Diff for /imach/src/imach.c between versions 1.13 and 1.138

version 1.13, 2002/02/20 17:02:08 version 1.138, 2010/04/30 18:19:40
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 1.138  2010/04/30 18:19:40  brouard
   individuals from different ages are interviewed on their health status    *** empty log message ***
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.137  2010/04/29 18:11:38  brouard
   Health expectancies are computed from the transistions observed between    (Module): Checking covariates for more complex models
   waves and are computed for each degree of severity of disability (number    than V1+V2. A lot of change to be done. Unstable.
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.136  2010/04/26 20:30:53  brouard
   The simplest model is the multinomial logistic model where pij is    (Module): merging some libgsl code. Fixing computation
   the probabibility to be observed in state j at the second wave conditional    of likelione (using inter/intrapolation if mle = 0) in order to
   to be observed in state i at the first wave. Therefore the model is:    get same likelihood as if mle=1.
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Some cleaning of code and comments added.
   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 1.135  2009/10/29 15:33:14  brouard
     *Covariates have to be included here again* invites you to do it.    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   More covariates you add, less is the speed of the convergence.  
     Revision 1.134  2009/10/29 13:18:53  brouard
   The advantage that this computer programme claims, comes from that if the    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   delay between waves is not identical for each individual, or if some  
   individual missed an interview, the information is not rounded or lost, but    Revision 1.133  2009/07/06 10:21:25  brouard
   taken into account using an interpolation or extrapolation.    just nforces
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    Revision 1.132  2009/07/06 08:22:05  brouard
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Many tings
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.131  2009/06/20 16:22:47  brouard
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Some dimensions resccaled
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.130  2009/05/26 06:44:34  brouard
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Max Covariate is now set to 20 instead of 8. A
   of the life expectancies. It also computes the prevalence limits.    lot of cleaning with variables initialized to 0. Trying to make
      V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.129  2007/08/31 13:49:27  lievre
   This software have been partly granted by Euro-REVES, a concerted action    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.128  2006/06/30 13:02:05  brouard
   software can be distributed freely for non commercial use. Latest version    (Module): Clarifications on computing e.j
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.127  2006/04/28 18:11:50  brouard
      (Module): Yes the sum of survivors was wrong since
 #include <math.h>    imach-114 because nhstepm was no more computed in the age
 #include <stdio.h>    loop. Now we define nhstepma in the age loop.
 #include <stdlib.h>    (Module): In order to speed up (in case of numerous covariates) we
 #include <unistd.h>    compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
 #define MAXLINE 256    deviation (needs data from the Hessian matrices) which slows the
 #define FILENAMELENGTH 80    computation.
 /*#define DEBUG*/    In the future we should be able to stop the program is only health
 #define windows    expectancies and graph are needed without standard deviations.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    imach-114 because nhstepm was no more computed in the age
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    loop. Now we define nhstepma in the age loop.
     Version 0.98h
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.125  2006/04/04 15:20:31  lievre
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Errors in calculation of health expectancies. Age was not initialized.
 #define NCOVMAX 8 /* Maximum number of covariates */    Forecasting file added.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.124  2006/03/22 17:13:53  lievre
 #define AGESUP 130    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define AGEBASE 40    The log-likelihood is printed in the log file
   
     Revision 1.123  2006/03/20 10:52:43  brouard
 int nvar;    * imach.c (Module): <title> changed, corresponds to .htm file
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    name. <head> headers where missing.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    * imach.c (Module): Weights can have a decimal point as for
 int ndeath=1; /* Number of dead states */    English (a comma might work with a correct LC_NUMERIC environment,
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 int *wav; /* Number of waves for this individuual 0 is possible */    1.
 int maxwav; /* Maxim number of waves */    Version 0.98g
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.122  2006/03/20 09:45:41  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Weights can have a decimal point as for
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    English (a comma might work with a correct LC_NUMERIC environment,
 double jmean; /* Mean space between 2 waves */    otherwise the weight is truncated).
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Modification of warning when the covariates values are not 0 or
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    1.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Version 0.98g
 FILE *ficgp, *fichtm,*ficresprob;  
 FILE *ficreseij;    Revision 1.121  2006/03/16 17:45:01  lievre
   char filerese[FILENAMELENGTH];    * imach.c (Module): Comments concerning covariates added
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    * imach.c (Module): refinements in the computation of lli if
  FILE  *ficresvpl;    status=-2 in order to have more reliable computation if stepm is
   char fileresvpl[FILENAMELENGTH];    not 1 month. Version 0.98f
   
 #define NR_END 1    Revision 1.120  2006/03/16 15:10:38  lievre
 #define FREE_ARG char*    (Module): refinements in the computation of lli if
 #define FTOL 1.0e-10    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 #define NRANSI  
 #define ITMAX 200    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
 #define TOL 2.0e-4    computed as likelihood omitting the logarithm. Version O.98e
   
 #define CGOLD 0.3819660    Revision 1.118  2006/03/14 18:20:07  brouard
 #define ZEPS 1.0e-10    (Module): varevsij Comments added explaining the second
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define GOLD 1.618034    (Module): Function pstamp added
 #define GLIMIT 100.0    (Module): Version 0.98d
 #define TINY 1.0e-20  
     Revision 1.117  2006/03/14 17:16:22  brouard
 static double maxarg1,maxarg2;    (Module): varevsij Comments added explaining the second
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    table of variances if popbased=1 .
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
      (Module): Function pstamp added
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Version 0.98d
 #define rint(a) floor(a+0.5)  
     Revision 1.116  2006/03/06 10:29:27  brouard
 static double sqrarg;    (Module): Variance-covariance wrong links and
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    varian-covariance of ej. is needed (Saito).
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.115  2006/02/27 12:17:45  brouard
 int imx;    (Module): One freematrix added in mlikeli! 0.98c
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
 int m,nb;    filename with strsep.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.113  2006/02/24 14:20:24  brouard
 double **pmmij, ***probs, ***mobaverage;    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 double *weight;    allocation too.
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.112  2006/01/30 09:55:26  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.111  2006/01/25 20:38:18  brouard
 double ftolhess; /* Tolerance for computing hessian */    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 /**************** split *************************/    can be a simple dot '.'.
 static  int split( char *path, char *dirc, char *name )  
 {    Revision 1.110  2006/01/25 00:51:50  brouard
    char *s;                             /* pointer */    (Module): Lots of cleaning and bugs added (Gompertz)
    int  l1, l2;                         /* length counters */  
     Revision 1.109  2006/01/24 19:37:15  brouard
    l1 = strlen( path );                 /* length of path */    (Module): Comments (lines starting with a #) are allowed in data.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.108  2006/01/19 18:05:42  lievre
    if ( s == NULL ) {                   /* no directory, so use current */    Gnuplot problem appeared...
 #if     defined(__bsd__)                /* get current working directory */    To be fixed
       extern char       *getwd( );  
     Revision 1.107  2006/01/19 16:20:37  brouard
       if ( getwd( dirc ) == NULL ) {    Test existence of gnuplot in imach path
 #else  
       extern char       *getcwd( );    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.105  2006/01/05 20:23:19  lievre
          return( GLOCK_ERROR_GETCWD );    *** empty log message ***
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.104  2005/09/30 16:11:43  lievre
    } else {                             /* strip direcotry from path */    (Module): sump fixed, loop imx fixed, and simplifications.
       s++;                              /* after this, the filename */    (Module): If the status is missing at the last wave but we know
       l2 = strlen( s );                 /* length of filename */    that the person is alive, then we can code his/her status as -2
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (instead of missing=-1 in earlier versions) and his/her
       strcpy( name, s );                /* save file name */    contributions to the likelihood is 1 - Prob of dying from last
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
       dirc[l1-l2] = 0;                  /* add zero */    the healthy state at last known wave). Version is 0.98
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.103  2005/09/30 15:54:49  lievre
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): sump fixed, loop imx fixed, and simplifications.
    return( 0 );                         /* we're done */  
 }    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
   
 /******************************************/    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 void replace(char *s, char*t)  
 {    Revision 1.100  2004/07/12 18:29:06  brouard
   int i;    Add version for Mac OS X. Just define UNIX in Makefile
   int lg=20;  
   i=0;    Revision 1.99  2004/06/05 08:57:40  brouard
   lg=strlen(t);    *** empty log message ***
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.98  2004/05/16 15:05:56  brouard
     if (t[i]== '\\') s[i]='/';    New version 0.97 . First attempt to estimate force of mortality
   }    directly from the data i.e. without the need of knowing the health
 }    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
 int nbocc(char *s, char occ)    other analysis, in order to test if the mortality estimated from the
 {    cross-longitudinal survey is different from the mortality estimated
   int i,j=0;    from other sources like vital statistic data.
   int lg=20;  
   i=0;    The same imach parameter file can be used but the option for mle should be -3.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Agnès, who wrote this part of the code, tried to keep most of the
   if  (s[i] == occ ) j++;    former routines in order to include the new code within the former code.
   }  
   return j;    The output is very simple: only an estimate of the intercept and of
 }    the slope with 95% confident intervals.
   
 void cutv(char *u,char *v, char*t, char occ)    Current limitations:
 {    A) Even if you enter covariates, i.e. with the
   int i,lg,j,p=0;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   i=0;    B) There is no computation of Life Expectancy nor Life Table.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.97  2004/02/20 13:25:42  lievre
   }    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.96  2003/07/15 15:38:55  brouard
     (u[j] = t[j]);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   }    rewritten within the same printf. Workaround: many printfs.
      u[p]='\0';  
     Revision 1.95  2003/07/08 07:54:34  brouard
    for(j=0; j<= lg; j++) {    * imach.c (Repository):
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Repository): Using imachwizard code to output a more meaningful covariance
   }    matrix (cov(a12,c31) instead of numbers.
 }  
     Revision 1.94  2003/06/27 13:00:02  brouard
 /********************** nrerror ********************/    Just cleaning
   
 void nrerror(char error_text[])    Revision 1.93  2003/06/25 16:33:55  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   fprintf(stderr,"ERREUR ...\n");    exist so I changed back to asctime which exists.
   fprintf(stderr,"%s\n",error_text);    (Module): Version 0.96b
   exit(1);  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
 /*********************** vector *******************/    (Module): On windows (cygwin) function asctime_r doesn't
 double *vector(int nl, int nh)    exist so I changed back to asctime which exists.
 {  
   double *v;    Revision 1.91  2003/06/25 15:30:29  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    * imach.c (Repository): Duplicated warning errors corrected.
   if (!v) nrerror("allocation failure in vector");    (Repository): Elapsed time after each iteration is now output. It
   return v-nl+NR_END;    helps to forecast when convergence will be reached. Elapsed time
 }    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   free((FREE_ARG)(v+nl-NR_END));    mle=-1 a template is output in file "or"mypar.txt with the design
 }    of the covariance matrix to be input.
   
 /************************ivector *******************************/    Revision 1.89  2003/06/24 12:30:52  brouard
 int *ivector(long nl,long nh)    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   int *v;    of the covariance matrix to be input.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.88  2003/06/23 17:54:56  brouard
   return v-nl+NR_END;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /******************free ivector **************************/    Version 0.96
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.86  2003/06/17 20:04:08  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 /******************* imatrix *******************************/    Revision 1.85  2003/06/17 13:12:43  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    * imach.c (Repository): Check when date of death was earlier that
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    current date of interview. It may happen when the death was just
 {    prior to the death. In this case, dh was negative and likelihood
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    was wrong (infinity). We still send an "Error" but patch by
   int **m;    assuming that the date of death was just one stepm after the
      interview.
   /* allocate pointers to rows */    (Repository): Because some people have very long ID (first column)
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    we changed int to long in num[] and we added a new lvector for
   if (!m) nrerror("allocation failure 1 in matrix()");    memory allocation. But we also truncated to 8 characters (left
   m += NR_END;    truncation)
   m -= nrl;    (Repository): No more line truncation errors.
    
      Revision 1.84  2003/06/13 21:44:43  brouard
   /* allocate rows and set pointers to them */    * imach.c (Repository): Replace "freqsummary" at a correct
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    place. It differs from routine "prevalence" which may be called
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    many times. Probs is memory consuming and must be used with
   m[nrl] += NR_END;    parcimony.
   m[nrl] -= ncl;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.83  2003/06/10 13:39:11  lievre
      *** empty log message ***
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.82  2003/06/05 15:57:20  brouard
 }    Add log in  imach.c and  fullversion number is now printed.
   
