Diff for /imach/src/imach.c between versions 1.13 and 1.146

version 1.13, 2002/02/20 17:02:08 version 1.146, 2014/06/16 10:20:28
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.146  2014/06/16 10:20:28  brouard
   individuals from different ages are interviewed on their health status    Summary: Merge
   or degree of  disability. At least a second wave of interviews    Author: Brouard
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Merge, before building revised version.
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.145  2014/06/10 21:23:15  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    Summary: Debugging with valgrind
   The simplest model is the multinomial logistic model where pij is    Author: Nicolas Brouard
   the probabibility to be observed in state j at the second wave conditional  
   to be observed in state i at the first wave. Therefore the model is:    Lot of changes in order to output the results with some covariates
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    After the Edimburgh REVES conference 2014, it seems mandatory to
   is a covariate. If you want to have a more complex model than "constant and    improve the code.
   age", you should modify the program where the markup    No more memory valgrind error but a lot has to be done in order to
     *Covariates have to be included here again* invites you to do it.    continue the work of splitting the code into subroutines.
   More covariates you add, less is the speed of the convergence.    Also, decodemodel has been improved. Tricode is still not
     optimal. nbcode should be improved. Documentation has been added in
   The advantage that this computer programme claims, comes from that if the    the source 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 1.143  2014/01/26 09:45:38  brouard
   taken into account using an interpolation or extrapolation.    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   x. The delay 'h' can be split into an exact number (nh*stepm) of    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.142  2014/01/26 03:57:36  brouard
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   and the contribution of each individual to the likelihood is simply hPijx.  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.141  2014/01/26 02:42:01  brouard
      * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.140  2011/09/02 10:37:54  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: times.h is ok with mingw32 now.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.139  2010/06/14 07:50:17  brouard
   software can be distributed freely for non commercial use. Latest version    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   can be accessed at http://euroreves.ined.fr/imach .    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   **********************************************************************/  
      Revision 1.138  2010/04/30 18:19:40  brouard
 #include <math.h>    *** empty log message ***
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.137  2010/04/29 18:11:38  brouard
 #include <unistd.h>    (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Revision 1.136  2010/04/26 20:30:53  brouard
 /*#define DEBUG*/    (Module): merging some libgsl code. Fixing computation
 #define windows    of likelione (using inter/intrapolation if mle = 0) in order to
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    get same likelihood as if mle=1.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Some cleaning of code and comments added.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.135  2009/10/29 15:33:14  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 #define NINTERVMAX 8    Revision 1.134  2009/10/29 13:18:53  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.133  2009/07/06 10:21:25  brouard
 #define MAXN 20000    just nforces
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.132  2009/07/06 08:22:05  brouard
 #define AGEBASE 40    Many tings
   
     Revision 1.131  2009/06/20 16:22:47  brouard
 int nvar;    Some dimensions resccaled
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.130  2009/05/26 06:44:34  brouard
 int nlstate=2; /* Number of live states */    (Module): Max Covariate is now set to 20 instead of 8. A
 int ndeath=1; /* Number of dead states */    lot of cleaning with variables initialized to 0. Trying to make
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.129  2007/08/31 13:49:27  lievre
 int maxwav; /* Maxim number of waves */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.128  2006/06/30 13:02:05  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Clarifications on computing e.j
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.127  2006/04/28 18:11:50  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Yes the sum of survivors was wrong since
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    imach-114 because nhstepm was no more computed in the age
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    loop. Now we define nhstepma in the age loop.
 FILE *ficgp, *fichtm,*ficresprob;    (Module): In order to speed up (in case of numerous covariates) we
 FILE *ficreseij;    compute health expectancies (without variances) in a first step
   char filerese[FILENAMELENGTH];    and then all the health expectancies with variances or standard
  FILE  *ficresvij;    deviation (needs data from the Hessian matrices) which slows the
   char fileresv[FILENAMELENGTH];    computation.
  FILE  *ficresvpl;    In the future we should be able to stop the program is only health
   char fileresvpl[FILENAMELENGTH];    expectancies and graph are needed without standard deviations.
   
