a pointer to pointers identical to out */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    long i, j, k;
           if(j==0) j=1;  /* Survives at least one month after exam */    for(i=nrl; i<= nrh; i++)
           k=k+1;      for(k=ncolol; k<=ncoloh; k++)
           if (j >= jmax) jmax=j;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           if (j <= jmin) jmin=j;          out[i][k] +=in[i][j]*b[j][k];
           sum=sum+j;  
           /* if (j<10) printf("j=%d num=%d ",j,i); */    return out;
           }  }
         }  
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  /************* Higher Matrix Product ***************/
           k=k+1;  
           if (j >= jmax) jmax=j;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           else if (j <= jmin)jmin=j;  {
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    /* Computes the transition matrix starting at age 'age' over 
           sum=sum+j;       'nhstepm*hstepm*stepm' months (i.e. until
         }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         jk= j/stepm;       nhstepm*hstepm matrices. 
         jl= j -jk*stepm;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         ju= j -(jk+1)*stepm;       (typically every 2 years instead of every month which is too big 
         if(jl <= -ju)       for the memory).
           dh[mi][i]=jk;       Model is determined by parameters x and covariates have to be 
         else       included manually here. 
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)       */
           dh[mi][i]=1; /* At least one step */  
       }    int i, j, d, h, k;
     }    double **out, cov[NCOVMAX+1];
   }    double **newm;
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    /* Hstepm could be zero and should return the unit matrix */
  }    for (i=1;i<=nlstate+ndeath;i++)
 /*********** Tricode ****************************/      for (j=1;j<=nlstate+ndeath;j++){
 void tricode(int *Tvar, int **nbcode, int imx)        oldm[i][j]=(i==j ? 1.0 : 0.0);
 {        po[i][j][0]=(i==j ? 1.0 : 0.0);
   int Ndum[20],ij=1, k, j, i;      }
   int cptcode=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   cptcoveff=0;    for(h=1; h <=nhstepm; h++){
        for(d=1; d <=hstepm; d++){
   for (k=0; k<19; k++) Ndum[k]=0;        newm=savm;
   for (k=1; k<=7; k++) ncodemax[k]=0;        /* Covariates have to be included here again */
         cov[1]=1.;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) 
       ij=(int)(covar[Tvar[j]][i]);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       Ndum[ij]++;        for (k=1; k<=cptcovage;k++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       if (ij > cptcode) cptcode=ij;        for (k=1; k<=cptcovprod;k++)
     }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     ij=1;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
     for (i=1; i<=ncodemax[j]; i++) {        oldm=newm;
       for (k=0; k<=19; k++) {      }
         if (Ndum[k] != 0) {      for(i=1; i<=nlstate+ndeath; i++)
           nbcode[Tvar[j]][ij]=k;        for(j=1;j<=nlstate+ndeath;j++) {
           ij++;          po[i][j][h]=newm[i][j];
         }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         if (ij > ncodemax[j]) break;        }
       }        /*printf("h=%d ",h);*/
     }    } /* end h */
   }    /*     printf("\n H=%d \n",h); */
     return po;
  for (k=0; k<19; k++) Ndum[k]=0;  }
   
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  /*************** log-likelihood *************/
       Ndum[ij]++;  double func( double *x)
     }  {
     int i, ii, j, k, mi, d, kk;
  ij=1;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
  for (i=1; i<=10; i++) {    double **out;
    if((Ndum[i]!=0) && (i<=ncov)){    double sw; /* Sum of weights */
      Tvaraff[ij]=i;    double lli; /* Individual log likelihood */
      ij++;    int s1, s2;
    }    double bbh, survp;
  }    long ipmx;
      /*extern weight */
     cptcoveff=ij-1;    /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 /*********** Health Expectancies ****************/      printf(" %d\n",s[4][i]);
     */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    cov[1]=1.;
 {  
   /* Health expectancies */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   int i, j, nhstepm, hstepm, h;  
   double age, agelim,hf;    if(mle==1){
   double ***p3mat;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          /* Computes the values of the ncovmodel covariates of the model
   fprintf(ficreseij,"# Health expectancies\n");           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   fprintf(ficreseij,"# Age");           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++)         */
       fprintf(ficreseij," %1d-%1d",i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficreseij,"\n");        /* 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] 
   hstepm=1*YEARM; /*  Every j years of age (in month) */           has been calculated etc */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   agelim=AGESUP;            for (j=1;j<=nlstate+ndeath;j++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* nhstepm age range expressed in number of stepm */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            }
     /* Typically if 20 years = 20*12/6=40 stepm */          for(d=0; d<dh[mi][i]; d++){
     if (stepm >= YEARM) hstepm=1;            newm=savm;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (kk=1; kk<=cptcovage;kk++) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(i=1; i<=nlstate;i++)            oldm=newm;
       for(j=1; j<=nlstate;j++)          } /* end mult */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        
           eij[i][j][(int)age] +=p3mat[i][j][h];          /*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.
               * If stepm is larger than one month (smallest stepm) and if the exact delay 
     hf=1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     if (stepm >= YEARM) hf=stepm/YEARM;           * the nearest (and in case of equal distance, to the lowest) interval but now
     fprintf(ficreseij,"%.0f",age );           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for(i=1; i<=nlstate;i++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       for(j=1; j<=nlstate;j++){           * probability in order to take into account the bias as a fraction of the way
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
     fprintf(ficreseij,"\n");           * For stepm=1 the results are the same as for previous versions of Imach.
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /************ Variance ******************/          bbh=(double)bh[mi][i]/(double)stepm; 
 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)          /* bias bh is positive if real duration
 {           * is higher than the multiple of stepm and negative otherwise.
   /* Variance of health expectancies */           */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double **newm;          if( s2 > nlstate){ 
   double **dnewm,**doldm;            /* i.e. if s2 is a death state and if the date of death is known 
   int i, j, nhstepm, hstepm, h;               then the contribution to the likelihood is the probability to 
   int k, cptcode;               die between last step unit time and current  step unit time, 
   double *xp;               which is also equal to probability to die before dh 
   double **gp, **gm;               minus probability to die before dh-stepm . 
   double ***gradg, ***trgradg;               In version up to 0.92 likelihood was computed
   double ***p3mat;          as if date of death was unknown. Death was treated as any other
   double age,agelim;          health state: the date of the interview describes the actual state
   int theta;          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
    fprintf(ficresvij,"# Covariances of life expectancies\n");          (healthy, disable or death) and IMaCh was corrected; but when we
   fprintf(ficresvij,"# Age");          introduced the exact date of death then we should have modified
   for(i=1; i<=nlstate;i++)          the contribution of an exact death to the likelihood. This new
     for(j=1; j<=nlstate;j++)          contribution is smaller and very dependent of the step unit
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          stepm. It is no more the probability to die between last interview
   fprintf(ficresvij,"\n");          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
   xp=vector(1,npar);          probability to die within a month. Thanks to Chris
   dnewm=matrix(1,nlstate,1,npar);          Jackson for correcting this bug.  Former versions increased
   doldm=matrix(1,nlstate,1,nlstate);          mortality artificially. The bad side is that we add another loop
            which slows down the processing. The difference can be up to 10%
   hstepm=1*YEARM; /* Every year of age */          lower mortality.
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            */
   agelim = AGESUP;            lli=log(out[s1][s2] - savm[s1][s2]);
   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;          } else if  (s2==-2) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (j=1,survp=0. ; j<=nlstate; j++) 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            /*survp += out[s1][j]; */
     gp=matrix(0,nhstepm,1,nlstate);            lli= log(survp);
     gm=matrix(0,nhstepm,1,nlstate);          }
           
     for(theta=1; theta <=npar; theta++){          else if  (s2==-4) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (j=3,survp=0. ; j<=nlstate; j++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
           else if  (s2==-5) { 
       if (popbased==1) {            for (j=1,survp=0. ; j<=2; j++)  
         for(i=1; i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           prlim[i][i]=probs[(int)age][i][ij];            lli= log(survp); 
       }          } 
                