 /****************** free_imatrix *************************/  */
 void free_imatrix(m,nrl,nrh,ncl,nch)  /*
       int **m;     Interpolated Markov Chain
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Short summary of the programme:
 {    
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    This program computes Healthy Life Expectancies from
   free((FREE_ARG) (m+nrl-NR_END));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 }    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 /******************* matrix *******************************/    case of a health survey which is our main interest) -2- at least a
 double **matrix(long nrl, long nrh, long ncl, long nch)    second wave of interviews ("longitudinal") which measure each change
 {    (if any) in individual health status.  Health expectancies are
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    computed from the time spent in each health state according to a
   double **m;    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    simplest model is the multinomial logistic model where pij is the
   if (!m) nrerror("allocation failure 1 in matrix()");    probability to be observed in state j at the second wave
   m += NR_END;    conditional to be observed in state i at the first wave. Therefore
   m -= nrl;    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
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    complex model than "constant and age", you should modify the program
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    where the markup *Covariates have to be included here again* invites
   m[nrl] += NR_END;    you to do it.  More covariates you add, slower the
   m[nrl] -= ncl;    convergence.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    The advantage of this computer programme, compared to a simple
   return m;    multinomial logistic model, is clear when the delay between waves is not
 }    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 /*************************free matrix ************************/    account using an interpolation or extrapolation.  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    hPijx is the probability to be observed in state i at age x+h
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    conditional to the observed state i at age x. The delay 'h' can be
   free((FREE_ARG)(m+nrl-NR_END));    split into an exact number (nh*stepm) of unobserved intermediate
 }    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 /******************* ma3x *******************************/    matrix is simply the matrix product of nh*stepm elementary matrices
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m += NR_END;             Institut national d'études démographiques, Paris.
   m -= nrl;    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    software can be distributed freely for non commercial use. Latest version
   m[nrl] += NR_END;    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl] -= ncl;  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
   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;    main
   m[nrl][ncl] -= nll;    read parameterfile
   for (j=ncl+1; j<=nch; j++)    read datafile
     m[nrl][j]=m[nrl][j-1]+nlay;    concatwav
      freqsummary
   for (i=nrl+1; i<=nrh; i++) {    if (mle >= 1)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      mlikeli
     for (j=ncl+1; j<=nch; j++)    print results files
       m[i][j]=m[i][j-1]+nlay;    if mle==1 
   }       computes hessian
   return m;    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 /*************************free ma3x ************************/    open html file
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    period (stable) prevalence
 {     for age prevalim()
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    h Pij x
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    variance of p varprob
   free((FREE_ARG)(m+nrl-NR_END));    forecasting if prevfcast==1 prevforecast call prevalence()
 }    health expectancies
     Variance-covariance of DFLE
 /***************** f1dim *************************/    prevalence()
 extern int ncom;     movingaverage()
 extern double *pcom,*xicom;    varevsij() 
 extern double (*nrfunc)(double []);    if popbased==1 varevsij(,popbased)
      total life expectancies
 double f1dim(double x)    Variance of period (stable) prevalence
 {   end
   int j;  */
   double f;  
   double *xt;  
    
   xt=vector(1,ncom);   
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #include <math.h>
   f=(*nrfunc)(xt);  #include <stdio.h>
   free_vector(xt,1,ncom);  #include <stdlib.h>
   return f;  #include <string.h>
 }  #include <unistd.h>
   
 /*****************brent *************************/  #include <limits.h>
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #include <sys/types.h>
 {  #include <sys/stat.h>
   int iter;  #include <errno.h>
   double a,b,d,etemp;  extern int errno;
   double fu,fv,fw,fx;  
   double ftemp;  /* #include <sys/time.h> */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #include <time.h>
   double e=0.0;  #include "timeval.h"
    
   a=(ax < cx ? ax : cx);  #ifdef GSL
   b=(ax > cx ? ax : cx);  #include <gsl/gsl_errno.h>
   x=w=v=bx;  #include <gsl/gsl_multimin.h>
   fw=fv=fx=(*f)(x);  #endif
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  /* #include <libintl.h> */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /* #define _(String) gettext (String) */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  #define MAXLINE 256
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  #define GNUPLOTPROGRAM "gnuplot"
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #endif  #define FILENAMELENGTH 132
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       return fx;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     }  
     ftemp=fu;  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
     if (fabs(e) > tol1) {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  #define NINTERVMAX 8
       p=(x-v)*q-(x-w)*r;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       q=2.0*(q-r);  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       if (q > 0.0) p = -p;  #define NCOVMAX 20 /* Maximum number of covariates */
       q=fabs(q);  #define MAXN 20000
       etemp=e;  #define YEARM 12. /* Number of months per year */
       e=d;  #define AGESUP 130
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define AGEBASE 40
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
       else {  #ifdef UNIX
         d=p/q;  #define DIRSEPARATOR '/'
         u=x+d;  #define CHARSEPARATOR "/"
         if (u-a < tol2 || b-u < tol2)  #define ODIRSEPARATOR '\\'
           d=SIGN(tol1,xm-x);  #else
       }  #define DIRSEPARATOR '\\'
     } else {  #define CHARSEPARATOR "\\"
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define ODIRSEPARATOR '/'
     }  #endif
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /* $Id$ */
     if (fu <= fx) {  /* $State$ */
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
         SHFT(fv,fw,fx,fu)  char fullversion[]="$Revision$ $Date$"; 
         } else {  char strstart[80];
           if (u < x) a=u; else b=u;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
           if (fu <= fw || w == x) {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
             v=w;  int nvar=0, nforce=0; /* Number of variables, number of forces */
             w=u;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
             fv=fw;  int npar=NPARMAX;
             fw=fu;  int nlstate=2; /* Number of live states */
           } else if (fu <= fv || v == x || v == w) {  int ndeath=1; /* Number of dead states */
             v=u;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
             fv=fu;  int popbased=0;
           }  
         }  int *wav; /* Number of waves for this individuual 0 is possible */
   }  int maxwav=0; /* Maxim number of waves */
   nrerror("Too many iterations in brent");  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   *xmin=x;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   return fx;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
 }                     to the likelihood and the sum of weights (done by funcone)*/
   int mle=1, weightopt=0;
 /****************** mnbrak ***********************/  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 */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
             double (*func)(double))             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 {  double jmean=1; /* Mean space between 2 waves */
   double ulim,u,r,q, dum;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double fu;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    /*FILE *fic ; */ /* Used in readdata only */
   *fa=(*func)(*ax);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   *fb=(*func)(*bx);  FILE *ficlog, *ficrespow;
   if (*fb > *fa) {  int globpr=0; /* Global variable for printing or not */
     SHFT(dum,*ax,*bx,dum)  double fretone; /* Only one call to likelihood */
       SHFT(dum,*fb,*fa,dum)  long ipmx=0; /* Number of contributions */
       }  double sw; /* Sum of weights */
   *cx=(*bx)+GOLD*(*bx-*ax);  char filerespow[FILENAMELENGTH];
   *fc=(*func)(*cx);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   while (*fb > *fc) {  FILE *ficresilk;
     r=(*bx-*ax)*(*fb-*fc);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     q=(*bx-*cx)*(*fb-*fa);  FILE *ficresprobmorprev;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  FILE *fichtm, *fichtmcov; /* Html File */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  FILE *ficreseij;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  char filerese[FILENAMELENGTH];
     if ((*bx-u)*(u-*cx) > 0.0) {  FILE *ficresstdeij;
       fu=(*func)(u);  char fileresstde[FILENAMELENGTH];
     } else if ((*cx-u)*(u-ulim) > 0.0) {  FILE *ficrescveij;
       fu=(*func)(u);  char filerescve[FILENAMELENGTH];
       if (fu < *fc) {  FILE  *ficresvij;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  char fileresv[FILENAMELENGTH];
           SHFT(*fb,*fc,fu,(*func)(u))  FILE  *ficresvpl;
           }  char fileresvpl[FILENAMELENGTH];
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  char title[MAXLINE];
       u=ulim;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       fu=(*func)(u);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     } else {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       u=(*cx)+GOLD*(*cx-*bx);  char command[FILENAMELENGTH];
       fu=(*func)(u);  int  outcmd=0;
     }  
     SHFT(*ax,*bx,*cx,u)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       SHFT(*fa,*fb,*fc,fu)  
       }  char filelog[FILENAMELENGTH]; /* Log file */
 }  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 /*************** linmin ************************/  char popfile[FILENAMELENGTH];
   
 int ncom;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
    struct timezone tzp;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double brent(double ax, double bx, double cx,  long time_value;
                double (*f)(double), double tol, double *xmin);  extern long time();
   double f1dim(double x);  char strcurr[80], strfor[80];
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  char *endptr;
   int j;  long lval;
   double xx,xmin,bx,ax;  double dval;
   double fx,fb,fa;  
    #define NR_END 1
   ncom=n;  #define FREE_ARG char*
   pcom=vector(1,n);  #define FTOL 1.0e-10
   xicom=vector(1,n);  
   nrfunc=func;  #define NRANSI 
   for (j=1;j<=n;j++) {  #define ITMAX 200 
     pcom[j]=p[j];  
     xicom[j]=xi[j];  #define TOL 2.0e-4 
   }  
   ax=0.0;  #define CGOLD 0.3819660 
   xx=1.0;  #define ZEPS 1.0e-10 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  #define GOLD 1.618034 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define GLIMIT 100.0 
 #endif  #define TINY 1.0e-20 
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  static double maxarg1,maxarg2;
     p[j] += xi[j];  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   free_vector(xicom,1,n);    
   free_vector(pcom,1,n);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
 /*************** powell ************************/  static double sqrarg;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
             double (*func)(double []))  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  int agegomp= AGEGOMP;
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  int imx; 
   int i,ibig,j;  int stepm=1;
   double del,t,*pt,*ptt,*xit;  /* Stepm, step in month: minimum step interpolation*/
   double fp,fptt;  
   double *xits;  int estepm;
   pt=vector(1,n);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   ptt=vector(1,n);  
   xit=vector(1,n);  int m,nb;
   xits=vector(1,n);  long *num;
   *fret=(*func)(p);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   for (j=1;j<=n;j++) pt[j]=p[j];  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   for (*iter=1;;++(*iter)) {  double **pmmij, ***probs;
     fp=(*fret);  double *ageexmed,*agecens;
     ibig=0;  double dateintmean=0;
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double *weight;
     for (i=1;i<=n;i++)  int **s; /* Status */
       printf(" %d %.12f",i, p[i]);  double *agedc, **covar, idx;
     printf("\n");  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     for (i=1;i<=n;i++) {  double *lsurv, *lpop, *tpop;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 #ifdef DEBUG  double ftolhess; /* Tolerance for computing hessian */
       printf("fret=%lf \n",*fret);  
 #endif  /**************** split *************************/
       printf("%d",i);fflush(stdout);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       linmin(p,xit,n,fret,func);  {
       if (fabs(fptt-(*fret)) > del) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         del=fabs(fptt-(*fret));       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         ibig=i;    */ 
       }    char  *ss;                            /* pointer */
 #ifdef DEBUG    int   l1, l2;                         /* length counters */
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {    l1 = strlen(path );                   /* length of path */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         printf(" x(%d)=%.12e",j,xit[j]);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       for(j=1;j<=n;j++)      strcpy( name, path );               /* we got the fullname name because no directory */
         printf(" p=%.12e",p[j]);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       printf("\n");        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 #endif      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 #ifdef DEBUG        return( GLOCK_ERROR_GETCWD );
       int k[2],l;      }
       k[0]=1;      /* got dirc from getcwd*/
       k[1]=-1;      printf(" DIRC = %s \n",dirc);
       printf("Max: %.12e",(*func)(p));    } else {                              /* strip direcotry from path */
       for (j=1;j<=n;j++)      ss++;                               /* after this, the filename */
         printf(" %.12e",p[j]);      l2 = strlen( ss );                  /* length of filename */
       printf("\n");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       for(l=0;l<=1;l++) {      strcpy( name, ss );         /* save file name */
         for (j=1;j<=n;j++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      dirc[l1-l2] = 0;                    /* add zero */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      printf(" DIRC2 = %s \n",dirc);
         }    }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    /* We add a separator at the end of dirc if not exists */
       }    l1 = strlen( dirc );                  /* length of directory */
 #endif    if( dirc[l1-1] != DIRSEPARATOR ){
       dirc[l1] =  DIRSEPARATOR;
       dirc[l1+1] = 0; 
       free_vector(xit,1,n);      printf(" DIRC3 = %s \n",dirc);
       free_vector(xits,1,n);    }
       free_vector(ptt,1,n);    ss = strrchr( name, '.' );            /* find last / */
       free_vector(pt,1,n);    if (ss >0){
       return;      ss++;
     }      strcpy(ext,ss);                     /* save extension */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      l1= strlen( name);
     for (j=1;j<=n;j++) {      l2= strlen(ss)+1;
       ptt[j]=2.0*p[j]-pt[j];      strncpy( finame, name, l1-l2);
       xit[j]=p[j]-pt[j];      finame[l1-l2]= 0;
       pt[j]=p[j];    }
     }  
     fptt=(*func)(ptt);    return( 0 );                          /* we're done */
     if (fptt < fp) {  }
       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 (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  void replace_back_to_slash(char *s, char*t)
           xi[j][n]=xit[j];  {
         }    int i;
 #ifdef DEBUG    int lg=0;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    i=0;
         for(j=1;j<=n;j++)    lg=strlen(t);
           printf(" %.12e",xit[j]);    for(i=0; i<= lg; i++) {
         printf("\n");      (s[i] = t[i]);
 #endif      if (t[i]== '\\') s[i]='/';
       }    }
     }  }
   }  
 }  char *trimbb(char *out, char *in)
   { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
 /**** Prevalence limit ****************/    char *s;
     s=out;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    while (*in != '\0'){
 {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        in++;
      matrix by transitions matrix until convergence is reached */      }
       *out++ = *in++;
   int i, ii,j,k;    }
   double min, max, maxmin, maxmax,sumnew=0.;    *out='\0';
   double **matprod2();    return s;
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     for (j=1;j<=nlstate+ndeath;j++){       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
    cov[1]=1.;    char *s, *t;
      t=in;s=in;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    while (*in != '\0'){
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      while( *in == occ){
     newm=savm;        *blocc++ = *in++;
     /* Covariates have to be included here again */        s=in;
      cov[2]=agefin;      }
        *blocc++ = *in++;
       for (k=1; k<=cptcovn;k++) {    }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (s == t) /* occ not found */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      *(blocc-(in-s))='\0';
       }    else
       for (k=1; k<=cptcovage;k++)      *(blocc-(in-s)-1)='\0';
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    in=s;
       for (k=1; k<=cptcovprod;k++)    while ( *in != '\0'){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      *alocc++ = *in++;
     }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    *alocc='\0';
     return s;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   
     savm=oldm;  int nbocc(char *s, char occ)
     oldm=newm;  {
     maxmax=0.;    int i,j=0;
     for(j=1;j<=nlstate;j++){    int lg=20;
       min=1.;    i=0;
       max=0.;    lg=strlen(s);
       for(i=1; i<=nlstate; i++) {    for(i=0; i<= lg; i++) {
         sumnew=0;    if  (s[i] == occ ) j++;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    }
         prlim[i][j]= newm[i][j]/(1-sumnew);    return j;
         max=FMAX(max,prlim[i][j]);  }
         min=FMIN(min,prlim[i][j]);  
       }  /* void cutv(char *u,char *v, char*t, char occ) */
       maxmin=max-min;  /* { */
       maxmax=FMAX(maxmax,maxmin);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     if(maxmax < ftolpl){  /*      gives u="abcdef2ghi" and v="j" *\/ */
       return prlim;  /*   int i,lg,j,p=0; */
     }  /*   i=0; */
   }  /*   lg=strlen(t); */
 }  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
 /*************** transition probabilities ***************/  /*   } */
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /*   for(j=0; j<p; j++) { */
 {  /*     (u[j] = t[j]); */
   double s1, s2;  /*   } */
   /*double t34;*/  /*      u[p]='\0'; */
   int i,j,j1, nc, ii, jj;  
   /*    for(j=0; j<= lg; j++) { */
     for(i=1; i<= nlstate; i++){  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     for(j=1; j<i;j++){  /*   } */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* } */
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /********************** nrerror ********************/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  void nrerror(char error_text[])
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    fprintf(stderr,"ERREUR ...\n");
     }    fprintf(stderr,"%s\n",error_text);
     for(j=i+1; j<=nlstate+ndeath;j++){    exit(EXIT_FAILURE);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*********************** vector *******************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  double *vector(int nl, int nh)
       }  {
       ps[i][j]=(s2);    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   }    if (!v) nrerror("allocation failure in vector");
     /*ps[3][2]=1;*/    return v-nl+NR_END;
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /************************ free vector ******************/
     for(j=1; j<i; j++)  void free_vector(double*v, int nl, int nh)
       s1+=exp(ps[i][j]);  {
     for(j=i+1; j<=nlstate+ndeath; j++)    free((FREE_ARG)(v+nl-NR_END));
       s1+=exp(ps[i][j]);  }
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  /************************ivector *******************************/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  int *ivector(long nl,long nh)
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       ps[i][j]= exp(ps[i][j])*ps[i][i];    int *v;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   } /* end i */    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /******************free ivector **************************/
       ps[ii][ii]=1;  void free_ivector(int *v, long nl, long nh)
     }  {
   }    free((FREE_ARG)(v+nl-NR_END));
   }
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  /************************lvector *******************************/
     for(jj=1; jj<= nlstate+ndeath; jj++){  long *lvector(long nl,long nh)
      printf("%lf ",ps[ii][jj]);  {
    }    long *v;
     printf("\n ");    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
     printf("\n ");printf("%lf ",cov[2]);*/    return v-nl+NR_END;
 /*  }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  /******************free lvector **************************/
     return ps;  void free_lvector(long *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /**************** Product of 2 matrices ******************/  }
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /******************* imatrix *******************************/
 {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  { 
   /* in, b, out are matrice of pointers which should have been initialized    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
      before: only the contents of out is modified. The function returns    int **m; 
      a pointer to pointers identical to out */    
   long i, j, k;    /* allocate pointers to rows */ 
   for(i=nrl; i<= nrh; i++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     for(k=ncolol; k<=ncoloh; k++)    if (!m) nrerror("allocation failure 1 in matrix()"); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    m += NR_END; 
         out[i][k] +=in[i][j]*b[j][k];    m -= nrl; 
     