 #define NR_END 1    Revision 1.126  2006/04/28 17:23:28  brouard
 #define FREE_ARG char*    (Module): Yes the sum of survivors was wrong since
 #define FTOL 1.0e-10    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 #define NRANSI    Version 0.98h
 #define ITMAX 200  
     Revision 1.125  2006/04/04 15:20:31  lievre
 #define TOL 2.0e-4    Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.124  2006/03/22 17:13:53  lievre
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.123  2006/03/20 10:52:43  brouard
 #define TINY 1.0e-20    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Module): Weights can have a decimal point as for
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    English (a comma might work with a correct LC_NUMERIC environment,
      otherwise the weight is truncated).
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Modification of warning when the covariates values are not 0 or
 #define rint(a) floor(a+0.5)    1.
     Version 0.98g
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.122  2006/03/20 09:45:41  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 int imx;    otherwise the weight is truncated).
 int stepm;    Modification of warning when the covariates values are not 0 or
 /* Stepm, step in month: minimum step interpolation*/    1.
     Version 0.98g
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.121  2006/03/16 17:45:01  lievre
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    * imach.c (Module): Comments concerning covariates added
 double **pmmij, ***probs, ***mobaverage;  
     * imach.c (Module): refinements in the computation of lli if
 double *weight;    status=-2 in order to have more reliable computation if stepm is
 int **s; /* Status */    not 1 month. Version 0.98f
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    status=-2 in order to have more reliable computation if stepm is
 double ftolhess; /* Tolerance for computing hessian */    not 1 month. Version 0.98f
   
 /**************** split *************************/    Revision 1.119  2006/03/15 17:42:26  brouard
 static  int split( char *path, char *dirc, char *name )    (Module): Bug if status = -2, the loglikelihood was
 {    computed as likelihood omitting the logarithm. Version O.98e
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
    l1 = strlen( path );                 /* length of path */    table of variances if popbased=1 .
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    s = strrchr( path, '\\' );           /* find last / */    (Module): Function pstamp added
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Version 0.98d
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
       if ( getwd( dirc ) == NULL ) {    table of variances if popbased=1 .
 #else    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
       extern char       *getcwd( );    (Module): Function pstamp added
     (Module): Version 0.98d
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.116  2006/03/06 10:29:27  brouard
          return( GLOCK_ERROR_GETCWD );    (Module): Variance-covariance wrong links and
       }    varian-covariance of ej. is needed (Saito).
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.115  2006/02/27 12:17:45  brouard
       s++;                              /* after this, the filename */    (Module): One freematrix added in mlikeli! 0.98c
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.114  2006/02/26 12:57:58  brouard
       strcpy( name, s );                /* save file name */    (Module): Some improvements in processing parameter
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    filename with strsep.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.113  2006/02/24 14:20:24  brouard
    l1 = strlen( dirc );                 /* length of directory */    (Module): Memory leaks checks with valgrind and:
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    datafile was not closed, some imatrix were not freed and on matrix
    return( 0 );                         /* we're done */    allocation too.
 }  
     Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
 /******************************************/  
     Revision 1.111  2006/01/25 20:38:18  brouard
 void replace(char *s, char*t)    (Module): Lots of cleaning and bugs added (Gompertz)
 {    (Module): Comments can be added in data file. Missing date values
   int i;    can be a simple dot '.'.
   int lg=20;  
   i=0;    Revision 1.110  2006/01/25 00:51:50  brouard
   lg=strlen(t);    (Module): Lots of cleaning and bugs added (Gompertz)
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.109  2006/01/24 19:37:15  brouard
     if (t[i]== '\\') s[i]='/';    (Module): Comments (lines starting with a #) are allowed in data.
   }  
 }    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 int nbocc(char *s, char occ)    To be fixed
 {  
   int i,j=0;    Revision 1.107  2006/01/19 16:20:37  brouard
   int lg=20;    Test existence of gnuplot in imach path
   i=0;  
   lg=strlen(s);    Revision 1.106  2006/01/19 13:24:36  brouard
   for(i=0; i<= lg; i++) {    Some cleaning and links added in html output
   if  (s[i] == occ ) j++;  
   }    Revision 1.105  2006/01/05 20:23:19  lievre
   return j;    *** empty log message ***
 }  
     Revision 1.104  2005/09/30 16:11:43  lievre
 void cutv(char *u,char *v, char*t, char occ)    (Module): sump fixed, loop imx fixed, and simplifications.
 {    (Module): If the status is missing at the last wave but we know
   int i,lg,j,p=0;    that the person is alive, then we can code his/her status as -2
   i=0;    (instead of missing=-1 in earlier versions) and his/her
   for(j=0; j<=strlen(t)-1; j++) {    contributions to the likelihood is 1 - Prob of dying from last
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   }    the healthy state at last known wave). Version is 0.98
   