       for(j=1; j<= nlstate; j++){          else{
         for(h=0; h<=nhstepm; h++){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          } 
         }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       }          /*if(lli ==000.0)*/
              /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       for(i=1; i<=npar; i++) /* Computes gradient */          ipmx +=1;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          sw += weight[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of wave */
       } /* end of individual */
       if (popbased==1) {    }  else if(mle==2){
         for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           prlim[i][i]=probs[(int)age][i][ij];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<= nlstate; j++){            for (j=1;j<=nlstate+ndeath;j++){
         for(h=0; h<=nhstepm; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }          for(d=0; d<=dh[mi][i]; d++){
       }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1; j<= nlstate; j++)            for (kk=1; kk<=cptcovage;kk++) {
         for(h=0; h<=nhstepm; h++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     } /* End theta */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            oldm=newm;
           } /* end mult */
     for(h=0; h<=nhstepm; h++)        
       for(j=1; j<=nlstate;j++)          s1=s[mw[mi][i]][i];
         for(theta=1; theta <=npar; theta++)          s2=s[mw[mi+1][i]][i];
           trgradg[h][j][theta]=gradg[h][theta][j];          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for(i=1;i<=nlstate;i++)          ipmx +=1;
       for(j=1;j<=nlstate;j++)          sw += weight[i];
         vareij[i][j][(int)age] =0.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(h=0;h<=nhstepm;h++){        } /* end of wave */
       for(k=0;k<=nhstepm;k++){      } /* end of individual */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    }  else if(mle==3){  /* exponential inter-extrapolation */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(i=1;i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(j=1;j<=nlstate;j++)        for(mi=1; mi<= wav[i]-1; mi++){
             vareij[i][j][(int)age] += doldm[i][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     h=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) h=stepm/YEARM;            }
     fprintf(ficresvij,"%.0f ",age );          for(d=0; d<dh[mi][i]; d++){
     for(i=1; i<=nlstate;i++)            newm=savm;
       for(j=1; j<=nlstate;j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficresvij,"\n");            }
     free_matrix(gp,0,nhstepm,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_matrix(gm,0,nhstepm,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            savm=oldm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            oldm=newm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } /* end mult */
   } /* End age */        
            s1=s[mw[mi][i]][i];
   free_vector(xp,1,npar);          s2=s[mw[mi+1][i]][i];
   free_matrix(doldm,1,nlstate,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_matrix(dnewm,1,nlstate,1,nlstate);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
 }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************ Variance of prevlim ******************/        } /* end of wave */
 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)      } /* end of individual */
 {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   /* Variance of prevalence limit */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **newm;        for(mi=1; mi<= wav[i]-1; mi++){
   double **dnewm,**doldm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, j, nhstepm, hstepm;            for (j=1;j<=nlstate+ndeath;j++){
   int k, cptcode;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *xp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *gp, *gm;            }
   double **gradg, **trgradg;          for(d=0; d<dh[mi][i]; d++){
   double age,agelim;            newm=savm;
   int theta;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficresvpl,"# Age");            }
   for(i=1; i<=nlstate;i++)          
       fprintf(ficresvpl," %1d-%1d",i,i);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficresvpl,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   xp=vector(1,npar);            oldm=newm;
   dnewm=matrix(1,nlstate,1,npar);          } /* end mult */
   doldm=matrix(1,nlstate,1,nlstate);        
            s1=s[mw[mi][i]][i];
   hstepm=1*YEARM; /* Every year of age */          s2=s[mw[mi+1][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          if( s2 > nlstate){ 
   agelim = AGESUP;            lli=log(out[s1][s2] - savm[s1][s2]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }else{
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     if (stepm >= YEARM) hstepm=1;          }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          ipmx +=1;
     gradg=matrix(1,npar,1,nlstate);          sw += weight[i];
     gp=vector(1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gm=vector(1,nlstate);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
     for(theta=1; theta <=npar; theta++){      } /* end of individual */
       for(i=1; i<=npar; i++){ /* Computes gradient */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(mi=1; mi<= wav[i]-1; mi++){
       for(i=1;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         gp[i] = prlim[i][i];            for (j=1;j<=nlstate+ndeath;j++){
                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++) /* Computes gradient */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(d=0; d<dh[mi][i]; d++){
       for(i=1;i<=nlstate;i++)            newm=savm;
         gm[i] = prlim[i][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
       for(i=1;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            }
     } /* End theta */          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     trgradg =matrix(1,nlstate,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(j=1; j<=nlstate;j++)            oldm=newm;
       for(theta=1; theta <=npar; theta++)          } /* end mult */
         trgradg[j][theta]=gradg[theta][j];        
           s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       varpl[i][(int)age] =0.;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          ipmx +=1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          sw += weight[i];
     for(i=1;i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
     fprintf(ficresvpl,"%.0f ",age );      } /* end of individual */
     for(i=1; i<=nlstate;i++)    } /* End of if */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     fprintf(ficresvpl,"\n");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     free_vector(gp,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_vector(gm,1,nlstate);    return -l;
     free_matrix(gradg,1,npar,1,nlstate);  }
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  /*************** log-likelihood *************/
   double funcone( double *x)
   free_vector(xp,1,npar);  {
   free_matrix(doldm,1,nlstate,1,npar);    /* Same as likeli but slower because of a lot of printf and if */
   free_matrix(dnewm,1,nlstate,1,nlstate);    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 }    double **out;
     double lli; /* Individual log likelihood */
 /************ Variance of one-step probabilities  ******************/    double llt;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    int s1, s2;
 {    double bbh, survp;
   int i, j;    /*extern weight */
   int k=0, cptcode;    /* We are differentiating ll according to initial status */
   double **dnewm,**doldm;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double *xp;    /*for(i=1;i<imx;i++) 
   double *gp, *gm;      printf(" %d\n",s[4][i]);
   double **gradg, **trgradg;    */
   double age,agelim, cov[NCOVMAX];    cov[1]=1.;
   int theta;  
   char fileresprob[FILENAMELENGTH];    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   strcpy(fileresprob,"prob");    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcat(fileresprob,fileres);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with resultfile: %s\n", fileresprob);        for (ii=1;ii<=nlstate+ndeath;ii++)
   }          for (j=1;j<=nlstate+ndeath;j++){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   xp=vector(1,npar);        for(d=0; d<dh[mi][i]; d++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          newm=savm;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for (kk=1; kk<=cptcovage;kk++) {
   cov[1]=1;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (age=bage; age<=fage; age ++){          }
     cov[2]=age;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gradg=matrix(1,npar,1,9);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     trgradg=matrix(1,9,1,npar);          savm=oldm;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          oldm=newm;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        } /* end mult */
            
     for(theta=1; theta <=npar; theta++){        s1=s[mw[mi][i]][i];
       for(i=1; i<=npar; i++)        s2=s[mw[mi+1][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        bbh=(double)bh[mi][i]/(double)stepm; 
              /* bias is positive if real duration
       pmij(pmmij,cov,ncovmodel,xp,nlstate);         * is higher than the multiple of stepm and negative otherwise.
             */
       k=0;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       for(i=1; i<= (nlstate+ndeath); i++){          lli=log(out[s1][s2] - savm[s1][s2]);
         for(j=1; j<=(nlstate+ndeath);j++){        } else if  (s2==-2) {
            k=k+1;          for (j=1,survp=0. ; j<=nlstate; j++) 
           gp[k]=pmmij[i][j];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         }          lli= log(survp);
       }        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(i=1; i<=npar; i++)        } else if(mle==2){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            } else if(mle==3){  /* exponential inter-extrapolation */
           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 */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       k=0;          lli=log(out[s1][s2]); /* Original formula */
       for(i=1; i<=(nlstate+ndeath); i++){        } else{  /* mle=0 back to 1 */
         for(j=1; j<=(nlstate+ndeath);j++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           k=k+1;          /*lli=log(out[s1][s2]); */ /* Original formula */
           gm[k]=pmmij[i][j];        } /* End of if */
         }        ipmx +=1;
       }        sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          if(globpr){
     }          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for(theta=1; theta <=npar; theta++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       trgradg[j][theta]=gradg[theta][j];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
              llt +=ll[k]*gipmx/gsw;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          }
           fprintf(ficresilk," %10.6f\n", -llt);
      pmij(pmmij,cov,ncovmodel,x,nlstate);        }
       } /* end of wave */
      k=0;    } /* end of individual */
      for(i=1; i<=(nlstate+ndeath); i++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        for(j=1; j<=(nlstate+ndeath);j++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          k=k+1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
          gm[k]=pmmij[i][j];    if(globpr==0){ /* First time we count the contributions and weights */
         }      gipmx=ipmx;
      }      gsw=sw;
          }
      /*printf("\n%d ",(int)age);    return -l;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  }
          