   return out;    
 }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 /************* Higher Matrix Product ***************/    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    
 {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    
      duration (i.e. until    /* return pointer to array of pointers to rows */ 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    return m; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  } 
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  /****************** free_imatrix *************************/
      included manually here.  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
      */        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   int i, j, d, h, k;  { 
   double **out, cov[NCOVMAX];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double **newm;    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /******************* matrix *******************************/
     for (j=1;j<=nlstate+ndeath;j++){  double **matrix(long nrl, long nrh, long ncl, long nch)
       oldm[i][j]=(i==j ? 1.0 : 0.0);  {
       po[i][j][0]=(i==j ? 1.0 : 0.0);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(d=1; d <=hstepm; d++){    if (!m) nrerror("allocation failure 1 in matrix()");
       newm=savm;    m += NR_END;
       /* Covariates have to be included here again */    m -= nrl;
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for (k=1; k<=cptcovage;k++)    m[nrl] += NR_END;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl] -= ncl;
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/     */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /*************************free matrix ************************/
       savm=oldm;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       oldm=newm;  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(i=1; i<=nlstate+ndeath; i++)    free((FREE_ARG)(m+nrl-NR_END));
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /******************* ma3x *******************************/
          */  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       }  {
   } /* end h */    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   return po;    double ***m;
 }  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /*************** log-likelihood *************/    m += NR_END;
 double func( double *x)    m -= nrl;
 {  
   int i, ii, j, k, mi, d, kk;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double **out;    m[nrl] += NR_END;
   double sw; /* Sum of weights */    m[nrl] -= ncl;
   double lli; /* Individual log likelihood */  
   long ipmx;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   /*extern weight */  
   /* We are differentiating ll according to initial status */    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   /*for(i=1;i<imx;i++)    m[nrl][ncl] += NR_END;
     printf(" %d\n",s[4][i]);    m[nrl][ncl] -= nll;
   */    for (j=ncl+1; j<=nch; j++) 
   cov[1]=1.;      m[nrl][j]=m[nrl][j-1]+nlay;
     
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for (i=nrl+1; i<=nrh; i++) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      for (j=ncl+1; j<=nch; j++) 
     for(mi=1; mi<= wav[i]-1; mi++){        m[i][j]=m[i][j-1]+nlay;
       for (ii=1;ii<=nlstate+ndeath;ii++)    }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return m; 
       for(d=0; d<dh[mi][i]; d++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         newm=savm;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    */
         for (kk=1; kk<=cptcovage;kk++) {  }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  /*************************free ma3x ************************/
          void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         savm=oldm;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         oldm=newm;    free((FREE_ARG)(m+nrl-NR_END));
          }
          
       } /* end mult */  /*************** function subdirf ***********/
        char *subdirf(char fileres[])
       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]]);*/    /* Caution optionfilefiname is hidden */
       ipmx +=1;    strcpy(tmpout,optionfilefiname);
       sw += weight[i];    strcat(tmpout,"/"); /* Add to the right */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    strcat(tmpout,fileres);
     } /* end of wave */    return tmpout;
   } /* end of individual */  }
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  /*************** function subdirf2 ***********/
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  char *subdirf2(char fileres[], char *preop)
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  {
   return -l;    
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 /*********** Maximum Likelihood Estimation ***************/    strcat(tmpout,preop);
     strcat(tmpout,fileres);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    return tmpout;
 {  }
   int i,j, iter;  
   double **xi,*delti;  /*************** function subdirf3 ***********/
   double fret;  char *subdirf3(char fileres[], char *preop, char *preop2)
   xi=matrix(1,npar,1,npar);  {
   for (i=1;i<=npar;i++)    
     for (j=1;j<=npar;j++)    /* Caution optionfilefiname is hidden */
       xi[i][j]=(i==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
   printf("Powell\n");    strcat(tmpout,"/");
   powell(p,xi,npar,ftol,&iter,&fret,func);    strcat(tmpout,preop);
     strcat(tmpout,preop2);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    strcat(tmpout,fileres);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    return tmpout;
   }
 }  
   /***************** f1dim *************************/
 /**** Computes Hessian and covariance matrix ***/  extern int ncom; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  extern double *pcom,*xicom;
 {  extern double (*nrfunc)(double []); 
   double  **a,**y,*x,pd;   
   double **hess;  double f1dim(double x) 
   int i, j,jk;  { 
   int *indx;    int j; 
     double f;
   double hessii(double p[], double delta, int theta, double delti[]);    double *xt; 
   double hessij(double p[], double delti[], int i, int j);   
   void lubksb(double **a, int npar, int *indx, double b[]) ;    xt=vector(1,ncom); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
   hess=matrix(1,npar,1,npar);    free_vector(xt,1,ncom); 
     return f; 
   printf("\nCalculation of the hessian matrix. Wait...\n");  } 
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  /*****************brent *************************/
     hess[i][i]=hessii(p,ftolhess,i,delti);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     /*printf(" %f ",p[i]);*/  { 
     /*printf(" %lf ",hess[i][i]);*/    int iter; 
   }    double a,b,d,etemp;
      double fu,fv,fw,fx;
   for (i=1;i<=npar;i++) {    double ftemp;
     for (j=1;j<=npar;j++)  {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       if (j>i) {    double e=0.0; 
         printf(".%d%d",i,j);fflush(stdout);   
         hess[i][j]=hessij(p,delti,i,j);    a=(ax < cx ? ax : cx); 
         hess[j][i]=hess[i][j];        b=(ax > cx ? ax : cx); 
         /*printf(" %lf ",hess[i][j]);*/    x=w=v=bx; 
       }    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
   }      xm=0.5*(a+b); 
   printf("\n");      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      printf(".");fflush(stdout);
        fprintf(ficlog,".");fflush(ficlog);
   a=matrix(1,npar,1,npar);  #ifdef DEBUG
   y=matrix(1,npar,1,npar);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   x=vector(1,npar);      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);
   indx=ivector(1,npar);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   ludcmp(a,npar,indx,&pd);        *xmin=x; 
         return fx; 
   for (j=1;j<=npar;j++) {      } 
     for (i=1;i<=npar;i++) x[i]=0;      ftemp=fu;
     x[j]=1;      if (fabs(e) > tol1) { 
     lubksb(a,npar,indx,x);        r=(x-w)*(fx-fv); 
     for (i=1;i<=npar;i++){        q=(x-v)*(fx-fw); 
       matcov[i][j]=x[i];        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
   }        if (q > 0.0) p = -p; 
         q=fabs(q); 
   printf("\n#Hessian matrix#\n");        etemp=e; 
   for (i=1;i<=npar;i++) {        e=d; 
     for (j=1;j<=npar;j++) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       printf("%.3e ",hess[i][j]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }        else { 
     printf("\n");          d=p/q; 
   }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
   /* Recompute Inverse */            d=SIGN(tol1,xm-x); 
   for (i=1;i<=npar;i++)        } 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      } else { 
   ludcmp(a,npar,indx,&pd);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
   /*  printf("\n#Hessian matrix recomputed#\n");      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
   for (j=1;j<=npar;j++) {      if (fu <= fx) { 
     for (i=1;i<=npar;i++) x[i]=0;        if (u >= x) a=x; else b=x; 
     x[j]=1;        SHFT(v,w,x,u) 
     lubksb(a,npar,indx,x);          SHFT(fv,fw,fx,fu) 
     for (i=1;i<=npar;i++){          } else { 
       y[i][j]=x[i];            if (u < x) a=u; else b=u; 
       printf("%.3e ",y[i][j]);            if (fu <= fw || w == x) { 
     }              v=w; 
     printf("\n");              w=u; 
   }              fv=fw; 
   */              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
   free_matrix(a,1,npar,1,npar);              v=u; 
   free_matrix(y,1,npar,1,npar);              fv=fu; 
   free_vector(x,1,npar);            } 
   free_ivector(indx,1,npar);          } 
   free_matrix(hess,1,npar,1,npar);    } 
     nrerror("Too many iterations in brent"); 
     *xmin=x; 
 }    return fx; 
   } 
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  /****************** mnbrak ***********************/
 {  
   int i;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   int l=1, lmax=20;              double (*func)(double)) 
   double k1,k2;  { 
   double p2[NPARMAX+1];    double ulim,u,r,q, dum;
   double res;    double fu; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;   
   double fx;    *fa=(*func)(*ax); 
   int k=0,kmax=10;    *fb=(*func)(*bx); 
   double l1;    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
   fx=func(x);        SHFT(dum,*fb,*fa,dum) 
   for (i=1;i<=npar;i++) p2[i]=x[i];        } 
   for(l=0 ; l <=lmax; l++){    *cx=(*bx)+GOLD*(*bx-*ax); 
     l1=pow(10,l);    *fc=(*func)(*cx); 
     delts=delt;    while (*fb > *fc) { 
     for(k=1 ; k <kmax; k=k+1){      r=(*bx-*ax)*(*fb-*fc); 
       delt = delta*(l1*k);      q=(*bx-*cx)*(*fb-*fa); 
       p2[theta]=x[theta] +delt;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       k1=func(p2)-fx;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       p2[theta]=x[theta]-delt;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       k2=func(p2)-fx;      if ((*bx-u)*(u-*cx) > 0.0) { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        fu=(*func)(u); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      } else if ((*cx-u)*(u-ulim) > 0.0) { 
              fu=(*func)(u); 
 #ifdef DEBUG        if (fu < *fc) { 
       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);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 #endif            SHFT(*fb,*fc,fu,(*func)(u)) 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            } 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         k=kmax;        u=ulim; 
       }        fu=(*func)(u); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      } else { 
         k=kmax; l=lmax*10.;        u=(*cx)+GOLD*(*cx-*bx); 
       }        fu=(*func)(u); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      } 
         delts=delt;      SHFT(*ax,*bx,*cx,u) 
       }        SHFT(*fa,*fb,*fc,fu) 
     }        } 
   }  } 
   delti[theta]=delts;  
   return res;  /*************** linmin ************************/
    