   lg=strlen(t);    Revision 1.103  2005/09/30 15:54:49  lievre
   for(j=0; j<p; j++) {    (Module): sump fixed, loop imx fixed, and simplifications.
     (u[j] = t[j]);  
   }    Revision 1.102  2004/09/15 17:31:30  brouard
      u[p]='\0';    Add the possibility to read data file including tab characters.
   
    for(j=0; j<= lg; j++) {    Revision 1.101  2004/09/15 10:38:38  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    Fix on curr_time
   }  
 }    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 /********************** nrerror ********************/  
     Revision 1.99  2004/06/05 08:57:40  brouard
 void nrerror(char error_text[])    *** empty log message ***
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.98  2004/05/16 15:05:56  brouard
   fprintf(stderr,"%s\n",error_text);    New version 0.97 . First attempt to estimate force of mortality
   exit(1);    directly from the data i.e. without the need of knowing the health
 }    state at each age, but using a Gompertz model: log u =a + b*age .
 /*********************** vector *******************/    This is the basic analysis of mortality and should be done before any
 double *vector(int nl, int nh)    other analysis, in order to test if the mortality estimated from the
 {    cross-longitudinal survey is different from the mortality estimated
   double *v;    from other sources like vital statistic data.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    The same imach parameter file can be used but the option for mle should be -3.
   return v-nl+NR_END;  
 }    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    The output is very simple: only an estimate of the intercept and of
 {    the slope with 95% confident intervals.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Current limitations:
     A) Even if you enter covariates, i.e. with the
 /************************ivector *******************************/    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int *ivector(long nl,long nh)    B) There is no computation of Life Expectancy nor Life Table.
 {  
   int *v;    Revision 1.97  2004/02/20 13:25:42  lievre
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Version 0.96d. Population forecasting command line is (temporarily)
   if (!v) nrerror("allocation failure in ivector");    suppressed.
   return v-nl+NR_END;  
 }    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 /******************free ivector **************************/    rewritten within the same printf. Workaround: many printfs.
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.95  2003/07/08 07:54:34  brouard
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Repository):
 }    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.94  2003/06/27 13:00:02  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Just cleaning
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.93  2003/06/25 16:33:55  brouard
   int **m;    (Module): On windows (cygwin) function asctime_r doesn't
      exist so I changed back to asctime which exists.
   /* allocate pointers to rows */    (Module): Version 0.96b
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.92  2003/06/25 16:30:45  brouard
   m += NR_END;    (Module): On windows (cygwin) function asctime_r doesn't
   m -= nrl;    exist so I changed back to asctime which exists.
    
      Revision 1.91  2003/06/25 15:30:29  brouard
   /* allocate rows and set pointers to them */    * imach.c (Repository): Duplicated warning errors corrected.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Repository): Elapsed time after each iteration is now output. It
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    helps to forecast when convergence will be reached. Elapsed time
   m[nrl] += NR_END;    is stamped in powell.  We created a new html file for the graphs
   m[nrl] -= ncl;    concerning matrix of covariance. It has extension -cov.htm.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.90  2003/06/24 12:34:15  brouard
      (Module): Some bugs corrected for windows. Also, when
   /* return pointer to array of pointers to rows */    mle=-1 a template is output in file "or"mypar.txt with the design
   return m;    of the covariance matrix to be input.
 }  
     Revision 1.89  2003/06/24 12:30:52  brouard
 /****************** free_imatrix *************************/    (Module): Some bugs corrected for windows. Also, when
 void free_imatrix(m,nrl,nrh,ncl,nch)    mle=-1 a template is output in file "or"mypar.txt with the design
       int **m;    of the covariance matrix to be input.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.88  2003/06/23 17:54:56  brouard
 {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.87  2003/06/18 12:26:01  brouard
 }    Version 0.96
   