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  /*************** function likelione ***********/
      }*/  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
   fprintf(ficresprob,"\n%d ",(int)age);    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){       to check the exact contribution to the likelihood.
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);       Plotting could be done.
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);     */
   }    int k;
   
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    if(*globpri !=0){ /* Just counts and sums, no printings */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      strcpy(fileresilk,"ilk"); 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      strcat(fileresilk,fileres);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 }        printf("Problem with resultfile: %s\n", fileresilk);
  free_vector(xp,1,npar);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 fclose(ficresprob);      }
  exit(0);      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");
 }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 /***********************************************/      for(k=1; k<=nlstate; k++) 
 /**************** Main Program *****************/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 /***********************************************/      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
 /*int main(int argc, char *argv[])*/  
 int main()    *fretone=(*funcone)(p);
 {    if(*globpri !=0){
       fclose(ficresilk);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double agedeb, agefin,hf;      fflush(fichtm); 
   double agemin=1.e20, agemax=-1.e20;    } 
     return;
   double fret;  }
   double **xi,tmp,delta;  
   
   double dum; /* Dummy variable */  /*********** Maximum Likelihood Estimation ***************/
   double ***p3mat;  
   int *indx;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   char line[MAXLINE], linepar[MAXLINE];  {
   char title[MAXLINE];    int i,j, iter;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    double **xi;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    double fret;
   char filerest[FILENAMELENGTH];    double fretone; /* Only one call to likelihood */
   char fileregp[FILENAMELENGTH];    /*  char filerespow[FILENAMELENGTH];*/
   char popfile[FILENAMELENGTH];    xi=matrix(1,npar,1,npar);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    for (i=1;i<=npar;i++)
   int firstobs=1, lastobs=10;      for (j=1;j<=npar;j++)
   int sdeb, sfin; /* Status at beginning and end */        xi[i][j]=(i==j ? 1.0 : 0.0);
   int c,  h , cpt,l;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int ju,jl, mi;    strcpy(filerespow,"pow"); 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    strcat(filerespow,fileres);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   int mobilav=0,popforecast=0;      printf("Problem with resultfile: %s\n", filerespow);
   int hstepm, nhstepm;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   int *popage;/*boolprev=0 if date and zero if wave*/    }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
   double bage, fage, age, agelim, agebase;      for(j=1;j<=nlstate+ndeath;j++)
   double ftolpl=FTOL;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double **prlim;    fprintf(ficrespow,"\n");
   double *severity;  
   double ***param; /* Matrix of parameters */    powell(p,xi,npar,ftol,&iter,&fret,func);
   double  *p;  
   double **matcov; /* Matrix of covariance */    free_matrix(xi,1,npar,1,npar);
   double ***delti3; /* Scale */    fclose(ficrespow);
   double *delti; /* Scale */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double ***eij, ***vareij;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **varpl; /* Variances of prevalence limits by age */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double *epj, vepp;  
   double kk1, kk2;  }
   double *popeffectif,*popcount;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;  /**** Computes Hessian and covariance matrix ***/
   double yp,yp1,yp2;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    double  **a,**y,*x,pd;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double **hess;
     int i, j,jk;
     int *indx;
   char z[1]="c", occ;  
 #include <sys/time.h>    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
 #include <time.h>    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    void lubksb(double **a, int npar, int *indx, double b[]) ;
      void ludcmp(double **a, int npar, int *indx, double *d) ;
   /* long total_usecs;    double gompertz(double p[]);
   struct timeval start_time, end_time;    hess=matrix(1,npar,1,npar);
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
   printf("\nIMACH, Version 0.7");      printf("%d",i);fflush(stdout);
   printf("\nEnter the parameter file name: ");      fprintf(ficlog,"%d",i);fflush(ficlog);
      
 #ifdef windows       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   scanf("%s",pathtot);      
   getcwd(pathcd, size);      /*  printf(" %f ",p[i]);
   /*cygwin_split_path(pathtot,path,optionfile);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    }
   /* cutv(path,optionfile,pathtot,'\\');*/    
     for (i=1;i<=npar;i++) {
 split(pathtot, path,optionfile);      for (j=1;j<=npar;j++)  {
   chdir(path);        if (j>i) { 
   replace(pathc,path);          printf(".%d%d",i,j);fflush(stdout);
 #endif          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 #ifdef unix          hess[i][j]=hessij(p,delti,i,j,func,npar);
   scanf("%s",optionfile);          
 #endif          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
 /*-------- arguments in the command line --------*/        }
       }
   strcpy(fileres,"r");    }
   strcat(fileres, optionfile);    printf("\n");
     fprintf(ficlog,"\n");
   /*---------arguments file --------*/  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     printf("Problem with optionfile %s\n",optionfile);    
     goto end;    a=matrix(1,npar,1,npar);
   }    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
   strcpy(filereso,"o");    indx=ivector(1,npar);
   strcat(filereso,fileres);    for (i=1;i<=npar;i++)
   if((ficparo=fopen(filereso,"w"))==NULL) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    ludcmp(a,npar,indx,&pd);
   }  
     for (j=1;j<=npar;j++) {
   /* Reads comments: lines beginning with '#' */      for (i=1;i<=npar;i++) x[i]=0;
   while((c=getc(ficpar))=='#' && c!= EOF){      x[j]=1;
     ungetc(c,ficpar);      lubksb(a,npar,indx,x);
     fgets(line, MAXLINE, ficpar);      for (i=1;i<=npar;i++){ 
     puts(line);        matcov[i][j]=x[i];
     fputs(line,ficparo);      }
   }    }
   ungetc(c,ficpar);  
     printf("\n#Hessian matrix#\n");
   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);    fprintf(ficlog,"\n#Hessian matrix#\n");
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    for (i=1;i<=npar;i++) { 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);      for (j=1;j<=npar;j++) { 
 while((c=getc(ficpar))=='#' && c!= EOF){        printf("%.3e ",hess[i][j]);
     ungetc(c,ficpar);        fprintf(ficlog,"%.3e ",hess[i][j]);
     fgets(line, MAXLINE, ficpar);      }
     puts(line);      printf("\n");
     fputs(line,ficparo);      fprintf(ficlog,"\n");
   }    }
   ungetc(c,ficpar);  
      /* Recompute Inverse */
        for (i=1;i<=npar;i++)
   covar=matrix(0,NCOVMAX,1,n);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   cptcovn=0;    ludcmp(a,npar,indx,&pd);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
     /*  printf("\n#Hessian matrix recomputed#\n");
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   /* Read guess parameters */      x[j]=1;
   /* Reads comments: lines beginning with '#' */      lubksb(a,npar,indx,x);
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1;i<=npar;i++){ 
     ungetc(c,ficpar);        y[i][j]=x[i];
     fgets(line, MAXLINE, ficpar);        printf("%.3e ",y[i][j]);
     puts(line);        fprintf(ficlog,"%.3e ",y[i][j]);
     fputs(line,ficparo);      }
   }      printf("\n");
   ungetc(c,ficpar);      fprintf(ficlog,"\n");
      }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    */
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(a,1,npar,1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    free_matrix(y,1,npar,1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    free_vector(x,1,npar);
       printf("%1d%1d",i,j);    free_ivector(indx,1,npar);
       for(k=1; k<=ncovmodel;k++){    free_matrix(hess,1,npar,1,npar);
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  }
       }  
       fscanf(ficpar,"\n");  /*************** hessian matrix ****************/
       printf("\n");  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       fprintf(ficparo,"\n");  {
     }    int i;
      int l=1, lmax=20;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
   p=param[1][1];    double res;
      double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   /* Reads comments: lines beginning with '#' */    double fx;
   while((c=getc(ficpar))=='#' && c!= EOF){    int k=0,kmax=10;
     ungetc(c,ficpar);    double l1;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    fx=func(x);
     fputs(line,ficparo);    for (i=1;i<=npar;i++) p2[i]=x[i];
   }    for(l=0 ; l <=lmax; l++){
   ungetc(c,ficpar);      l1=pow(10,l);
       delts=delt;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(k=1 ; k <kmax; k=k+1){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        delt = delta*(l1*k);
   for(i=1; i <=nlstate; i++){        p2[theta]=x[theta] +delt;
     for(j=1; j <=nlstate+ndeath-1; j++){        k1=func(p2)-fx;
       fscanf(ficpar,"%1d%1d",&i1,&j1);        p2[theta]=x[theta]-delt;
       printf("%1d%1d",i,j);        k2=func(p2)-fx;
       fprintf(ficparo,"%1d%1d",i1,j1);        /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(k=1; k<=ncovmodel;k++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         fscanf(ficpar,"%le",&delti3[i][j][k]);        
         printf(" %le",delti3[i][j][k]);  #ifdef DEBUGHESS
         fprintf(ficparo," %le",delti3[i][j][k]);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }        fprintf(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);
       fscanf(ficpar,"\n");  #endif
       printf("\n");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       fprintf(ficparo,"\n");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     }          k=kmax;
   }        }
   delti=delti3[1][1];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
            k=kmax; l=lmax*10.;
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     ungetc(c,ficpar);          delts=delt;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      }
     fputs(line,ficparo);    }
   }    delti[theta]=delts;
   ungetc(c,ficpar);    return res; 
      