 }  int ncom; 
   double *pcom,*xicom;
 double hessij( double x[], double delti[], int thetai,int thetaj)  double (*nrfunc)(double []); 
 {   
   int i;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   int l=1, l1, lmax=20;  { 
   double k1,k2,k3,k4,res,fx;    double brent(double ax, double bx, double cx, 
   double p2[NPARMAX+1];                 double (*f)(double), double tol, double *xmin); 
   int k;    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   fx=func(x);                double *fc, double (*func)(double)); 
   for (k=1; k<=2; k++) {    int j; 
     for (i=1;i<=npar;i++) p2[i]=x[i];    double xx,xmin,bx,ax; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    double fx,fb,fa;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;   
     k1=func(p2)-fx;    ncom=n; 
      pcom=vector(1,n); 
     p2[thetai]=x[thetai]+delti[thetai]/k;    xicom=vector(1,n); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    nrfunc=func; 
     k2=func(p2)-fx;    for (j=1;j<=n;j++) { 
        pcom[j]=p[j]; 
     p2[thetai]=x[thetai]-delti[thetai]/k;      xicom[j]=xi[j]; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    } 
     k3=func(p2)-fx;    ax=0.0; 
      xx=1.0; 
     p2[thetai]=x[thetai]-delti[thetai]/k;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     k4=func(p2)-fx;  #ifdef DEBUG
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 #ifdef DEBUG    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  #endif
 #endif    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
   return res;      p[j] += xi[j]; 
 }    } 
     free_vector(xicom,1,n); 
 /************** Inverse of matrix **************/    free_vector(pcom,1,n); 
 void ludcmp(double **a, int n, int *indx, double *d)  } 
 {  
   int i,imax,j,k;  char *asc_diff_time(long time_sec, char ascdiff[])
   double big,dum,sum,temp;  {
   double *vv;    long sec_left, days, hours, minutes;
      days = (time_sec) / (60*60*24);
   vv=vector(1,n);    sec_left = (time_sec) % (60*60*24);
   *d=1.0;    hours = (sec_left) / (60*60) ;
   for (i=1;i<=n;i++) {    sec_left = (sec_left) %(60*60);
     big=0.0;    minutes = (sec_left) /60;
     for (j=1;j<=n;j++)    sec_left = (sec_left) % (60);
       if ((temp=fabs(a[i][j])) > big) big=temp;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    return ascdiff;
     vv[i]=1.0/big;  }
   }  
   for (j=1;j<=n;j++) {  /*************** powell ************************/
     for (i=1;i<j;i++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       sum=a[i][j];              double (*func)(double [])) 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  { 
       a[i][j]=sum;    void linmin(double p[], double xi[], int n, double *fret, 
     }                double (*func)(double [])); 
     big=0.0;    int i,ibig,j; 
     for (i=j;i<=n;i++) {    double del,t,*pt,*ptt,*xit;
       sum=a[i][j];    double fp,fptt;
       for (k=1;k<j;k++)    double *xits;
         sum -= a[i][k]*a[k][j];    int niterf, itmp;
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {    pt=vector(1,n); 
         big=dum;    ptt=vector(1,n); 
         imax=i;    xit=vector(1,n); 
       }    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     if (j != imax) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
       for (k=1;k<=n;k++) {    for (*iter=1;;++(*iter)) { 
         dum=a[imax][k];      fp=(*fret); 
         a[imax][k]=a[j][k];      ibig=0; 
         a[j][k]=dum;      del=0.0; 
       }      last_time=curr_time;
       *d = -(*d);      (void) gettimeofday(&curr_time,&tzp);
       vv[imax]=vv[j];      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     }      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);
     indx[j]=imax;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     if (a[j][j] == 0.0) a[j][j]=TINY;     for (i=1;i<=n;i++) {
     if (j != n) {        printf(" %d %.12f",i, p[i]);
       dum=1.0/(a[j][j]);        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        fprintf(ficrespow," %.12lf", p[i]);
     }      }
   }      printf("\n");
   free_vector(vv,1,n);  /* Doesn't work */      fprintf(ficlog,"\n");
 ;      fprintf(ficrespow,"\n");fflush(ficrespow);
 }      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
 void lubksb(double **a, int n, int *indx, double b[])        strcpy(strcurr,asctime(&tm));
 {  /*       asctime_r(&tm,strcurr); */
   int i,ii=0,ip,j;        forecast_time=curr_time; 
   double sum;        itmp = strlen(strcurr);
          if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   for (i=1;i<=n;i++) {          strcurr[itmp-1]='\0';
     ip=indx[i];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     sum=b[ip];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     b[ip]=b[i];        for(niterf=10;niterf<=30;niterf+=10){
     if (ii)          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          tmf = *localtime(&forecast_time.tv_sec);
     else if (sum) ii=i;  /*      asctime_r(&tmf,strfor); */
     b[i]=sum;          strcpy(strfor,asctime(&tmf));
   }          itmp = strlen(strfor);
   for (i=n;i>=1;i--) {          if(strfor[itmp-1]=='\n')
     sum=b[i];          strfor[itmp-1]='\0';
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          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);
     b[i]=sum/a[i][i];          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   }        }
 }      }
       for (i=1;i<=n;i++) { 
 /************ Frequencies ********************/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)        fptt=(*fret); 
 {  /* Some frequencies */  #ifdef DEBUG
          printf("fret=%lf \n",*fret);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        fprintf(ficlog,"fret=%lf \n",*fret);
   double ***freq; /* Frequencies */  #endif
   double *pp;        printf("%d",i);fflush(stdout);
   double pos;        fprintf(ficlog,"%d",i);fflush(ficlog);
   FILE *ficresp;        linmin(p,xit,n,fret,func); 
   char fileresp[FILENAMELENGTH];        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
   pp=vector(1,nlstate);          ibig=i; 
  probs= ma3x(1,130 ,1,8, 1,8);        } 
   strcpy(fileresp,"p");  #ifdef DEBUG
   strcat(fileresp,fileres);        printf("%d %.12e",i,(*fret));
   if((ficresp=fopen(fileresp,"w"))==NULL) {        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for (j=1;j<=n;j++) {
     exit(0);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   }          printf(" x(%d)=%.12e",j,xit[j]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   j1=0;        }
         for(j=1;j<=n;j++) {
   j=cptcoveff;          printf(" p=%.12e",p[j]);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          fprintf(ficlog," p=%.12e",p[j]);
         }
   for(k1=1; k1<=j;k1++){        printf("\n");
    for(i1=1; i1<=ncodemax[k1];i1++){        fprintf(ficlog,"\n");
        j1++;  #endif
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      } 
          scanf("%d", i);*/      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         for (i=-1; i<=nlstate+ndeath; i++)    #ifdef DEBUG
          for (jk=-1; jk<=nlstate+ndeath; jk++)          int k[2],l;
            for(m=agemin; m <= agemax+3; m++)        k[0]=1;
              freq[i][jk][m]=0;        k[1]=-1;
                printf("Max: %.12e",(*func)(p));
        for (i=1; i<=imx; i++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
          bool=1;        for (j=1;j<=n;j++) {
          if  (cptcovn>0) {          printf(" %.12e",p[j]);
            for (z1=1; z1<=cptcoveff; z1++)          fprintf(ficlog," %.12e",p[j]);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
                bool=0;        printf("\n");
          }        fprintf(ficlog,"\n");
           if (bool==1) {        for(l=0;l<=1;l++) {
            for(m=firstpass; m<=lastpass-1; m++){          for (j=1;j<=n;j++) {
              if(agev[m][i]==0) agev[m][i]=agemax+1;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
              if(agev[m][i]==1) agev[m][i]=agemax+2;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          }
            }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
          }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
        }        }
         if  (cptcovn>0) {  #endif
          fprintf(ficresp, "\n#********** Variable ");  
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
        fprintf(ficresp, "**********\n#");        free_vector(xit,1,n); 
         }        free_vector(xits,1,n); 
        for(i=1; i<=nlstate;i++)        free_vector(ptt,1,n); 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        free_vector(pt,1,n); 
        fprintf(ficresp, "\n");        return; 
              } 
   for(i=(int)agemin; i <= (int)agemax+3; i++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     if(i==(int)agemax+3)      for (j=1;j<=n;j++) { 
       printf("Total");        ptt[j]=2.0*p[j]-pt[j]; 
     else        xit[j]=p[j]-pt[j]; 
       printf("Age %d", i);        pt[j]=p[j]; 
     for(jk=1; jk <=nlstate ; jk++){      } 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      fptt=(*func)(ptt); 
         pp[jk] += freq[jk][m][i];      if (fptt < fp) { 
     }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for(jk=1; jk <=nlstate ; jk++){        if (t < 0.0) { 
       for(m=-1, pos=0; m <=0 ; m++)          linmin(p,xit,n,fret,func); 
         pos += freq[jk][m][i];          for (j=1;j<=n;j++) { 
       if(pp[jk]>=1.e-10)            xi[j][ibig]=xi[j][n]; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            xi[j][n]=xit[j]; 
       else          }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  #ifdef DEBUG
     }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)          for(j=1;j<=n;j++){
         pp[jk] += freq[jk][m][i];            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
     for(jk=1,pos=0; jk <=nlstate ; jk++)          }
       pos += pp[jk];          printf("\n");
     for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog,"\n");
       if(pos>=1.e-5)  #endif
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        }
       else      } 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    } 
       if( i <= (int) agemax){  } 
         if(pos>=1.e-5){  
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /**** Prevalence limit (stable or period prevalence)  ****************/
           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]);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         }  {
       else    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);       matrix by transitions matrix until convergence is reached */
       }  
     }    int i, ii,j,k;
     for(jk=-1; jk <=nlstate+ndeath; jk++)    double min, max, maxmin, maxmax,sumnew=0.;
       for(m=-1; m <=nlstate+ndeath; m++)    double **matprod2();
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    double **out, cov[NCOVMAX+1], **pmij();
     if(i <= (int) agemax)    double **newm;
       fprintf(ficresp,"\n");    double agefin, delaymax=50 ; /* Max number of years to converge */
     printf("\n");  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
  }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        }
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);     cov[1]=1.;
   free_vector(pp,1,nlstate);   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 }  /* End of Freq */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 /************* Waves Concatenation ***************/      /* Covariates have to be included here again */
       cov[2]=agefin;
 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 (k=1; k<=cptcovn;k++) {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      Death is a valid wave (if date is known).        /*        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]]);*/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      and mw[mi+1][i]. dh depends on stepm.      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]]];
       
   int i, mi, m;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
      double sum=0., jmean=0.;*/      /*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);
   int j, k=0,jk, ju, jl;      
   double sum=0.;      savm=oldm;
   jmin=1e+5;      oldm=newm;
   jmax=-1;      maxmax=0.;
   jmean=0.;      for(j=1;j<=nlstate;j++){
   for(i=1; i<=imx; i++){        min=1.;
     mi=0;        max=0.;
     m=firstpass;        for(i=1; i<=nlstate; i++) {
     while(s[m][i] <= nlstate){          sumnew=0;
       if(s[m][i]>=1)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         mw[++mi][i]=m;          prlim[i][j]= newm[i][j]/(1-sumnew);
       if(m >=lastpass)          max=FMAX(max,prlim[i][j]);
         break;          min=FMIN(min,prlim[i][j]);
       else        }
         m++;        maxmin=max-min;
     }/* end while */        maxmax=FMAX(maxmax,maxmin);
     if (s[m][i] > nlstate){      }
       mi++;     /* Death is another wave */      if(maxmax < ftolpl){
       /* if(mi==0)  never been interviewed correctly before death */        return prlim;
          /* Only death is a correct wave */      }
       mw[mi][i]=m;    }
     }  }
   
     wav[i]=mi;  /*************** transition probabilities ***************/ 
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  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,
   for(i=1; i<=imx; i++){       computes the probability to be observed in state j being in state i by appying the
     for(mi=1; mi<wav[i];mi++){       model to the ncovmodel covariates (including constant and age).
       if (stepm <=0)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         dh[mi][i]=1;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
       else{       ncth covariate in the global vector x is given by the formula:
         if (s[mw[mi+1][i]][i] > nlstate) {       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           if (agedc[i] < 2*AGESUP) {       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
           if(j==0) j=1;  /* Survives at least one month after exam */       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
           k=k+1;       Outputs ps[i][j] the probability to be observed in j being in j according to
           if (j >= jmax) jmax=j;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           if (j <= jmin) jmin=j;    */
           sum=sum+j;    double s1, lnpijopii;
           /* if (j<10) printf("j=%d num=%d ",j,i); */    /*double t34;*/
           }    int i,j,j1, nc, ii, jj;
         }  
         else{      for(i=1; i<= nlstate; i++){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        for(j=1; j<i;j++){
           k=k+1;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           if (j >= jmax) jmax=j;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
           else if (j <= jmin)jmin=j;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           sum=sum+j;          }
         }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         jk= j/stepm;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         jl= j -jk*stepm;        }
         ju= j -(jk+1)*stepm;        for(j=i+1; j<=nlstate+ndeath;j++){
         if(jl <= -ju)          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           dh[mi][i]=jk;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
         else            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
           dh[mi][i]=jk+1;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         if(dh[mi][i]==0)          }
           dh[mi][i]=1; /* At least one step */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       }        }
     }      }
   }      
   jmean=sum/k;      for(i=1; i<= nlstate; i++){
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        s1=0;
  }        for(j=1; j<i; j++){
 /*********** Tricode ****************************/          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
 void tricode(int *Tvar, int **nbcode, int imx)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
 {        }
   int Ndum[20],ij=1, k, j, i;        for(j=i+1; j<=nlstate+ndeath; j++){
   int cptcode=0;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   cptcoveff=0;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
          }
   for (k=0; k<19; k++) Ndum[k]=0;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   for (k=1; k<=7; k++) ncodemax[k]=0;        ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        for(j=1; j<i; j++)
     for (i=1; i<=imx; i++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
       ij=(int)(covar[Tvar[j]][i]);        for(j=i+1; j<=nlstate+ndeath; j++)
       Ndum[ij]++;          ps[i][j]= exp(ps[i][j])*ps[i][i];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       if (ij > cptcode) cptcode=ij;      } /* end i */
     }      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for (i=0; i<=cptcode; i++) {        for(jj=1; jj<= nlstate+ndeath; jj++){
       if(Ndum[i]!=0) ncodemax[j]++;          ps[ii][jj]=0;
     }          ps[ii][ii]=1;
     ij=1;        }
       }
       
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         if (Ndum[k] != 0) {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
           nbcode[Tvar[j]][ij]=k;  /*         printf("ddd %lf ",ps[ii][jj]); */
           ij++;  /*       } */
         }  /*       printf("\n "); */
         if (ij > ncodemax[j]) break;  /*        } */
       }    /*        printf("\n ");printf("%lf ",cov[2]); */
     }         /*
   }          for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
  for (k=0; k<19; k++) Ndum[k]=0;      return ps;
   }
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];  /**************** Product of 2 matrices ******************/
       Ndum[ij]++;  
     }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
  ij=1;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
  for (i=1; i<=10; i++) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
    if((Ndum[i]!=0) && (i<=ncov)){    /* in, b, out are matrice of pointers which should have been initialized 
      Tvaraff[ij]=i;       before: only the contents of out is modified. The function returns
      ij++;       a pointer to pointers identical to out */
    }    long i, j, k;
  }    for(i=nrl; i<= nrh; i++)
        for(k=ncolol; k<=ncoloh; k++)
     cptcoveff=ij-1;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 }          out[i][k] +=in[i][j]*b[j][k];
   