   matcov=matrix(1,npar,1,npar);  }
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     printf("%s",str);  {
     fprintf(ficparo,"%s",str);    int i;
     for(j=1; j <=i; j++){    int l=1, l1, lmax=20;
       fscanf(ficpar," %le",&matcov[i][j]);    double k1,k2,k3,k4,res,fx;
       printf(" %.5le",matcov[i][j]);    double p2[MAXPARM+1];
       fprintf(ficparo," %.5le",matcov[i][j]);    int k;
     }  
     fscanf(ficpar,"\n");    fx=func(x);
     printf("\n");    for (k=1; k<=2; k++) {
     fprintf(ficparo,"\n");      for (i=1;i<=npar;i++) p2[i]=x[i];
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
   for(i=1; i <=npar; i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(j=i+1;j<=npar;j++)      k1=func(p2)-fx;
       matcov[i][j]=matcov[j][i];    
          p2[thetai]=x[thetai]+delti[thetai]/k;
   printf("\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     
     /*-------- data file ----------*/      p2[thetai]=x[thetai]-delti[thetai]/k;
     if((ficres =fopen(fileres,"w"))==NULL) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       printf("Problem with resultfile: %s\n", fileres);goto end;      k3=func(p2)-fx;
     }    
     fprintf(ficres,"#%s\n",version);      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if((fic=fopen(datafile,"r"))==NULL)    {      k4=func(p2)-fx;
       printf("Problem with datafile: %s\n", datafile);goto end;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     }  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     n= lastobs;      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);
     severity = vector(1,maxwav);  #endif
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    return res;
     moisnais=vector(1,n);  }
     annais=vector(1,n);  
     moisdc=vector(1,n);  /************** Inverse of matrix **************/
     andc=vector(1,n);  void ludcmp(double **a, int n, int *indx, double *d) 
     agedc=vector(1,n);  { 
     cod=ivector(1,n);    int i,imax,j,k; 
     weight=vector(1,n);    double big,dum,sum,temp; 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double *vv; 
     mint=matrix(1,maxwav,1,n);   
     anint=matrix(1,maxwav,1,n);    vv=vector(1,n); 
     s=imatrix(1,maxwav+1,1,n);    *d=1.0; 
     adl=imatrix(1,maxwav+1,1,n);        for (i=1;i<=n;i++) { 
     tab=ivector(1,NCOVMAX);      big=0.0; 
     ncodemax=ivector(1,8);      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
     i=1;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     while (fgets(line, MAXLINE, fic) != NULL)    {      vv[i]=1.0/big; 
       if ((i >= firstobs) && (i <=lastobs)) {    } 
            for (j=1;j<=n;j++) { 
         for (j=maxwav;j>=1;j--){      for (i=1;i<j;i++) { 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        sum=a[i][j]; 
           strcpy(line,stra);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        a[i][j]=sum; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         }      big=0.0; 
              for (i=j;i<=n;i++) { 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        sum=a[i][j]; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        a[i][j]=sum; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          imax=i; 
         for (j=ncov;j>=1;j--){        } 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         }      if (j != imax) { 
         num[i]=atol(stra);        for (k=1;k<=n;k++) { 
                  dum=a[imax][k]; 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          a[imax][k]=a[j][k]; 
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          a[j][k]=dum; 
         } 
         i=i+1;        *d = -(*d); 
       }        vv[imax]=vv[j]; 
     }      } 
     /* printf("ii=%d", ij);      indx[j]=imax; 
        scanf("%d",i);*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
   imx=i-1; /* Number of individuals */      if (j != n) { 
         dum=1.0/(a[j][j]); 
   /* for (i=1; i<=imx; i++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      } 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    } 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
   } 
     for (i=1; i<=imx; i++)  
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
   /* Calculation of the number of parameter from char model*/    int i,ii=0,ip,j; 
   Tvar=ivector(1,15);    double sum; 
   Tprod=ivector(1,15);   
   Tvaraff=ivector(1,15);    for (i=1;i<=n;i++) { 
   Tvard=imatrix(1,15,1,2);      ip=indx[i]; 
   Tage=ivector(1,15);            sum=b[ip]; 
          b[ip]=b[i]; 
   if (strlen(model) >1){      if (ii) 
     j=0, j1=0, k1=1, k2=1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     j=nbocc(model,'+');      else if (sum) ii=i; 
     j1=nbocc(model,'*');      b[i]=sum; 
     cptcovn=j+1;    } 
     cptcovprod=j1;    for (i=n;i>=1;i--) { 
          sum=b[i]; 
          for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     strcpy(modelsav,model);      b[i]=sum/a[i][i]; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    } 
       printf("Error. Non available option model=%s ",model);  } 
       goto end;  
     }  void pstamp(FILE *fichier)
      {
     for(i=(j+1); i>=1;i--){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       cutv(stra,strb,modelsav,'+');  }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  /************ Frequencies ********************/
       /*scanf("%d",i);*/  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[])
       if (strchr(strb,'*')) {  {  /* Some frequencies */
         cutv(strd,strc,strb,'*');    
         if (strcmp(strc,"age")==0) {    int i, m, jk, k1,i1, j1, bool, z1,j;
           cptcovprod--;    int first;
           cutv(strb,stre,strd,'V');    double ***freq; /* Frequencies */
           Tvar[i]=atoi(stre);    double *pp, **prop;
           cptcovage++;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             Tage[cptcovage]=i;    char fileresp[FILENAMELENGTH];
             /*printf("stre=%s ", stre);*/    
         }    pp=vector(1,nlstate);
         else if (strcmp(strd,"age")==0) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
           cptcovprod--;    strcpy(fileresp,"p");
           cutv(strb,stre,strc,'V');    strcat(fileresp,fileres);
           Tvar[i]=atoi(stre);    if((ficresp=fopen(fileresp,"w"))==NULL) {
           cptcovage++;      printf("Problem with prevalence resultfile: %s\n", fileresp);
           Tage[cptcovage]=i;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         }      exit(0);
         else {    }
           cutv(strb,stre,strc,'V');    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           Tvar[i]=ncov+k1;    j1=0;
           cutv(strb,strc,strd,'V');    
           Tprod[k1]=i;    j=cptcoveff;
           Tvard[k1][1]=atoi(strc);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];    first=1;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)    for(k1=1; k1<=j;k1++){
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for(i1=1; i1<=ncodemax[k1];i1++){
           k1++;        j1++;
           k2=k2+2;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         }          scanf("%d", i);*/
       }        for (i=-5; i<=nlstate+ndeath; i++)  
       else {          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            for(m=iagemin; m <= iagemax+3; m++)
        /*  scanf("%d",i);*/              freq[i][jk][m]=0;
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);      for (i=1; i<=nlstate; i++)  
       }        for(m=iagemin; m <= iagemax+3; m++)
       strcpy(modelsav,stra);            prop[i][m]=0;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        
         scanf("%d",i);*/        dateintsum=0;
     }        k2cpt=0;
 }        for (i=1; i<=imx; i++) {
            bool=1;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          if  (cptcovn>0) {
   printf("cptcovprod=%d ", cptcovprod);            for (z1=1; z1<=cptcoveff; z1++) 
   scanf("%d ",i);*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fclose(fic);                bool=0;
           }
     /*  if(mle==1){*/          if (bool==1){
     if (weightopt != 1) { /* Maximisation without weights*/            for(m=firstpass; m<=lastpass; m++){
       for(i=1;i<=n;i++) weight[i]=1.0;              k2=anint[m][i]+(mint[m][i]/12.);
     }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     /*-calculation of age at interview from date of interview and age at death -*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     agev=matrix(1,maxwav,1,imx);                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];
    for (i=1; i<=imx; i++)                if (m<lastpass) {
      for(m=2; (m<= maxwav); m++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
          anint[m][i]=9999;                }
          s[m][i]=-1;                
        }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                      dateintsum=dateintsum+k2;
     for (i=1; i<=imx; i++)  {                  k2cpt++;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                }
       for(m=1; (m<= maxwav); m++){                /*}*/
         if(s[m][i] >0){            }
           if (s[m][i] == nlstate+1) {          }
             if(agedc[i]>0)        }
               if(moisdc[i]!=99 && andc[i]!=9999)         
               agev[m][i]=agedc[i];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             else {        pstamp(ficresp);
               if (andc[i]!=9999){        if  (cptcovn>0) {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          fprintf(ficresp, "\n#********** Variable "); 
               agev[m][i]=-1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               }          fprintf(ficresp, "**********\n#");
             }        }
           }        for(i=1; i<=nlstate;i++) 
           else if(s[m][i] !=9){ /* Should no more exist */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        fprintf(ficresp, "\n");
             if(mint[m][i]==99 || anint[m][i]==9999)        
               agev[m][i]=1;        for(i=iagemin; i <= iagemax+3; i++){
             else if(agev[m][i] <agemin){          if(i==iagemax+3){
               agemin=agev[m][i];            fprintf(ficlog,"Total");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          }else{
             }            if(first==1){
             else if(agev[m][i] >agemax){              first=0;
               agemax=agev[m][i];              printf("See log file for details...\n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            }
             }            fprintf(ficlog,"Age %d", i);
             /*agev[m][i]=anint[m][i]-annais[i];*/          }
             /*   agev[m][i] = age[i]+2*m;*/          for(jk=1; jk <=nlstate ; jk++){
           }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           else { /* =9 */              pp[jk] += freq[jk][m][i]; 
             agev[m][i]=1;          }
             s[m][i]=-1;          for(jk=1; jk <=nlstate ; jk++){
           }            for(m=-1, pos=0; m <=0 ; m++)
         }              pos += freq[jk][m][i];
         else /*= 0 Unknown */            if(pp[jk]>=1.e-10){
           agev[m][i]=1;              if(first==1){
       }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
     }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for (i=1; i<=imx; i++)  {            }else{
       for(m=1; (m<= maxwav); m++){              if(first==1)
         if (s[m][i] > (nlstate+ndeath)) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           printf("Error: Wrong value in nlstate or ndeath\n");                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           goto end;            }
         }          }
       }  
     }          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              pp[jk] += freq[jk][m][i];
           }       
     free_vector(severity,1,maxwav);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     free_imatrix(outcome,1,maxwav+1,1,n);            pos += pp[jk];
     free_vector(moisnais,1,n);            posprop += prop[jk][i];
     free_vector(annais,1,n);          }
     /* free_matrix(mint,1,maxwav,1,n);          for(jk=1; jk <=nlstate ; jk++){
        free_matrix(anint,1,maxwav,1,n);*/            if(pos>=1.e-5){
     free_vector(moisdc,1,n);              if(first==1)
     free_vector(andc,1,n);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                }else{
     wav=ivector(1,imx);              if(first==1)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                }
     /* Concatenates waves */            if( i <= iagemax){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
       Tcode=ivector(1,100);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              }
       ncodemax[1]=1;              else
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                  }
    codtab=imatrix(1,100,1,10);          }
    h=0;          
    m=pow(2,cptcoveff);          for(jk=-1; jk <=nlstate+ndeath; jk++)
              for(m=-1; m <=nlstate+ndeath; m++)
    for(k=1;k<=cptcoveff; k++){              if(freq[jk][m][i] !=0 ) {
      for(i=1; i <=(m/pow(2,k));i++){              if(first==1)
        for(j=1; j <= ncodemax[k]; j++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
            h++;              }
            if (h>m) h=1;codtab[h][k]=j;          if(i <= iagemax)
          }            fprintf(ficresp,"\n");
        }          if(first==1)
      }            printf("Others in log...\n");
    }          fprintf(ficlog,"\n");
            }
    /* Calculates basic frequencies. Computes observed prevalence at single age      }
        and prints on file fileres'p'. */    }
     dateintmean=dateintsum/k2cpt; 
       
        fclose(ficresp);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_vector(pp,1,nlstate);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* End of Freq */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  }
        
     /* For Powell, parameters are in a vector p[] starting at p[1]  /************ Prevalence ********************/
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  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)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     if(mle==1){       in each health status at the date of interview (if between dateprev1 and dateprev2).
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       We still use firstpass and lastpass as another selection.
     }    */
       
     /*--------- results files --------------*/    int i, m, jk, k1, i1, j1, bool, z1,j;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    double ***freq; /* Frequencies */
      double *pp, **prop;
     double pos,posprop; 
    jk=1;    double  y2; /* in fractional years */
    fprintf(ficres,"# Parameters\n");    int iagemin, iagemax;
    printf("# Parameters\n");  
    for(i=1,jk=1; i <=nlstate; i++){    iagemin= (int) agemin;
      for(k=1; k <=(nlstate+ndeath); k++){    iagemax= (int) agemax;
        if (k != i)    /*pp=vector(1,nlstate);*/
          {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
            printf("%d%d ",i,k);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
            fprintf(ficres,"%1d%1d ",i,k);    j1=0;
            for(j=1; j <=ncovmodel; j++){    
              printf("%f ",p[jk]);    j=cptcoveff;
              fprintf(ficres,"%f ",p[jk]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
              jk++;    
            }    for(k1=1; k1<=j;k1++){
            printf("\n");      for(i1=1; i1<=ncodemax[k1];i1++){
            fprintf(ficres,"\n");        j1++;
          }        
      }        for (i=1; i<=nlstate; i++)  
    }          for(m=iagemin; m <= iagemax+3; m++)
  if(mle==1){            prop[i][m]=0.0;
     /* Computing hessian and covariance matrix */       
     ftolhess=ftol; /* Usually correct */        for (i=1; i<=imx; i++) { /* Each individual */
     hesscov(matcov, p, npar, delti, ftolhess, func);          bool=1;
  }          if  (cptcovn>0) {
     fprintf(ficres,"# Scales\n");            for (z1=1; z1<=cptcoveff; z1++) 
     printf("# Scales\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      for(i=1,jk=1; i <=nlstate; i++){                bool=0;
       for(j=1; j <=nlstate+ndeath; j++){          } 
         if (j!=i) {          if (bool==1) { 
           fprintf(ficres,"%1d%1d",i,j);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           printf("%1d%1d",i,j);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           for(k=1; k<=ncovmodel;k++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
             printf(" %.5e",delti[jk]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             fprintf(ficres," %.5e",delti[jk]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             jk++;                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); 
           }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           printf("\n");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
           fprintf(ficres,"\n");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
       }                } 
      }              }
                } /* end selection of waves */
     k=1;          }
     fprintf(ficres,"# Covariance\n");        }
     printf("# Covariance\n");        for(i=iagemin; i <= iagemax+3; i++){  
     for(i=1;i<=npar;i++){          
       /*  if (k>nlstate) k=1;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       i1=(i-1)/(ncovmodel*nlstate)+1;            posprop += prop[jk][i]; 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          } 
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);          for(jk=1; jk <=nlstate ; jk++){     
       printf("%3d",i);            if( i <=  iagemax){ 
       for(j=1; j<=i;j++){              if(posprop>=1.e-5){ 
         fprintf(ficres," %.5e",matcov[i][j]);                probs[i][jk][j1]= prop[jk][i]/posprop;
         printf(" %.5e",matcov[i][j]);              } else
       }                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
       fprintf(ficres,"\n");            } 
       printf("\n");          }/* end jk */ 
       k++;        }/* end i */ 
     }      } /* end i1 */
        } /* end k1 */
     while((c=getc(ficpar))=='#' && c!= EOF){    
       ungetc(c,ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       fgets(line, MAXLINE, ficpar);    /*free_vector(pp,1,nlstate);*/
       puts(line);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fputs(line,ficparo);  }  /* End of prevalence */
     }  
     ungetc(c,ficpar);  /************* Waves Concatenation ***************/
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
      {
     if (fage <= 2) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       bage = agemin;       Death is a valid wave (if date is known).
       fage = agemax;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
     fprintf(ficres,"# agemin agemax for life expectancy.\n");       */
   