 /*********** Health Expectancies ****************/    return out;
   }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  
 {  
   /* Health expectancies */  /************* Higher Matrix Product ***************/
   int i, j, nhstepm, hstepm, h;  
   double age, agelim,hf;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double ***p3mat;  {
      /* Computes the transition matrix starting at age 'age' over 
   fprintf(ficreseij,"# Health expectancies\n");       'nhstepm*hstepm*stepm' months (i.e. until
   fprintf(ficreseij,"# Age");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   for(i=1; i<=nlstate;i++)       nhstepm*hstepm matrices. 
     for(j=1; j<=nlstate;j++)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       fprintf(ficreseij," %1d-%1d",i,j);       (typically every 2 years instead of every month which is too big 
   fprintf(ficreseij,"\n");       for the memory).
        Model is determined by parameters x and covariates have to be 
   hstepm=1*YEARM; /*  Every j years of age (in month) */       included manually here. 
   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 */    int i, j, d, h, k;
     /* nhstepm age range expressed in number of stepm */    double **out, cov[NCOVMAX+1];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    double **newm;
     /* Typically if 20 years = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;    /* Hstepm could be zero and should return the unit matrix */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    for (i=1;i<=nlstate+ndeath;i++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=nlstate+ndeath;j++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        oldm[i][j]=(i==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        po[i][j][0]=(i==j ? 1.0 : 0.0);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
     for(i=1; i<=nlstate;i++)      for(d=1; d <=hstepm; d++){
       for(j=1; j<=nlstate;j++)        newm=savm;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        /* Covariates have to be included here again */
           eij[i][j][(int)age] +=p3mat[i][j][h];        cov[1]=1.;
         }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
            for (k=1; k<=cptcovn;k++) 
     hf=1;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     if (stepm >= YEARM) hf=stepm/YEARM;        for (k=1; k<=cptcovage;k++)
     fprintf(ficreseij,"%.0f",age );          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovprod;k++)
       for(j=1; j<=nlstate;j++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  
       }  
     fprintf(ficreseij,"\n");        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 /************ Variance ******************/        oldm=newm;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      }
 {      for(i=1; i<=nlstate+ndeath; i++)
   /* Variance of health expectancies */        for(j=1;j<=nlstate+ndeath;j++) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          po[i][j][h]=newm[i][j];
   double **newm;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   double **dnewm,**doldm;        }
   int i, j, nhstepm, hstepm, h;      /*printf("h=%d ",h);*/
   int k, cptcode;    } /* end h */
   double *xp;  /*     printf("\n H=%d \n",h); */
   double **gp, **gm;    return po;
   double ***gradg, ***trgradg;  }
   double ***p3mat;  
   double age,agelim;  
   int theta;  /*************** log-likelihood *************/
   double func( double *x)
    fprintf(ficresvij,"# Covariances of life expectancies\n");  {
   fprintf(ficresvij,"# Age");    int i, ii, j, k, mi, d, kk;
   for(i=1; i<=nlstate;i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(j=1; j<=nlstate;j++)    double **out;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    double sw; /* Sum of weights */
   fprintf(ficresvij,"\n");    double lli; /* Individual log likelihood */
     int s1, s2;
   xp=vector(1,npar);    double bbh, survp;
   dnewm=matrix(1,nlstate,1,npar);    long ipmx;
   doldm=matrix(1,nlstate,1,nlstate);    /*extern weight */
      /* We are differentiating ll according to initial status */
   hstepm=1*YEARM; /* Every year of age */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /*for(i=1;i<imx;i++) 
   agelim = AGESUP;      printf(" %d\n",s[4][i]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    cov[1]=1.;
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for(k=1; k<=nlstate; k++) ll[k]=0.;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    if(mle==1){
     gp=matrix(0,nhstepm,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gm=matrix(0,nhstepm,1,nlstate);        /* Computes the values of the ncovmodel covariates of the model
            depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
     for(theta=1; theta <=npar; theta++){           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       for(i=1; i<=npar; i++){ /* Computes gradient */           to be observed in j being in i according to the model.
         xp[i] = x[i] + (i==theta ?delti[theta]:0);         */
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       for(j=1; j<= nlstate; j++){           has been calculated etc */
         for(h=0; h<=nhstepm; h++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
       for(i=1; i<=npar; i++) /* Computes gradient */          for(d=0; d<dh[mi][i]; d++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            newm=savm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<= nlstate; j++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       }            oldm=newm;
       for(j=1; j<= nlstate; j++)          } /* end mult */
         for(h=0; h<=nhstepm; h++){        
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          /*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.
     } /* End theta */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for(h=0; h<=nhstepm; h++)           * (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
         for(theta=1; theta <=npar; theta++)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           trgradg[h][j][theta]=gradg[h][theta][j];           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
     for(i=1;i<=nlstate;i++)           * For stepm > 1 the results are less biased than in previous versions. 
       for(j=1;j<=nlstate;j++)           */
         vareij[i][j][(int)age] =0.;          s1=s[mw[mi][i]][i];
     for(h=0;h<=nhstepm;h++){          s2=s[mw[mi+1][i]][i];
       for(k=0;k<=nhstepm;k++){          bbh=(double)bh[mi][i]/(double)stepm; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          /* bias bh is positive if real duration
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);           * is higher than the multiple of stepm and negative otherwise.
         for(i=1;i<=nlstate;i++)           */
           for(j=1;j<=nlstate;j++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
             vareij[i][j][(int)age] += doldm[i][j];          if( s2 > nlstate){ 
       }            /* i.e. if s2 is a death state and if the date of death is known 
     }               then the contribution to the likelihood is the probability to 
     h=1;               die between last step unit time and current  step unit time, 
     if (stepm >= YEARM) h=stepm/YEARM;               which is also equal to probability to die before dh 
     fprintf(ficresvij,"%.0f ",age );               minus probability to die before dh-stepm . 
     for(i=1; i<=nlstate;i++)               In version up to 0.92 likelihood was computed
       for(j=1; j<=nlstate;j++){          as if date of death was unknown. Death was treated as any other
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          health state: the date of the interview describes the actual state
       }          and not the date of a change in health state. The former idea was
     fprintf(ficresvij,"\n");          to consider that at each interview the state was recorded
     free_matrix(gp,0,nhstepm,1,nlstate);          (healthy, disable or death) and IMaCh was corrected; but when we
     free_matrix(gm,0,nhstepm,1,nlstate);          introduced the exact date of death then we should have modified
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          the contribution of an exact death to the likelihood. This new
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          contribution is smaller and very dependent of the step unit
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          stepm. It is no more the probability to die between last interview
   } /* End age */          and month of death but the probability to survive from last
            interview up to one month before death multiplied by the
   free_vector(xp,1,npar);          probability to die within a month. Thanks to Chris
   free_matrix(doldm,1,nlstate,1,npar);          Jackson for correcting this bug.  Former versions increased
   free_matrix(dnewm,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%
 }          lower mortality.
             */
 /************ Variance of prevlim ******************/            lli=log(out[s1][s2] - savm[s1][s2]);
 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)  
 {  
   /* Variance of prevalence limit */          } else if  (s2==-2) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (j=1,survp=0. ; j<=nlstate; j++) 
   double **newm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double **dnewm,**doldm;            /*survp += out[s1][j]; */
   int i, j, nhstepm, hstepm;            lli= log(survp);
   int k, cptcode;          }
   double *xp;          
   double *gp, *gm;          else if  (s2==-4) { 
   double **gradg, **trgradg;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double age,agelim;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int theta;            lli= log(survp); 
              } 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");          else if  (s2==-5) { 
   for(i=1; i<=nlstate;i++)            for (j=1,survp=0. ; j<=2; j++)  
       fprintf(ficresvpl," %1d-%1d",i,i);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fprintf(ficresvpl,"\n");            lli= log(survp); 
           } 
   xp=vector(1,npar);          
   dnewm=matrix(1,nlstate,1,npar);          else{
   doldm=matrix(1,nlstate,1,nlstate);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
              /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   hstepm=1*YEARM; /* Every year of age */          } 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   agelim = AGESUP;          /*if(lli ==000.0)*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          /*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); */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          ipmx +=1;
     if (stepm >= YEARM) hstepm=1;          sw += weight[i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gradg=matrix(1,npar,1,nlstate);        } /* end of wave */
     gp=vector(1,nlstate);      } /* end of individual */
     gm=vector(1,nlstate);    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(theta=1; theta <=npar; theta++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(mi=1; mi<= wav[i]-1; mi++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         gp[i] = prlim[i][i];            }
              for(d=0; d<=dh[mi][i]; d++){
       for(i=1; i<=npar; i++) /* Computes gradient */            newm=savm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (kk=1; kk<=cptcovage;kk++) {
       for(i=1;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         gm[i] = prlim[i][i];            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            savm=oldm;
     } /* End theta */            oldm=newm;
           } /* end mult */
     trgradg =matrix(1,nlstate,1,npar);        
           s1=s[mw[mi][i]][i];
     for(j=1; j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
       for(theta=1; theta <=npar; theta++)          bbh=(double)bh[mi][i]/(double)stepm; 
         trgradg[j][theta]=gradg[theta][j];          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
     for(i=1;i<=nlstate;i++)          sw += weight[i];
       varpl[i][(int)age] =0.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        } /* end of wave */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      } /* end of individual */
     for(i=1;i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficresvpl,"%.0f ",age );        for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1; i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresvpl,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_vector(gp,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_vector(gm,1,nlstate);            }
     free_matrix(gradg,1,npar,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     free_matrix(trgradg,1,nlstate,1,npar);            newm=savm;
   } /* End age */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   free_vector(xp,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(doldm,1,nlstate,1,npar);            }
   free_matrix(dnewm,1,nlstate,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /************ Variance of one-step probabilities  ******************/          } /* end mult */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        
 {          s1=s[mw[mi][i]][i];
   int i, j;          s2=s[mw[mi+1][i]][i];
   int k=0, cptcode;          bbh=(double)bh[mi][i]/(double)stepm; 
   double **dnewm,**doldm;          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 */
   double *xp;          ipmx +=1;
   double *gp, *gm;          sw += weight[i];
   double **gradg, **trgradg;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim, cov[NCOVMAX];        } /* end of wave */
   int theta;      } /* end of individual */
   char fileresprob[FILENAMELENGTH];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(fileresprob,"prob");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(fileresprob,fileres);        for(mi=1; mi<= wav[i]-1; mi++){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with resultfile: %s\n", fileresprob);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
           for(d=0; d<dh[mi][i]; d++){
   xp=vector(1,npar);            newm=savm;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   cov[1]=1;            }
   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);          if( s2 > nlstate){ 
                  lli=log(out[s1][s2] - savm[s1][s2]);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          }else{
                lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       k=0;          }
       for(i=1; i<= (nlstate+ndeath); i++){          ipmx +=1;
         for(j=1; j<=(nlstate+ndeath);j++){          sw += weight[i];
            k=k+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           gp[k]=pmmij[i][j];  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         }        } /* end of wave */
       }      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(i=1; i<=npar; i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
       k=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=(nlstate+ndeath); i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(j=1; j<=(nlstate+ndeath);j++){            }
           k=k+1;          for(d=0; d<dh[mi][i]; d++){
           gm[k]=pmmij[i][j];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            savm=oldm;
       for(theta=1; theta <=npar; theta++)            oldm=newm;
       trgradg[j][theta]=gradg[theta][j];          } /* end mult */
          
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          s1=s[mw[mi][i]][i];
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
      pmij(pmmij,cov,ncovmodel,x,nlstate);          ipmx +=1;
           sw += weight[i];
      k=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      for(i=1; i<=(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]);*/
        for(j=1; j<=(nlstate+ndeath);j++){        } /* end of wave */
          k=k+1;      } /* end of individual */
          gm[k]=pmmij[i][j];    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      /*printf("\n%d ",(int)age);    return -l;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  }
          
   /*************** log-likelihood *************/
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  double funcone( double *x)
      }*/  {
     /* Same as likeli but slower because of a lot of printf and if */
   fprintf(ficresprob,"\n%d ",(int)age);    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double **out;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    double lli; /* Individual log likelihood */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    double llt;
   }    int s1, s2;
     double bbh, survp;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    /*extern weight */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    /* We are differentiating ll according to initial status */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*for(i=1;i<imx;i++) 
 }      printf(" %d\n",s[4][i]);
  free_vector(xp,1,npar);    */
 fclose(ficresprob);    cov[1]=1.;
  exit(0);  
 }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 /***********************************************/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /**************** Main Program *****************/      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++)
 /*int main(int argc, char *argv[])*/          for (j=1;j<=nlstate+ndeath;j++){
 int main()            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        for(d=0; d<dh[mi][i]; d++){
   double agedeb, agefin,hf;          newm=savm;
   double agemin=1.e20, agemax=-1.e20;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
   double fret;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **xi,tmp,delta;          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double dum; /* Dummy variable */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***p3mat;          savm=oldm;
   int *indx;          oldm=newm;
   char line[MAXLINE], linepar[MAXLINE];        } /* end mult */
   char title[MAXLINE];        
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];        s1=s[mw[mi][i]][i];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];        s2=s[mw[mi+1][i]][i];
   char filerest[FILENAMELENGTH];        bbh=(double)bh[mi][i]/(double)stepm; 
   char fileregp[FILENAMELENGTH];        /* bias is positive if real duration
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];         * is higher than the multiple of stepm and negative otherwise.
   int firstobs=1, lastobs=10;         */
   int sdeb, sfin; /* Status at beginning and end */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   int c,  h , cpt,l;          lli=log(out[s1][s2] - savm[s1][s2]);
   int ju,jl, mi;        } else if  (s2==-2) {
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for (j=1,survp=0. ; j<=nlstate; j++) 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
            lli= log(survp);
   int hstepm, nhstepm;        }else if (mle==1){
   double bage, fage, age, agelim, agebase;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double ftolpl=FTOL;        } else if(mle==2){
   double **prlim;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double *severity;        } else if(mle==3){  /* exponential inter-extrapolation */
   double ***param; /* Matrix of parameters */          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 */
   double  *p;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **matcov; /* Matrix of covariance */          lli=log(out[s1][s2]); /* Original formula */
   double ***delti3; /* Scale */        } else{  /* mle=0 back to 1 */
   double *delti; /* Scale */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double ***eij, ***vareij;          /*lli=log(out[s1][s2]); */ /* Original formula */
   double **varpl; /* Variances of prevalence limits by age */        } /* End of if */
   double *epj, vepp;        ipmx +=1;
   double kk1;        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";        /*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]); */
   char *alph[]={"a","a","b","c","d","e"}, str[4];        if(globpr){
           fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
   char z[1]="c", occ;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 #include <sys/time.h>                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 #include <time.h>          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            llt +=ll[k]*gipmx/gsw;
   /* long total_usecs;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   struct timeval start_time, end_time;          }
            fprintf(ficresilk," %10.6f\n", -llt);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
       } /* end of wave */
     } /* end of individual */
   printf("\nIMACH, Version 0.64b");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   printf("\nEnter the parameter file name: ");    /* 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 */
 #ifdef windows    if(globpr==0){ /* First time we count the contributions and weights */
   scanf("%s",pathtot);      gipmx=ipmx;
   getcwd(pathcd, size);      gsw=sw;
   /*cygwin_split_path(pathtot,path,optionfile);    }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    return -l;
   /* cutv(path,optionfile,pathtot,'\\');*/  }
   