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int i, mi, m;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         double sum=0., jmean=0.;*/
     while((c=getc(ficpar))=='#' && c!= EOF){    int first;
     ungetc(c,ficpar);    int j, k=0,jk, ju, jl;
     fgets(line, MAXLINE, ficpar);    double sum=0.;
     puts(line);    first=0;
     fputs(line,ficparo);    jmin=1e+5;
   }    jmax=-1;
   ungetc(c,ficpar);    jmean=0.;
      for(i=1; i<=imx; i++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);      mi=0;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      m=firstpass;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      while(s[m][i] <= nlstate){
              if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   while((c=getc(ficpar))=='#' && c!= EOF){          mw[++mi][i]=m;
     ungetc(c,ficpar);        if(m >=lastpass)
     fgets(line, MAXLINE, ficpar);          break;
     puts(line);        else
     fputs(line,ficparo);          m++;
   }      }/* end while */
   ungetc(c,ficpar);      if (s[m][i] > nlstate){
          mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;           /* Only death is a correct wave */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        mw[mi][i]=m;
       }
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
    fprintf(ficparo,"pop_based=%d\n",popbased);        wav[i]=mi;
    fprintf(ficres,"pop_based=%d\n",popbased);        if(mi==0){
         nbwarn++;
   while((c=getc(ficpar))=='#' && c!= EOF){        if(first==0){
     ungetc(c,ficpar);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fgets(line, MAXLINE, ficpar);          first=1;
     puts(line);        }
     fputs(line,ficparo);        if(first==1){
   }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   ungetc(c,ficpar);        }
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);      } /* end mi==0 */
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    } /* End individuals */
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
     for(i=1; i<=imx; i++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
  /*------------ gnuplot -------------*/          dh[mi][i]=1;
 chdir(pathcd);        else{
   if((ficgp=fopen("graph.plt","w"))==NULL) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     printf("Problem with file graph.gp");goto end;            if (agedc[i] < 2*AGESUP) {
   }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 #ifdef windows              if(j==0) j=1;  /* Survives at least one month after exam */
   fprintf(ficgp,"cd \"%s\" \n",pathc);              else if(j<0){
 #endif                nberr++;
 m=pow(2,cptcoveff);                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]);
                  j=1; /* Temporary Dangerous patch */
  /* 1eme*/                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);
   for (cpt=1; cpt<= nlstate ; cpt ++) {                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    for (k1=1; k1<= m ; k1 ++) {                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);
               }
 #ifdef windows              k=k+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);              if (j >= jmax){
 #endif                jmax=j;
 #ifdef unix                ijmax=i;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);              }
 #endif              if (j <= jmin){
                 jmin=j;
 for (i=1; i<= nlstate ; i ++) {                ijmin=i;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");              sum=sum+j;
 }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          else{
 }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            k=k+1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if (j >= jmax) {
 }                jmax=j;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));              ijmax=i;
 #ifdef unix            }
 fprintf(ficgp,"\nset ter gif small size 400,300");            else if (j <= jmin){
 #endif              jmin=j;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              ijmin=i;
    }            }
   }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   /*2 eme*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
   for (k1=1; k1<= m ; k1 ++) {              nberr++;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for (i=1; i<= nlstate+1 ; i ++) {            }
       k=2*i;            sum=sum+j;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {          jk= j/stepm;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          jl= j -jk*stepm;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          ju= j -(jk+1)*stepm;
 }            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            if(jl==0){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              dh[mi][i]=jk;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              bh[mi][i]=0;
       for (j=1; j<= nlstate+1 ; j ++) {            }else{ /* We want a negative bias in order to only have interpolation ie
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                    * to avoid the price of an extra matrix product in likelihood */
         else fprintf(ficgp," \%%*lf (\%%*lf)");              dh[mi][i]=jk+1;
 }                bh[mi][i]=ju;
       fprintf(ficgp,"\" t\"\" w l 0,");            }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          }else{
       for (j=1; j<= nlstate+1 ; j ++) {            if(jl <= -ju){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              dh[mi][i]=jk;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              bh[mi][i]=jl;       /* bias is positive if real duration
 }                                     * is higher than the multiple of stepm and negative otherwise.
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                                   */
       else fprintf(ficgp,"\" t\"\" w l 0,");            }
     }            else{
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
              }
   /*3eme*/            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
   for (k1=1; k1<= m ; k1 ++) {              bh[mi][i]=ju; /* At least one step */
     for (cpt=1; cpt<= nlstate ; cpt ++) {              /*  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);*/
       k=2+nlstate*(cpt-1);            }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          } /* end if mle */
       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);      } /* end wave */
       }    }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    jmean=sum/k;
     }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   }    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     }
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {  /*********** Tricode ****************************/
     for (cpt=1; cpt<nlstate ; cpt ++) {  void tricode(int *Tvar, int **nbcode, int imx)
       k=3;  {
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    /* Uses cptcovn+2*cptcovprod as the number of covariates */
       for (i=1; i< nlstate ; i ++)    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
          int modmaxcovj=0; /* Modality max of covariates j */
       l=3+(nlstate+ndeath)*cpt;    cptcoveff=0; 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);   
       for (i=1; i< nlstate ; i ++) {    for (k=0; k<maxncov; k++) Ndum[k]=0;
         l=3+(nlstate+ndeath)*cpt;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
         fprintf(ficgp,"+$%d",l+i+1);  
       }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                                 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
   }                                          modality of the nth covariate of individual i. */
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   /* proba elementaires */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
    for(i=1,jk=1; i <=nlstate; i++){        if (ij > modmaxcovj) modmaxcovj=ij; 
     for(k=1; k <=(nlstate+ndeath); k++){        /* getting the maximum value of the modality of the covariate
       if (k != i) {           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         for(j=1; j <=ncovmodel; j++){           female is 1, then modmaxcovj=1.*/
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      }
           /*fprintf(ficgp,"%s",alph[1]);*/      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
           jk++;        if( Ndum[i] != 0 )
           fprintf(ficgp,"\n");          ncodemax[j]++; 
         }        /* Number of modalities of the j th covariate. In fact
       }           ncodemax[j]=2 (dichotom. variables only) but it could be more for
     }           historical reasons */
     }      } /* Ndum[-1] number of undefined modalities */
   
   for(jk=1; jk <=m; jk++) {      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      ij=1; 
    i=1;      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
    for(k2=1; k2<=nlstate; k2++) {        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
      k3=i;          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
      for(k=1; k<=(nlstate+ndeath); k++) {            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
        if (k != k2){                                       k is a modality. If we have model=V1+V1*sex 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
 ij=1;            ij++;
         for(j=3; j <=ncovmodel; j++) {          }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          if (ij > ncodemax[j]) break; 
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        }  /* end of loop on */
             ij++;      } /* end of loop on modality */ 
           }    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
           else    
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for (k=0; k< maxncov; k++) Ndum[k]=0;
         }    
           fprintf(ficgp,")/(1");    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
             /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         for(k1=1; k1 <=nlstate; k1++){       ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);     Ndum[ij]++;
 ij=1;   }
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {   ij=1;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
             ij++;     if((Ndum[i]!=0) && (i<=ncovcol)){
           }       Tvaraff[ij]=i; /*For printing */
           else       ij++;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);     }
           }   }
           fprintf(ficgp,")");   ij--;
         }   cptcoveff=ij; /*Number of simple covariates*/
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;  /*********** Health Expectancies ****************/
        }  
      }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  {
   }    /* Health expectancies, no variances */
        int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   fclose(ficgp);    int nhstepma, nstepma; /* Decreasing with age */
        double age, agelim, hf;
 chdir(path);    double ***p3mat;
        double eip;
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    pstamp(ficreseij);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     free_ivector(num,1,n);    fprintf(ficreseij,"# Age");
     free_vector(agedc,1,n);    for(i=1; i<=nlstate;i++){
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      for(j=1; j<=nlstate;j++){
     fclose(ficparo);        fprintf(ficreseij," e%1d%1d ",i,j);
     fclose(ficres);      }
     /*  }*/      fprintf(ficreseij," e%1d. ",i);
        }
    /*________fin mle=1_________*/    fprintf(ficreseij,"\n");
      