 split(pathtot, path,optionfile);  
   chdir(path);  /*************** function likelione ***********/
   replace(pathc,path);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 #endif  {
 #ifdef unix    /* This routine should help understanding what is done with 
   scanf("%s",optionfile);       the selection of individuals/waves and
 #endif       to check the exact contribution to the likelihood.
        Plotting could be done.
 /*-------- arguments in the command line --------*/     */
     int k;
   strcpy(fileres,"r");  
   strcat(fileres, optionfile);    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   /*---------arguments file --------*/      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        printf("Problem with resultfile: %s\n", fileresilk);
     printf("Problem with optionfile %s\n",optionfile);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     goto end;      }
   }      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 ");
   strcpy(filereso,"o");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   strcat(filereso,fileres);      for(k=1; k<=nlstate; k++) 
   if((ficparo=fopen(filereso,"w"))==NULL) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   
   /* Reads comments: lines beginning with '#' */    *fretone=(*funcone)(p);
   while((c=getc(ficpar))=='#' && c!= EOF){    if(*globpri !=0){
     ungetc(c,ficpar);      fclose(ficresilk);
     fgets(line, MAXLINE, ficpar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     puts(line);      fflush(fichtm); 
     fputs(line,ficparo);    } 
   }    return;
   ungetc(c,ficpar);  }
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);  /*********** Maximum Likelihood Estimation ***************/
   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);  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   covar=matrix(0,NCOVMAX,1,n);  {
   cptcovn=0;    int i,j, iter;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    double **xi;
     double fret;
   ncovmodel=2+cptcovn;    double fretone; /* Only one call to likelihood */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    /*  char filerespow[FILENAMELENGTH];*/
      xi=matrix(1,npar,1,npar);
   /* Read guess parameters */    for (i=1;i<=npar;i++)
   /* Reads comments: lines beginning with '#' */      for (j=1;j<=npar;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){        xi[i][j]=(i==j ? 1.0 : 0.0);
     ungetc(c,ficpar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     fgets(line, MAXLINE, ficpar);    strcpy(filerespow,"pow"); 
     puts(line);    strcat(filerespow,fileres);
     fputs(line,ficparo);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for(i=1; i <=nlstate; i++)    for (i=1;i<=nlstate;i++)
     for(j=1; j <=nlstate+ndeath-1; j++){      for(j=1;j<=nlstate+ndeath;j++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficrespow,"\n");
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    powell(p,xi,npar,ftol,&iter,&fret,func);
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);    free_matrix(xi,1,npar,1,npar);
         fprintf(ficparo," %lf",param[i][j][k]);    fclose(ficrespow);
       }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       fscanf(ficpar,"\n");    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       printf("\n");    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficparo,"\n");  
     }  }
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   p=param[1][1];  {
      double  **a,**y,*x,pd;
   /* Reads comments: lines beginning with '#' */    double **hess;
   while((c=getc(ficpar))=='#' && c!= EOF){    int i, j,jk;
     ungetc(c,ficpar);    int *indx;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fputs(line,ficparo);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
   ungetc(c,ficpar);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    hess=matrix(1,npar,1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){    printf("\nCalculation of the hessian matrix. Wait...\n");
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (i=1;i<=npar;i++){
       printf("%1d%1d",i,j);      printf("%d",i);fflush(stdout);
       fprintf(ficparo,"%1d%1d",i1,j1);      fprintf(ficlog,"%d",i);fflush(ficlog);
       for(k=1; k<=ncovmodel;k++){     
         fscanf(ficpar,"%le",&delti3[i][j][k]);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         printf(" %le",delti3[i][j][k]);      
         fprintf(ficparo," %le",delti3[i][j][k]);      /*  printf(" %f ",p[i]);
       }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       fscanf(ficpar,"\n");    }
       printf("\n");    
       fprintf(ficparo,"\n");    for (i=1;i<=npar;i++) {
     }      for (j=1;j<=npar;j++)  {
   }        if (j>i) { 
   delti=delti3[1][1];          printf(".%d%d",i,j);fflush(stdout);
            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   /* Reads comments: lines beginning with '#' */          hess[i][j]=hessij(p,delti,i,j,func,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);          hess[j][i]=hess[i][j];    
     fgets(line, MAXLINE, ficpar);          /*printf(" %lf ",hess[i][j]);*/
     puts(line);        }
     fputs(line,ficparo);      }
   }    }
   ungetc(c,ficpar);    printf("\n");
      fprintf(ficlog,"\n");
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fscanf(ficpar,"%s",&str);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     printf("%s",str);    
     fprintf(ficparo,"%s",str);    a=matrix(1,npar,1,npar);
     for(j=1; j <=i; j++){    y=matrix(1,npar,1,npar);
       fscanf(ficpar," %le",&matcov[i][j]);    x=vector(1,npar);
       printf(" %.5le",matcov[i][j]);    indx=ivector(1,npar);
       fprintf(ficparo," %.5le",matcov[i][j]);    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     fscanf(ficpar,"\n");    ludcmp(a,npar,indx,&pd);
     printf("\n");  
     fprintf(ficparo,"\n");    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   for(i=1; i <=npar; i++)      x[j]=1;
     for(j=i+1;j<=npar;j++)      lubksb(a,npar,indx,x);
       matcov[i][j]=matcov[j][i];      for (i=1;i<=npar;i++){ 
            matcov[i][j]=x[i];
   printf("\n");      }
     }
   
     /*-------- data file ----------*/    printf("\n#Hessian matrix#\n");
     if((ficres =fopen(fileres,"w"))==NULL) {    fprintf(ficlog,"\n#Hessian matrix#\n");
       printf("Problem with resultfile: %s\n", fileres);goto end;    for (i=1;i<=npar;i++) { 
     }      for (j=1;j<=npar;j++) { 
     fprintf(ficres,"#%s\n",version);        printf("%.3e ",hess[i][j]);
            fprintf(ficlog,"%.3e ",hess[i][j]);
     if((fic=fopen(datafile,"r"))==NULL)    {      }
       printf("Problem with datafile: %s\n", datafile);goto end;      printf("\n");
     }      fprintf(ficlog,"\n");
     }
     n= lastobs;  
     severity = vector(1,maxwav);    /* Recompute Inverse */
     outcome=imatrix(1,maxwav+1,1,n);    for (i=1;i<=npar;i++)
     num=ivector(1,n);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     moisnais=vector(1,n);    ludcmp(a,npar,indx,&pd);
     annais=vector(1,n);  
     moisdc=vector(1,n);    /*  printf("\n#Hessian matrix recomputed#\n");
     andc=vector(1,n);  
     agedc=vector(1,n);    for (j=1;j<=npar;j++) {
     cod=ivector(1,n);      for (i=1;i<=npar;i++) x[i]=0;
     weight=vector(1,n);      x[j]=1;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      lubksb(a,npar,indx,x);
     mint=matrix(1,maxwav,1,n);      for (i=1;i<=npar;i++){ 
     anint=matrix(1,maxwav,1,n);        y[i][j]=x[i];
     s=imatrix(1,maxwav+1,1,n);        printf("%.3e ",y[i][j]);
     adl=imatrix(1,maxwav+1,1,n);            fprintf(ficlog,"%.3e ",y[i][j]);
     tab=ivector(1,NCOVMAX);      }
     ncodemax=ivector(1,8);      printf("\n");
       fprintf(ficlog,"\n");
     i=1;    }
     while (fgets(line, MAXLINE, fic) != NULL)    {    */
       if ((i >= firstobs) && (i <=lastobs)) {  
            free_matrix(a,1,npar,1,npar);
         for (j=maxwav;j>=1;j--){    free_matrix(y,1,npar,1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    free_vector(x,1,npar);
           strcpy(line,stra);    free_ivector(indx,1,npar);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(hess,1,npar,1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  
          }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    int i;
     int l=1, lmax=20;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    double k1,k2;
         for (j=ncov;j>=1;j--){    double p2[MAXPARM+1]; /* identical to x */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double res;
         }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         num[i]=atol(stra);    double fx;
            int k=0,kmax=10;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double l1;
           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;}*/  
     fx=func(x);
         i=i+1;    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){
     }      l1=pow(10,l);
     /* printf("ii=%d", ij);      delts=delt;
        scanf("%d",i);*/      for(k=1 ; k <kmax; k=k+1){
   imx=i-1; /* Number of individuals */        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   /* for (i=1; i<=imx; i++){        k1=func(p2)-fx;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        p2[theta]=x[theta]-delt;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        k2=func(p2)-fx;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        
   #ifdef DEBUGHESS
   /* Calculation of the number of parameter from char model*/        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);
   Tvar=ivector(1,15);        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);
   Tprod=ivector(1,15);  #endif
   Tvaraff=ivector(1,15);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   Tvard=imatrix(1,15,1,2);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   Tage=ivector(1,15);                k=kmax;
            }
   if (strlen(model) >1){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     j=0, j1=0, k1=1, k2=1;          k=kmax; l=lmax*10.;
     j=nbocc(model,'+');        }
     j1=nbocc(model,'*');        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     cptcovn=j+1;          delts=delt;
     cptcovprod=j1;        }
          }
        }
     strcpy(modelsav,model);    delti[theta]=delts;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    return res; 
       printf("Error. Non available option model=%s ",model);    
       goto end;  }
     }  
      double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(i=(j+1); i>=1;i--){  {
       cutv(stra,strb,modelsav,'+');    int i;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    int l=1, l1, lmax=20;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    double k1,k2,k3,k4,res,fx;
       /*scanf("%d",i);*/    double p2[MAXPARM+1];
       if (strchr(strb,'*')) {    int k;
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {    fx=func(x);
           cptcovprod--;    for (k=1; k<=2; k++) {
           cutv(strb,stre,strd,'V');      for (i=1;i<=npar;i++) p2[i]=x[i];
           Tvar[i]=atoi(stre);      p2[thetai]=x[thetai]+delti[thetai]/k;
           cptcovage++;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             Tage[cptcovage]=i;      k1=func(p2)-fx;
             /*printf("stre=%s ", stre);*/    
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
         else if (strcmp(strd,"age")==0) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           cptcovprod--;      k2=func(p2)-fx;
           cutv(strb,stre,strc,'V');    
           Tvar[i]=atoi(stre);      p2[thetai]=x[thetai]-delti[thetai]/k;
           cptcovage++;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           Tage[cptcovage]=i;      k3=func(p2)-fx;
         }    
         else {      p2[thetai]=x[thetai]-delti[thetai]/k;
           cutv(strb,stre,strc,'V');      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           Tvar[i]=ncov+k1;      k4=func(p2)-fx;
           cutv(strb,strc,strd,'V');      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           Tprod[k1]=i;  #ifdef DEBUG
           Tvard[k1][1]=atoi(strc);      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);
           Tvard[k1][2]=atoi(stre);      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);
           Tvar[cptcovn+k2]=Tvard[k1][1];  #endif
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    }
           for (k=1; k<=lastobs;k++)    return res;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  }
           k1++;  
           k2=k2+2;  /************** Inverse of matrix **************/
         }  void ludcmp(double **a, int n, int *indx, double *d) 
       }  { 
       else {    int i,imax,j,k; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double big,dum,sum,temp; 
        /*  scanf("%d",i);*/    double *vv; 
       cutv(strd,strc,strb,'V');   
       Tvar[i]=atoi(strc);    vv=vector(1,n); 
       }    *d=1.0; 
       strcpy(modelsav,stra);      for (i=1;i<=n;i++) { 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      big=0.0; 
         scanf("%d",i);*/      for (j=1;j<=n;j++) 
     }        if ((temp=fabs(a[i][j])) > big) big=temp; 
 }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        vv[i]=1.0/big; 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    } 
   printf("cptcovprod=%d ", cptcovprod);    for (j=1;j<=n;j++) { 
   scanf("%d ",i);*/      for (i=1;i<j;i++) { 
     fclose(fic);        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     /*  if(mle==1){*/        a[i][j]=sum; 
     if (weightopt != 1) { /* Maximisation without weights*/      } 
       for(i=1;i<=n;i++) weight[i]=1.0;      big=0.0; 
     }      for (i=j;i<=n;i++) { 
     /*-calculation of age at interview from date of interview and age at death -*/        sum=a[i][j]; 
     agev=matrix(1,maxwav,1,imx);        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
    for (i=1; i<=imx; i++)        a[i][j]=sum; 
      for(m=2; (m<= maxwav); m++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          big=dum; 
          anint[m][i]=9999;          imax=i; 
          s[m][i]=-1;        } 
        }      } 
          if (j != imax) { 
     for (i=1; i<=imx; i++)  {        for (k=1;k<=n;k++) { 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          dum=a[imax][k]; 
       for(m=1; (m<= maxwav); m++){          a[imax][k]=a[j][k]; 
         if(s[m][i] >0){          a[j][k]=dum; 
           if (s[m][i] == nlstate+1) {        } 
             if(agedc[i]>0)        *d = -(*d); 
               if(moisdc[i]!=99 && andc[i]!=9999)        vv[imax]=vv[j]; 
               agev[m][i]=agedc[i];      } 
             else {      indx[j]=imax; 
               if (andc[i]!=9999){      if (a[j][j] == 0.0) a[j][j]=TINY; 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      if (j != n) { 
               agev[m][i]=-1;        dum=1.0/(a[j][j]); 
               }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
             }      } 
           }    } 
           else if(s[m][i] !=9){ /* Should no more exist */    free_vector(vv,1,n);  /* Doesn't work */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  ;
             if(mint[m][i]==99 || anint[m][i]==9999)  } 
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){  void lubksb(double **a, int n, int *indx, double b[]) 
               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);*/    int i,ii=0,ip,j; 
             }    double sum; 
             else if(agev[m][i] >agemax){   
               agemax=agev[m][i];    for (i=1;i<=n;i++) { 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      ip=indx[i]; 
             }      sum=b[ip]; 
             /*agev[m][i]=anint[m][i]-annais[i];*/      b[ip]=b[i]; 
             /*   agev[m][i] = age[i]+2*m;*/      if (ii) 
           }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           else { /* =9 */      else if (sum) ii=i; 
             agev[m][i]=1;      b[i]=sum; 
             s[m][i]=-1;    } 
           }    for (i=n;i>=1;i--) { 
         }      sum=b[i]; 
         else /*= 0 Unknown */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           agev[m][i]=1;      b[i]=sum/a[i][i]; 
       }    } 
      } 
     }  
     for (i=1; i<=imx; i++)  {  void pstamp(FILE *fichier)
       for(m=1; (m<= maxwav); m++){  {
         if (s[m][i] > (nlstate+ndeath)) {    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
           printf("Error: Wrong value in nlstate or ndeath\n");    }
           goto end;  
         }  /************ Frequencies ********************/
       }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     }  {  /* Some frequencies */
     
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    int i, m, jk, k1,i1, j1, bool, z1,j;
     int first;
     free_vector(severity,1,maxwav);    double ***freq; /* Frequencies */
     free_imatrix(outcome,1,maxwav+1,1,n);    double *pp, **prop;
     free_vector(moisnais,1,n);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     free_vector(annais,1,n);    char fileresp[FILENAMELENGTH];
     free_matrix(mint,1,maxwav,1,n);    
     free_matrix(anint,1,maxwav,1,n);    pp=vector(1,nlstate);
     free_vector(moisdc,1,n);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     free_vector(andc,1,n);    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
        if((ficresp=fopen(fileresp,"w"))==NULL) {
     wav=ivector(1,imx);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      exit(0);
        }
     /* Concatenates waves */    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    j1=0;
     
     j=cptcoveff;
       Tcode=ivector(1,100);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    first=1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
          for(k1=1; k1<=j;k1++){
    codtab=imatrix(1,100,1,10);      for(i1=1; i1<=ncodemax[k1];i1++){
    h=0;        j1++;
    m=pow(2,cptcoveff);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
    for(k=1;k<=cptcoveff; k++){        for (i=-5; i<=nlstate+ndeath; i++)  
      for(i=1; i <=(m/pow(2,k));i++){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
        for(j=1; j <= ncodemax[k]; j++){            for(m=iagemin; m <= iagemax+3; m++)
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              freq[i][jk][m]=0;
            h++;  
            if (h>m) h=1;codtab[h][k]=j;      for (i=1; i<=nlstate; i++)  
          }        for(m=iagemin; m <= iagemax+3; m++)
        }          prop[i][m]=0;
      }        
    }        dateintsum=0;
         k2cpt=0;
         for (i=1; i<=imx; i++) {
    /*for(i=1; i <=m ;i++){          bool=1;
      for(k=1; k <=cptcovn; k++){          if  (cptcovn>0) {
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);            for (z1=1; z1<=cptcoveff; z1++) 
      }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      printf("\n");                bool=0;
    }          }
    scanf("%d",i);*/          if (bool==1){
                for(m=firstpass; m<=lastpass; m++){
    /* Calculates basic frequencies. Computes observed prevalence at single age              k2=anint[m][i]+(mint[m][i]/12.);
        and prints on file fileres'p'. */              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if (m<lastpass) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                }
                      
     /* For Powell, parameters are in a vector p[] starting at p[1]                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                  dateintsum=dateintsum+k2;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                  k2cpt++;
                 }
     if(mle==1){                /*}*/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            }
     }          }
            }
     /*--------- results files --------------*/         
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
            pstamp(ficresp);
    jk=1;        if  (cptcovn>0) {
    fprintf(ficres,"# Parameters\n");          fprintf(ficresp, "\n#********** Variable "); 
    printf("# Parameters\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresp, "**********\n#");
      for(k=1; k <=(nlstate+ndeath); k++){        }
        if (k != i)        for(i=1; i<=nlstate;i++) 
          {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
            printf("%d%d ",i,k);        fprintf(ficresp, "\n");
            fprintf(ficres,"%1d%1d ",i,k);        
            for(j=1; j <=ncovmodel; j++){        for(i=iagemin; i <= iagemax+3; i++){
              printf("%f ",p[jk]);          if(i==iagemax+3){
              fprintf(ficres,"%f ",p[jk]);            fprintf(ficlog,"Total");
              jk++;          }else{
            }            if(first==1){
            printf("\n");              first=0;
            fprintf(ficres,"\n");              printf("See log file for details...\n");
          }            }
      }            fprintf(ficlog,"Age %d", i);
    }          }
  if(mle==1){          for(jk=1; jk <=nlstate ; jk++){
     /* Computing hessian and covariance matrix */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     ftolhess=ftol; /* Usually correct */              pp[jk] += freq[jk][m][i]; 
     hesscov(matcov, p, npar, delti, ftolhess, func);          }
  }          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficres,"# Scales\n");            for(m=-1, pos=0; m <=0 ; m++)
     printf("# Scales\n");              pos += freq[jk][m][i];
      for(i=1,jk=1; i <=nlstate; i++){            if(pp[jk]>=1.e-10){
       for(j=1; j <=nlstate+ndeath; j++){              if(first==1){
         if (j!=i) {                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           fprintf(ficres,"%1d%1d",i,j);              }
           printf("%1d%1d",i,j);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           for(k=1; k<=ncovmodel;k++){            }else{
             printf(" %.5e",delti[jk]);              if(first==1)
             fprintf(ficres," %.5e",delti[jk]);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             jk++;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           }            }
           printf("\n");          }
           fprintf(ficres,"\n");  
         }          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       }              pp[jk] += freq[jk][m][i];
              }       
     k=1;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     fprintf(ficres,"# Covariance\n");            pos += pp[jk];
     printf("# Covariance\n");            posprop += prop[jk][i];
     for(i=1;i<=npar;i++){          }
       /*  if (k>nlstate) k=1;          for(jk=1; jk <=nlstate ; jk++){
       i1=(i-1)/(ncovmodel*nlstate)+1;            if(pos>=1.e-5){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              if(first==1)
       printf("%s%d%d",alph[k],i1,tab[i]);*/                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficres,"%3d",i);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       printf("%3d",i);            }else{
       for(j=1; j<=i;j++){              if(first==1)
         fprintf(ficres," %.5e",matcov[i][j]);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         printf(" %.5e",matcov[i][j]);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
       fprintf(ficres,"\n");            if( i <= iagemax){
       printf("\n");              if(pos>=1.e-5){
       k++;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     }                /*probs[i][jk][j1]= pp[jk]/pos;*/
                    /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     while((c=getc(ficpar))=='#' && c!= EOF){              }
       ungetc(c,ficpar);              else
       fgets(line, MAXLINE, ficpar);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       puts(line);            }
       fputs(line,ficparo);          }
     }          
     ungetc(c,ficpar);          for(jk=-1; jk <=nlstate+ndeath; jk++)
              for(m=-1; m <=nlstate+ndeath; m++)
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
     if (fage <= 2) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       bage = agemin;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       fage = agemax;              }
     }          if(i <= iagemax)
             fprintf(ficresp,"\n");
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          if(first==1)
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            printf("Others in log...\n");
           fprintf(ficlog,"\n");
            }
 /*------------ gnuplot -------------*/      }
 chdir(pathcd);    }
   if((ficgp=fopen("graph.plt","w"))==NULL) {    dateintmean=dateintsum/k2cpt; 
     printf("Problem with file graph.gp");goto end;   
   }    fclose(ficresp);
 #ifdef windows    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   fprintf(ficgp,"cd \"%s\" \n",pathc);    free_vector(pp,1,nlstate);
 #endif    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 m=pow(2,cptcoveff);    /* End of Freq */
    }
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {  /************ Prevalence ********************/
    for (k1=1; k1<= m ; k1 ++) {  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)
   {  
 #ifdef windows    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     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);       in each health status at the date of interview (if between dateprev1 and dateprev2).
 #endif       We still use firstpass and lastpass as another selection.
 #ifdef unix    */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);   
 #endif    int i, m, jk, k1, i1, j1, bool, z1,j;
     double ***freq; /* Frequencies */
 for (i=1; i<= nlstate ; i ++) {    double *pp, **prop;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double pos,posprop; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double  y2; /* in fractional years */
 }    int iagemin, iagemax;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {    iagemin= (int) agemin;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    iagemax= (int) agemax;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*pp=vector(1,nlstate);*/
 }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      for (i=1; i<= nlstate ; i ++) {    j1=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    j=cptcoveff;
 }      if (cptcovn<1) {j=1;ncodemax[1]=1;}
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    
 #ifdef unix    for(k1=1; k1<=j;k1++){
 fprintf(ficgp,"\nset ter gif small size 400,300");      for(i1=1; i1<=ncodemax[k1];i1++){
 #endif        j1++;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        
    }        for (i=1; i<=nlstate; i++)  
   }          for(m=iagemin; m <= iagemax+3; m++)
   /*2 eme*/            prop[i][m]=0.0;
        
   for (k1=1; k1<= m ; k1 ++) {        for (i=1; i<=imx; i++) { /* Each individual */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          bool=1;
              if  (cptcovn>0) {
     for (i=1; i<= nlstate+1 ; i ++) {            for (z1=1; z1<=cptcoveff; z1++) 
       k=2*i;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                bool=0;
       for (j=1; j<= nlstate+1 ; j ++) {          } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (bool==1) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 }                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       for (j=1; j<= nlstate+1 ; j ++) {                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         else fprintf(ficgp," \%%*lf (\%%*lf)");                  /*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]]);*/
 }                    prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,"\" t\"\" w l 0,");                  prop[s[m][i]][iagemax+3] += weight[i]; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                } 
       for (j=1; j<= nlstate+1 ; j ++) {              }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            } /* end selection of waves */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for(i=iagemin; i <= iagemax+3; i++){  
       else fprintf(ficgp,"\" t\"\" w l 0,");          
     }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            posprop += prop[jk][i]; 
   }          } 
    