     
      if(estepm < stepm){
     /* No more information from the sample is required now */      printf ("Problem %d lower than %d\n",estepm, stepm);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    else  hstepm=estepm;   
     ungetc(c,ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
     fgets(line, MAXLINE, ficpar);     * This is mainly to measure the difference between two models: for example
     puts(line);     * if stepm=24 months pijx are given only every 2 years and by summing them
     fputs(line,ficparo);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }     * progression in between and thus overestimating or underestimating according
   ungetc(c,ficpar);     * 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
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);     * to compare the new estimate of Life expectancy with the same linear 
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);     * hypothesis. A more precise result, taking into account a more precise
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     * curvature will be obtained if estepm is as small as stepm. */
 /*--------- index.htm --------*/  
     /* For example we decided to compute the life expectancy with the smallest unit */
   strcpy(optionfilehtm,optionfile);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(optionfilehtm,".htm");       nhstepm is the number of hstepm from age to agelim 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with %s \n",optionfilehtm);goto end;       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
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">       survival function given by stepm (the optimization length). Unfortunately it
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>       means that if the survival funtion is printed only each two years of age and if
 Total number of observations=%d <br>       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>       results. So we changed our mind and took the option of the best precision.
 <hr  size=\"2\" color=\"#EC5E5E\">    */
 <li>Outputs files<br><br>\n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         - 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>    agelim=AGESUP;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    /* If stepm=6 months */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  /* nhstepm age range expressed in number of stepm */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    /* if (stepm >= YEARM) hstepm=1;*/
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fprintf(fichtm," <li>Graphs</li><p>");  
     for (age=bage; age<=fage; age ++){ 
  m=cptcoveff;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
  j1=0;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      /* If stepm=6 months */
        j1++;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        if (cptcovn > 0) {         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      
          for (cpt=1; cpt<=cptcoveff;cpt++)      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        }      
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      printf("%d|",(int)age);fflush(stdout);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(cpt=1; cpt<nlstate;cpt++){      
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      /* Computing expectancies */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      for(i=1; i<=nlstate;i++)
        }        for(j=1; j<=nlstate;j++)
     for(cpt=1; cpt<=nlstate;cpt++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 interval) in state (%d): v%s%d%d.gif <br>            
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {          }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      fprintf(ficreseij,"%3.0f",age );
      }      for(i=1; i<=nlstate;i++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        eip=0;
 health expectancies in states (1) and (2): e%s%d.gif<br>        for(j=1; j<=nlstate;j++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          eip +=eij[i][j][(int)age];
 fprintf(fichtm,"\n</body>");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
    }        }
  }        fprintf(ficreseij,"%9.4f", eip );
 fclose(fichtm);      }
       fprintf(ficreseij,"\n");
   /*--------------- Prevalence limit --------------*/      
      }
   strcpy(filerespl,"pl");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(filerespl,fileres);    printf("\n");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fprintf(ficlog,"\n");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    
   }  }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\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[] )
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  {
   fprintf(ficrespl,"\n");    /* Covariances of health expectancies eij and of total life expectancies according
       to initial status i, ei. .
   prlim=matrix(1,nlstate,1,nlstate);    */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int nhstepma, nstepma; /* Decreasing with age */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double age, agelim, hf;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***p3matp, ***p3matm, ***varhe;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double **dnewm,**doldm;
   k=0;    double *xp, *xm;
   agebase=agemin;    double **gp, **gm;
   agelim=agemax;    double ***gradg, ***trgradg;
   ftolpl=1.e-10;    int theta;
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    double eip, vip;
   
   for(cptcov=1;cptcov<=i1;cptcov++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    xp=vector(1,npar);
         k=k+1;    xm=vector(1,npar);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
         fprintf(ficrespl,"\n#******");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         for(j=1;j<=cptcoveff;j++)    
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    pstamp(ficresstdeij);
         fprintf(ficrespl,"******\n");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
            fprintf(ficresstdeij,"# Age");
         for (age=agebase; age<=agelim; age++){    for(i=1; i<=nlstate;i++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      for(j=1; j<=nlstate;j++)
           fprintf(ficrespl,"%.0f",age );        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
           for(i=1; i<=nlstate;i++)      fprintf(ficresstdeij," e%1d. ",i);
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");    fprintf(ficresstdeij,"\n");
         }  
       }    pstamp(ficrescveij);
     }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   fclose(ficrespl);    fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
   /*------------- h Pij x at various ages ------------*/      for(j=1; j<=nlstate;j++){
          cptj= (j-1)*nlstate+i;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        for(i2=1; i2<=nlstate;i2++)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          for(j2=1; j2<=nlstate;j2++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            cptj2= (j2-1)*nlstate+i2;
   }            if(cptj2 <= cptj)
   printf("Computing pij: result on file '%s' \n", filerespij);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
            }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }
   /*if (stepm<=24) stepsize=2;*/    fprintf(ficrescveij,"\n");
     
   agelim=AGESUP;    if(estepm < stepm){
   hstepm=stepsize*YEARM; /* Every year of age */      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
      else  hstepm=estepm;   
   k=0;    /* We compute the life expectancy from trapezoids spaced every estepm months
   for(cptcov=1;cptcov<=i1;cptcov++){     * This is mainly to measure the difference between two models: for example
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * if stepm=24 months pijx are given only every 2 years and by summing them
       k=k+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
         fprintf(ficrespij,"\n#****** ");     * progression in between and thus overestimating or underestimating according
         for(j=1;j<=cptcoveff;j++)     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficrespij,"******\n");     * to compare the new estimate of Life expectancy with the same linear 
             * hypothesis. A more precise result, taking into account a more precise
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     * curvature will be obtained if estepm is as small as stepm. */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /* For example we decided to compute the life expectancy with the smallest unit */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           oldm=oldms;savm=savms;       nhstepm is the number of hstepm from age to agelim 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         nstepm is the number of stepm from age to agelin. 
           fprintf(ficrespij,"# Age");       Look at hpijx to understand the reason of that which relies in memory size
           for(i=1; i<=nlstate;i++)       and note for a fixed period like estepm months */
             for(j=1; j<=nlstate+ndeath;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               fprintf(ficrespij," %1d-%1d",i,j);       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficrespij,"\n");       means that if the survival funtion is printed only each two years of age and if
           for (h=0; h<=nhstepm; h++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       results. So we changed our mind and took the option of the best precision.
             for(i=1; i<=nlstate;i++)    */
               for(j=1; j<=nlstate+ndeath;j++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    /* If stepm=6 months */
           }    /* nhstepm age range expressed in number of stepm */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    agelim=AGESUP;
           fprintf(ficrespij,"\n");    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 */
     
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficrespij);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   /*---------- Forecasting ------------------*/    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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 */ 
   strcpy(fileresf,"f");      /* if (stepm >= YEARM) hstepm=1;*/
   strcat(fileresf,fileres);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      /* If stepm=6 months */
   }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   printf("Computing forecasting: result on file '%s' \n", fileresf);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
   free_matrix(mint,1,maxwav,1,n);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   free_matrix(anint,1,maxwav,1,n);  
   free_matrix(agev,1,maxwav,1,imx);      /* Computing  Variances of health expectancies */
   /* Mobile average */      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
   if (mobilav==1) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)        }
       for (i=1; i<=nlstate;i++)        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
           mobaverage[(int)agedeb][i][cptcod]=0.;    
            for(j=1; j<= nlstate; j++){
     for (agedeb=bage+4; agedeb<=fage; agedeb++){          for(i=1; i<=nlstate; i++){
       for (i=1; i<=nlstate;i++){            for(h=0; h<=nhstepm-1; h++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           for (cpt=0;cpt<=4;cpt++){              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            }
           }          }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }
         }       
       }        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];
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }/* End theta */
   if (stepm<=12) stepsize=1;      
       