   /*3eme*/          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
   for (k1=1; k1<= m ; k1 ++) {              if(posprop>=1.e-5){ 
     for (cpt=1; cpt<= nlstate ; cpt ++) {                probs[i][jk][j1]= prop[jk][i]/posprop;
       k=2+nlstate*(cpt-1);              } else
       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);                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
       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 jk */ 
       }        }/* end i */ 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      } /* end i1 */
     }    } /* end k1 */
   }    
      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /* CV preval stat */    /*free_vector(pp,1,nlstate);*/
   for (k1=1; k1<= m ; k1 ++) {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for (cpt=1; cpt<nlstate ; cpt ++) {  }  /* End of prevalence */
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  /************* Waves Concatenation ***************/
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  {
          /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       l=3+(nlstate+ndeath)*cpt;       Death is a valid wave (if date is known).
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for (i=1; i< nlstate ; i ++) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         l=3+(nlstate+ndeath)*cpt;       and mw[mi+1][i]. dh depends on stepm.
         fprintf(ficgp,"+$%d",l+i+1);       */
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      int i, mi, m;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     }       double sum=0., jmean=0.;*/
   }      int first;
     int j, k=0,jk, ju, jl;
   /* proba elementaires */    double sum=0.;
    for(i=1,jk=1; i <=nlstate; i++){    first=0;
     for(k=1; k <=(nlstate+ndeath); k++){    jmin=1e+5;
       if (k != i) {    jmax=-1;
         for(j=1; j <=ncovmodel; j++){    jmean=0.;
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    for(i=1; i<=imx; i++){
           /*fprintf(ficgp,"%s",alph[1]);*/      mi=0;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      m=firstpass;
           jk++;      while(s[m][i] <= nlstate){
           fprintf(ficgp,"\n");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         }          mw[++mi][i]=m;
       }        if(m >=lastpass)
     }          break;
     }        else
           m++;
   for(jk=1; jk <=m; jk++) {      }/* end while */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      if (s[m][i] > nlstate){
    i=1;        mi++;     /* Death is another wave */
    for(k2=1; k2<=nlstate; k2++) {        /* if(mi==0)  never been interviewed correctly before death */
      k3=i;           /* Only death is a correct wave */
      for(k=1; k<=(nlstate+ndeath); k++) {        mw[mi][i]=m;
        if (k != k2){      }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;      wav[i]=mi;
         for(j=3; j <=ncovmodel; j++) {      if(mi==0){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        nbwarn++;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        if(first==0){
             ij++;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           }          first=1;
           else        }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        if(first==1){
         }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           fprintf(ficgp,")/(1");        }
              } /* end mi==0 */
         for(k1=1; k1 <=nlstate; k1++){      } /* End individuals */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
 ij=1;    for(i=1; i<=imx; i++){
           for(j=3; j <=ncovmodel; j++){      for(mi=1; mi<wav[i];mi++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        if (stepm <=0)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          dh[mi][i]=1;
             ij++;        else{
           }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           else            if (agedc[i] < 2*AGESUP) {
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           }              if(j==0) j=1;  /* Survives at least one month after exam */
           fprintf(ficgp,")");              else if(j<0){
         }                nberr++;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                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]);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                j=1; /* Temporary Dangerous patch */
         i=i+ncovmodel;                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
        }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
    }              }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              k=k+1;
   }              if (j >= jmax){
                    jmax=j;
   fclose(ficgp);                ijmax=i;
                  }
 chdir(path);              if (j <= jmin){
     free_matrix(agev,1,maxwav,1,imx);                jmin=j;
     free_ivector(wav,1,imx);                ijmin=i;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              sum=sum+j;
                  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     free_imatrix(s,1,maxwav+1,1,n);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                }
              }
     free_ivector(num,1,n);          else{
     free_vector(agedc,1,n);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     free_vector(weight,1,n);  /*        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]); */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);            k=k+1;
     fclose(ficres);            if (j >= jmax) {
     /*  }*/              jmax=j;
                  ijmax=i;
    /*________fin mle=1_________*/            }
                else if (j <= jmin){
               jmin=j;
                ijmin=i;
     /* No more information from the sample is required now */            }
   /* Reads comments: lines beginning with '#' */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   while((c=getc(ficpar))=='#' && c!= EOF){            /*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]);*/
     ungetc(c,ficpar);            if(j<0){
     fgets(line, MAXLINE, ficpar);              nberr++;
     puts(line);              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]);
     fputs(line,ficparo);              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]);
   }            }
   ungetc(c,ficpar);            sum=sum+j;
            }
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          jk= j/stepm;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          jl= j -jk*stepm;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          ju= j -(jk+1)*stepm;
 /*--------- index.htm --------*/          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
   strcpy(optionfilehtm,optionfile);              dh[mi][i]=jk;
   strcat(optionfilehtm,".htm");              bh[mi][i]=0;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            }else{ /* We want a negative bias in order to only have interpolation ie
     printf("Problem with %s \n",optionfilehtm);goto end;                    * to avoid the price of an extra matrix product in likelihood */
   }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">            }
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          }else{
 Total number of observations=%d <br>            if(jl <= -ju){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>              dh[mi][i]=jk;
 <hr  size=\"2\" color=\"#EC5E5E\">              bh[mi][i]=jl;       /* bias is positive if real duration
 <li>Outputs files<br><br>\n                                   * is higher than the multiple of stepm and negative otherwise.
         - 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>            }
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            else{
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>              dh[mi][i]=jk+1;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              bh[mi][i]=ju;
         - 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>            if(dh[mi][i]==0){
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              dh[mi][i]=1; /* At least one step */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
  fprintf(fichtm," <li>Graphs</li><p>");            }
           } /* end if mle */
  m=cptcoveff;        }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      } /* end wave */
     }
  j1=0;    jmean=sum/k;
  for(k1=1; k1<=m;k1++){    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
        j1++;   }
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  /*********** Tricode ****************************/
          for (cpt=1; cpt<=cptcoveff;cpt++)  void tricode(int *Tvar, int **nbcode, int imx)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  {
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /* Uses cptcovn+2*cptcovprod as the number of covariates */
        }    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
        for(cpt=1; cpt<nlstate;cpt++){    int modmaxcovj=0; /* Modality max of covariates j */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    cptcoveff=0; 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);   
        }    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for(cpt=1; cpt<=nlstate;cpt++) {    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
      }                                 modality of this covariate Vj*/ 
      for(cpt=1; cpt<=nlstate;cpt++) {        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>                                        modality of the nth covariate of individual i. */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
      }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        if (ij > modmaxcovj) modmaxcovj=ij; 
 health expectancies in states (1) and (2): e%s%d.gif<br>        /* getting the maximum value of the modality of the covariate
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
 fprintf(fichtm,"\n</body>");           female is 1, then modmaxcovj=1.*/
    }      }
  }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
 fclose(fichtm);      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
         if( Ndum[i] != 0 )
   /*--------------- Prevalence limit --------------*/          ncodemax[j]++; 
          /* Number of modalities of the j th covariate. In fact
   strcpy(filerespl,"pl");           ncodemax[j]=2 (dichotom. variables only) but it could be more for
   strcat(filerespl,fileres);           historical reasons */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      } /* Ndum[-1] number of undefined modalities */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      ij=1; 
   fprintf(ficrespl,"#Prevalence limit\n");      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
   fprintf(ficrespl,"#Age ");        for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   fprintf(ficrespl,"\n");            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                         k is a modality. If we have model=V1+V1*sex 
   prlim=matrix(1,nlstate,1,nlstate);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            ij++;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if (ij > ncodemax[j]) break; 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }  /* end of loop on */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      } /* end of loop on modality */ 
   k=0;    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   agebase=agemin;    
   agelim=agemax;    for (k=0; k< maxncov; k++) Ndum[k]=0;
   ftolpl=1.e-10;    
   i1=cptcoveff;    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
   if (cptcovn < 1){i1=1;}     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
   for(cptcov=1;cptcov<=i1;cptcov++){     Ndum[ij]++;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   }
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   ij=1;
         fprintf(ficrespl,"\n#******");   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
         for(j=1;j<=cptcoveff;j++)     if((Ndum[i]!=0) && (i<=ncovcol)){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       Tvaraff[ij]=i; /*For printing */
         fprintf(ficrespl,"******\n");       ij++;
             }
         for (age=agebase; age<=agelim; age++){   }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   ij--;
           fprintf(ficrespl,"%.0f",age );   cptcoveff=ij; /*Number of simple covariates*/
           for(i=1; i<=nlstate;i++)  }
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");  /*********** 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[] )
     }  
   fclose(ficrespl);  {
     /* Health expectancies, no variances */
   /*------------- h Pij x at various ages ------------*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
      int nhstepma, nstepma; /* Decreasing with age */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double age, agelim, hf;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double ***p3mat;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    double eip;
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);    pstamp(ficreseij);
      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficreseij,"# Age");
   /*if (stepm<=24) stepsize=2;*/    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
   agelim=AGESUP;        fprintf(ficreseij," e%1d%1d ",i,j);
   hstepm=stepsize*YEARM; /* Every year of age */      }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      fprintf(ficreseij," e%1d. ",i);
      }
   k=0;    fprintf(ficreseij,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    if(estepm < stepm){
         fprintf(ficrespij,"\n#****** ");      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(j=1;j<=cptcoveff;j++)    }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    else  hstepm=estepm;   
         fprintf(ficrespij,"******\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
             * This is mainly to measure the difference between two models: for example
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     * if stepm=24 months pijx are given only every 2 years and by summing them
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     * we are calculating an estimate of the Life Expectancy assuming a linear 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */     * progression in between and thus overestimating or underestimating according
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * to the curvature of the survival function. If, for the same date, we 
           oldm=oldms;savm=savms;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * to compare the new estimate of Life expectancy with the same linear 
           fprintf(ficrespij,"# Age");     * hypothesis. A more precise result, taking into account a more precise
           for(i=1; i<=nlstate;i++)     * curvature will be obtained if estepm is as small as stepm. */
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);    /* For example we decided to compute the life expectancy with the smallest unit */
           fprintf(ficrespij,"\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           for (h=0; h<=nhstepm; h++){       nhstepm is the number of hstepm from age to agelim 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       nstepm is the number of stepm from age to agelin. 
             for(i=1; i<=nlstate;i++)       Look at hpijx to understand the reason of that which relies in memory size
               for(j=1; j<=nlstate+ndeath;j++)       and note for a fixed period like estepm months */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             fprintf(ficrespij,"\n");       survival function given by stepm (the optimization length). Unfortunately it
           }       means that if the survival funtion is printed only each two years of age and if
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           fprintf(ficrespij,"\n");       results. So we changed our mind and took the option of the best precision.
         }    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
     agelim=AGESUP;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
   fclose(ficrespij);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   exit(0);  /* nhstepm age range expressed in number of stepm */
   /*---------- Forecasting ------------------*/    nstepm=(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);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if((ficresf=fopen(fileresf,"w"))==NULL) {    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;  
   }    for (age=bage; age<=fage; age ++){ 
   printf("Computing forecasting: result on file '%s' \n", fileresf);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /* Mobile average */      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   /* for (agedeb=bage; agedeb<=fage; agedeb++)  
     for (i=1; i<=nlstate;i++)      /* If stepm=6 months */
       for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++)      /* Computed by stepm unit matrices, product of hstepma matrices, stored
       printf("%f %d i=%d j1=%d\n", probs[(int)agedeb][i][cptcod],(int) agedeb,i,cptcod);*/         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
   mobaverage= ma3x(1,130 ,1,8, 1,8);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      
     for (i=1; i<=nlstate;i++)      printf("%d|",(int)age);fflush(stdout);
       for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         mobaverage[(int)agedeb][i][cptcod]=0.;      
        /* Computing expectancies */
   for (agedeb=bage+4; agedeb<=fage; agedeb++){      for(i=1; i<=nlstate;i++)
     for (i=1; i<=nlstate;i++){        for(j=1; j<=nlstate;j++)
       for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         for (cpt=0;cpt<=4;cpt++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            
           }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
       }          }
     }  
   }      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
 /* if (cptcod==2) printf("m=%f p=%f %d age=%d ",mobaverage[(int)agedeb-2][i][cptcod],probs[(int)agedeb-cpt][i][cptcod],cpt,(int)agedeb-2);*/        eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   if (stepm<=24) stepsize=2;        }
         fprintf(ficreseij,"%9.4f", eip );
   agelim=AGESUP;      }
   hstepm=stepsize*YEARM; /* Every year of age */      fprintf(ficreseij,"\n");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      
   hstepm=12;    }
    k=0;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for(cptcov=1;cptcov<=i1;cptcov++){    printf("\n");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficlog,"\n");
       k=k+1;    
       fprintf(ficresf,"\n#****** ");  }
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  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(ficresf,"******\n");    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");    */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
       for (agedeb=fage; agedeb>=bage; agedeb--){    double age, agelim, hf;
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);    double ***p3matp, ***p3matm, ***varhe;
         for(j=1; j<=nlstate;j++)    double **dnewm,**doldm;
           fprintf(ficresf,"%.3f ",mobaverage[(int)agedeb][j][cptcod]);    double *xp, *xm;
       }    double **gp, **gm;
       for(j=1; j<=ndeath;j++) fprintf(ficresf,"0.");    double ***gradg, ***trgradg;
     int theta;
       for (cpt=1; cpt<=8;cpt++)    
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    double eip, vip;
          
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    xp=vector(1,npar);
         /*printf("stepm=%d hstepm=%d nhstepm=%d \n",stepm,hstepm,nhstepm);*/    xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         oldm=oldms;savm=savms;    
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      pstamp(ficresstdeij);
                    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         for (h=0; h<=nhstepm; h++){    fprintf(ficresstdeij,"# Age");
            for(i=1; i<=nlstate;i++){
           if (h*hstepm/YEARM*stepm==cpt)      for(j=1; j<=nlstate;j++)
  fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
                fprintf(ficresstdeij," e%1d. ",i);
           for(j=1; j<=nlstate+ndeath;j++) {    }
             kk1=0.;    fprintf(ficresstdeij,"\n");
             for(i=1; i<=nlstate;i++) {          
               /*   kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];*/    pstamp(ficrescveij);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
             }    fprintf(ficrescveij,"# Age");
                for(i=1; i<=nlstate;i++)
             if (h*hstepm/YEARM*stepm==cpt)      for(j=1; j<=nlstate;j++){
               fprintf(ficresf," %.5f ", kk1);        cptj= (j-1)*nlstate+i;
           }        for(i2=1; i2<=nlstate;i2++)
           }          for(j2=1; j2<=nlstate;j2++){
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cptj2= (j2-1)*nlstate+i2;
         }            if(cptj2 <= cptj)
       }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     }          }
   fclose(ficresf);      }
     fprintf(ficrescveij,"\n");
   /*---------- Health expectancies and variances ------------*/    
     if(estepm < stepm){
   strcpy(filerest,"t");      printf ("Problem %d lower than %d\n",estepm, stepm);
   strcat(filerest,fileres);    }
   if((ficrest=fopen(filerest,"w"))==NULL) {    else  hstepm=estepm;   
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * This is mainly to measure the difference between two models: for example
   printf("Computing Total LEs with variances: file '%s' \n", filerest);     * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   strcpy(filerese,"e");     * to the curvature of the survival function. If, for the same date, we 
   strcat(filerese,fileres);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   if((ficreseij=fopen(filerese,"w"))==NULL) {     * to compare the new estimate of Life expectancy with the same linear 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
     /* For example we decided to compute the life expectancy with the smallest unit */
  strcpy(fileresv,"v");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(fileresv,fileres);       nhstepm is the number of hstepm from age to agelim 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   k=0;       means that if the survival funtion is printed only each two years of age and if
   for(cptcov=1;cptcov<=i1;cptcov++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       results. So we changed our mind and took the option of the best precision.
       k=k+1;    */
       fprintf(ficrest,"\n#****** ");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* If stepm=6 months */
       fprintf(ficrest,"******\n");    /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
       fprintf(ficreseij,"\n#****** ");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
       for(j=1;j<=cptcoveff;j++)    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficreseij,"******\n");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
       fprintf(ficresvij,"\n#****** ");    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1;j<=cptcoveff;j++)    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       fprintf(ficresvij,"******\n");    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      for (age=bage; age<=fage; age ++){ 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       oldm=oldms;savm=savms;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      /* if (stepm >= YEARM) hstepm=1;*/
            nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      /* If stepm=6 months */
       fprintf(ficrest,"\n");      /* Computed by stepm unit matrices, product of hstepma matrices, stored
                 in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       hf=1;      
       if (stepm >= YEARM) hf=stepm/YEARM;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){      /* Computing  Variances of health expectancies */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         fprintf(ficrest," %.0f",age);         decrease memory allocation */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      for(theta=1; theta <=npar; theta++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        for(i=1; i<=npar; i++){ 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           epj[nlstate+1] +=epj[j];        }
         }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         for(i=1, vepp=0.;i <=nlstate;i++)        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
           for(j=1;j <=nlstate;j++)    
             vepp += vareij[i][j][(int)age];        for(j=1; j<= nlstate; j++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          for(i=1; i<=nlstate; i++){
         for(j=1;j <=nlstate;j++){            for(h=0; h<=nhstepm-1; h++){
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         }              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
         fprintf(ficrest,"\n");            }
       }          }
     }        }
   }       
                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];
           }
  fclose(ficreseij);      }/* End theta */
  fclose(ficresvij);      
   fclose(ficrest);      
   fclose(ficpar);      for(h=0; h<=nhstepm-1; h++)
   free_vector(epj,1,nlstate+1);        for(j=1; j<=nlstate*nlstate;j++)
   /*  scanf("%d ",i); */          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   /*------- Variance limit prevalence------*/        
   
 strcpy(fileresvpl,"vpl");       for(ij=1;ij<=nlstate*nlstate;ij++)
   strcat(fileresvpl,fileres);        for(ji=1;ji<=nlstate*nlstate;ji++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          varhe[ij][ji][(int)age] =0.;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
  k=0;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  for(cptcov=1;cptcov<=i1;cptcov++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for(ij=1;ij<=nlstate*nlstate;ij++)
      k=k+1;            for(ji=1;ji<=nlstate*nlstate;ji++)
      fprintf(ficresvpl,"\n#****** ");              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
      for(j=1;j<=cptcoveff;j++)        }
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
      fprintf(ficresvpl,"******\n");  
            /* Computing expectancies */
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
      oldm=oldms;savm=savms;      for(i=1; i<=nlstate;i++)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(j=1; j<=nlstate;j++)
    }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
  }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
   fclose(ficresvpl);            /* 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]);*/
   
   /*---------- End : free ----------------*/          }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
        fprintf(ficresstdeij,"%3.0f",age );
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for(i=1; i<=nlstate;i++){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        eip=0.;
          vip=0.;
          for(j=1; j<=nlstate;j++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          eip += eij[i][j][(int)age];
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
          }
   free_matrix(matcov,1,npar,1,npar);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   free_vector(delti,1,npar);      }
        fprintf(ficresstdeij,"\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
       fprintf(ficrescveij,"%3.0f",age );
   printf("End of Imach\n");      for(i=1; i<=nlstate;i++)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        for(j=1; j<=nlstate;j++){
            cptj= (j-1)*nlstate+i;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          for(i2=1; i2<=nlstate;i2++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/            for(j2=1; j2<=nlstate;j2++){
   /*------ End -----------*/              cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
  end:            }
 #ifdef windows        }
  chdir(pathcd);      fprintf(ficrescveij,"\n");
 #endif     
      }
  system("..\\gp37mgw\\wgnuplot graph.plt");    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 #ifdef windows    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   while (z[0] != 'q') {    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     chdir(pathcd);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     scanf("%s",z);    printf("\n");
     if (z[0] == 'c') system("./imach");    fprintf(ficlog,"\n");
     else if (z[0] == 'e') {  
       chdir(path);    free_vector(xm,1,npar);
       system(optionfilehtm);    free_vector(xp,1,npar);
     }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     else if (z[0] == 'q') exit(0);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 #endif  }
 }  
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 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;
                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 %ld 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 %ld 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 %ld 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 %ld 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 %ld 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 %ld 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 %ld 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 %ld 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 %ld 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 %ld 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 %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%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 '%d' at line number %ld 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 '%d' at line number %ld 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 '%d' at line number %ld 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 '%d' at line number %ld 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;
       }
       
       /* 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(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\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++;
       puts(line);
       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++;
       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++;
         puts(line);
         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++;
         puts(line);
         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++;
         puts(line);
         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); 
     /* 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); /* For V3*V2 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");
     }
     /*  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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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);
         puts(line);
         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);
       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 %d 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 %d 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.1.13  
changed lines
  Added in v.1.138


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