   agelim=AGESUP;      for(h=0; h<=nhstepm-1; h++)
   /*hstepm=stepsize*YEARM; *//* Every year of age */        for(j=1; j<=nlstate*nlstate;j++)
   hstepm=1;          for(theta=1; theta <=npar; theta++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */            trgradg[h][j][theta]=gradg[h][theta][j];
   yp1=modf(dateintmean,&yp);      
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);       for(ij=1;ij<=nlstate*nlstate;ij++)
   mprojmean=yp;        for(ji=1;ji<=nlstate*nlstate;ji++)
   yp1=modf((yp2*30.5),&yp);          varhe[ij][ji][(int)age] =0.;
   jprojmean=yp;  
   fprintf(ficresf,"Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   if (popforecast==1) {       for(h=0;h<=nhstepm-1;h++){
     if((ficpop=fopen(popfile,"r"))==NULL)    {        for(k=0;k<=nhstepm-1;k++){
       printf("Problem with population file : %s\n",popfile);goto end;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     popage=ivector(0,AGESUP);          for(ij=1;ij<=nlstate*nlstate;ij++)
     popeffectif=vector(0,AGESUP);            for(ji=1;ji<=nlstate*nlstate;ji++)
     popcount=vector(0,AGESUP);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
     i=1;        }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)  
       {      /* Computing expectancies */
         i=i+1;      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       }      for(i=1; i<=nlstate;i++)
     imx=i;        for(j=1; j<=nlstate;j++)
              for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   }            
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
       k=k+1;  
       fprintf(ficresf,"\n#******");      fprintf(ficresstdeij,"%3.0f",age );
       for(j=1;j<=cptcoveff;j++) {      for(i=1; i<=nlstate;i++){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        eip=0.;
       }        vip=0.;
       fprintf(ficresf,"******\n");        for(j=1; j<=nlstate;j++){
       fprintf(ficresf,"# StartingAge FinalAge");          eip += eij[i][j][(int)age];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
       if (popforecast==1)  fprintf(ficresf," [Population]");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
            fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       for (cpt=0; cpt<=1;cpt++) {        }
         fprintf(ficresf,"\n");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   fprintf(ficresf,"\nForecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        }
       for (agedeb=(fage-(1/12.)); agedeb>=(bage-(1/12.)); agedeb--){ /* If stepm=6 months */      fprintf(ficresstdeij,"\n");
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
         nhstepm = nhstepm/hstepm;      fprintf(ficrescveij,"%3.0f",age );
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          cptj= (j-1)*nlstate+i;
         oldm=oldms;savm=savms;          for(i2=1; i2<=nlstate;i2++)
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(j2=1; j2<=nlstate;j2++){
                              cptj2= (j2-1)*nlstate+i2;
         for (h=0; h<=nhstepm; h++){              if(cptj2 <= cptj)
           if (h==(int) (calagedate+12*cpt)) {                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             fprintf(ficresf,"h=%d ", h);            }
             fprintf(ficresf,"\n %f %f ",agedeb,agedeb+h*hstepm/YEARM*stepm);        }
           }      fprintf(ficrescveij,"\n");
           for(j=1; j<=nlstate+ndeath;j++) {     
             kk1=0.;kk2=0;    }
             for(i=1; i<=nlstate;i++) {            free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               if (mobilav==1)    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
               else {    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 /*  fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h],probs[(int)(agedeb)+1][i][cptcod]);*/    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               }    printf("\n");
     fprintf(ficlog,"\n");
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];  
             }    free_vector(xm,1,npar);
              free_vector(xp,1,npar);
             if (h==(int)(calagedate+12*cpt)){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
               fprintf(ficresf," %.3f", kk1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                  free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);  }
             }  
           }  /************ 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[])
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
       }    /* 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;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **dnewmp,**doldmp;
   if (popforecast==1) {    int i, j, nhstepm, hstepm, h, nstepm ;
     free_ivector(popage,0,AGESUP);    int k, cptcode;
     free_vector(popeffectif,0,AGESUP);    double *xp;
     free_vector(popcount,0,AGESUP);    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
   free_imatrix(s,1,maxwav+1,1,n);    double **gradgp, **trgradgp; /* for var p point j */
   free_vector(weight,1,n);    double *gpp, *gmp; /* for var p point j */
   fclose(ficresf);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   /*---------- Health expectancies and variances ------------*/    double ***p3mat;
     double age,agelim, hf;
   strcpy(filerest,"t");    double ***mobaverage;
   strcat(filerest,fileres);    int theta;
   if((ficrest=fopen(filerest,"w"))==NULL) {    char digit[4];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    char digitp[25];
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
   strcpy(filerese,"e");      if(mobilav!=0)
   strcat(filerese,fileres);        strcpy(digitp,"-populbased-mobilav-");
   if((ficreseij=fopen(filerese,"w"))==NULL) {      else strcpy(digitp,"-populbased-nomobil-");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    }
   }    else 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      strcpy(digitp,"-stablbased-");
   
  strcpy(fileresv,"v");    if (mobilav!=0) {
   strcat(fileresv,fileres);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      }
     }
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    strcpy(fileresprobmorprev,"prmorprev"); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    sprintf(digit,"%-d",ij);
       k=k+1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       fprintf(ficrest,"\n#****** ");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for(j=1;j<=cptcoveff;j++)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcat(fileresprobmorprev,fileres);
       fprintf(ficrest,"******\n");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficreseij,"\n#****** ");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficreseij,"******\n");   
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficresvij,"\n#****** ");    pstamp(ficresprobmorprev);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficresvij,"******\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(i=1; i<=nlstate;i++)
       oldm=oldms;savm=savms;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      }  
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficresprobmorprev,"\n");
       oldm=oldms;savm=savms;    fprintf(ficgp,"\n# Routine varevsij");
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /* 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(ficrest,"#Total LEs with variances: e.. (std) ");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  /*   } */
       fprintf(ficrest,"\n");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            pstamp(ficresvij);
       hf=1;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
       if (stepm >= YEARM) hf=stepm/YEARM;    if(popbased==1)
       epj=vector(1,nlstate+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);
       for(age=bage; age <=fage ;age++){    else
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
         if (popbased==1) {    fprintf(ficresvij,"# Age");
           for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][k];      for(j=1; j<=nlstate;j++)
         }        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
            fprintf(ficresvij,"\n");
         fprintf(ficrest," %.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    xp=vector(1,npar);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    dnewm=matrix(1,nlstate,1,npar);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    doldm=matrix(1,nlstate,1,nlstate);
           }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           epj[nlstate+1] +=epj[j];    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           for(j=1;j <=nlstate;j++)    gpp=vector(nlstate+1,nlstate+ndeath);
             vepp += vareij[i][j][(int)age];    gmp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         for(j=1;j <=nlstate;j++){    
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficrest,"\n");    }
       }    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
  fclose(ficreseij);       survival function given by stepm (the optimization length). Unfortunately it
  fclose(ficresvij);       means that if the survival funtion is printed every two years of age and if
   fclose(ficrest);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fclose(ficpar);       results. So we changed our mind and took the option of the best precision.
   free_vector(epj,1,nlstate+1);    */
   /*  scanf("%d ",i); */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   /*------- Variance limit prevalence------*/      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 strcpy(fileresvpl,"vpl");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   strcat(fileresvpl,fileres);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      gp=matrix(0,nhstepm,1,nlstate);
     exit(0);      gm=matrix(0,nhstepm,1,nlstate);
   }  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
       for(theta=1; theta <=npar; theta++){
  k=0;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
  for(cptcov=1;cptcov<=i1;cptcov++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
      k=k+1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      fprintf(ficresvpl,"\n#****** ");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      for(j=1;j<=cptcoveff;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if (popbased==1) {
      fprintf(ficresvpl,"******\n");          if(mobilav ==0){
                  for(i=1; i<=nlstate;i++)
      varpl=matrix(1,nlstate,(int) bage, (int) fage);              prlim[i][i]=probs[(int)age][i][ij];
      oldm=oldms;savm=savms;          }else{ /* mobilav */ 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            for(i=1; i<=nlstate;i++)
    }              prlim[i][i]=mobaverage[(int)age][i][ij];
  }          }
         }
   fclose(ficresvpl);    
         for(j=1; j<= nlstate; j++){
   /*---------- End : free ----------------*/          for(h=0; h<=nhstepm; h++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
          /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);           as a weighted average of prlim.
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   free_matrix(matcov,1,npar,1,npar);        }    
   free_vector(delti,1,npar);        /* end probability of death */
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   printf("End of Imach\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        if (popbased==1) {
   /*printf("Total time was %d uSec.\n", total_usecs);*/          if(mobilav ==0){
   /*------ End -----------*/            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
  end:            for(i=1; i<=nlstate;i++)
 #ifdef windows              prlim[i][i]=mobaverage[(int)age][i][ij];
  chdir(pathcd);          }
 #endif        }
    
  system("..\\gp37mgw\\wgnuplot graph.plt");        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
 #ifdef windows            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   while (z[0] != 'q') {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     chdir(pathcd);          }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        }
     scanf("%s",z);        /* This for computing probability of death (h=1 means
     if (z[0] == 'c') system("./imach");           computed over hstepm matrices product = hstepm*stepm months) 
     else if (z[0] == 'e') {           as a weighted average of prlim.
       chdir(path);        */
       system(optionfilehtm);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     else if (z[0] == 'q') exit(0);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   }        }    
 #endif        /* end probability of death */
 }  
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %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.1.19  
changed lines
  Added in v.1.141


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>