 /******************* matrix *******************************/    Revision 1.86  2003/06/17 20:04:08  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    (Module): Change position of html and gnuplot routines and added
 {    routine fileappend.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    current date of interview. It may happen when the death was just
   if (!m) nrerror("allocation failure 1 in matrix()");    prior to the death. In this case, dh was negative and likelihood
   m += NR_END;    was wrong (infinity). We still send an "Error" but patch by
   m -= nrl;    assuming that the date of death was just one stepm after the
     interview.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Repository): Because some people have very long ID (first column)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    we changed int to long in num[] and we added a new lvector for
   m[nrl] += NR_END;    memory allocation. But we also truncated to 8 characters (left
   m[nrl] -= ncl;    truncation)
     (Repository): No more line truncation errors.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.84  2003/06/13 21:44:43  brouard
 }    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 /*************************free matrix ************************/    many times. Probs is memory consuming and must be used with
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    parcimony.
 {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /******************* ma3x *******************************/    Revision 1.82  2003/06/05 15:57:20  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Add log in  imach.c and  fullversion number is now printed.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  */
   double ***m;  /*
      Interpolated Markov Chain
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Short summary of the programme:
   m += NR_END;    
   m -= nrl;    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    first survey ("cross") where individuals from different ages are
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    interviewed on their health status or degree of disability (in the
   m[nrl] += NR_END;    case of a health survey which is our main interest) -2- at least a
   m[nrl] -= ncl;    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Maximum Likelihood of the parameters involved in the model.  The
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    simplest model is the multinomial logistic model where pij is the
   m[nrl][ncl] += NR_END;    probability to be observed in state j at the second wave
   m[nrl][ncl] -= nll;    conditional to be observed in state i at the first wave. Therefore
   for (j=ncl+1; j<=nch; j++)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     m[nrl][j]=m[nrl][j-1]+nlay;    'age' is age and 'sex' is a covariate. If you want to have a more
      complex model than "constant and age", you should modify the program
   for (i=nrl+1; i<=nrh; i++) {    where the markup *Covariates have to be included here again* invites
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    you to do it.  More covariates you add, slower the
     for (j=ncl+1; j<=nch; j++)    convergence.
       m[i][j]=m[i][j-1]+nlay;  
   }    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 ma3x ************************/    account using an interpolation or extrapolation.  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    hPijx is the probability to be observed in state i at age x+h
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    conditional to the observed state i at age x. The delay 'h' can be
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    split into an exact number (nh*stepm) of unobserved intermediate
   free((FREE_ARG)(m+nrl-NR_END));    states. This elementary transition (by month, quarter,
 }    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 /***************** f1dim *************************/    and the contribution of each individual to the likelihood is simply
 extern int ncom;    hPijx.
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Also this programme outputs the covariance matrix of the parameters but also
      of the life expectancies. It also computes the period (stable) prevalence. 
 double f1dim(double x)    
 {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   int j;             Institut national d'études démographiques, Paris.
   double f;    This software have been partly granted by Euro-REVES, a concerted action
   double *xt;    from the European Union.
      It is copyrighted identically to a GNU software product, ie programme and
   xt=vector(1,ncom);    software can be distributed freely for non commercial use. Latest version
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    can be accessed at http://euroreves.ined.fr/imach .
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   return f;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 }    
     **********************************************************************/
 /*****************brent *************************/  /*
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    main
 {    read parameterfile
   int iter;    read datafile
   double a,b,d,etemp;    concatwav
   double fu,fv,fw,fx;    freqsummary
   double ftemp;    if (mle >= 1)
   double p,q,r,tol1,tol2,u,v,w,x,xm;      mlikeli
   double e=0.0;    print results files
      if mle==1 
   a=(ax < cx ? ax : cx);       computes hessian
   b=(ax > cx ? ax : cx);    read end of parameter file: agemin, agemax, bage, fage, estepm
   x=w=v=bx;        begin-prev-date,...
   fw=fv=fx=(*f)(x);    open gnuplot file
   for (iter=1;iter<=ITMAX;iter++) {    open html file
     xm=0.5*(a+b);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     printf(".");fflush(stdout);      freexexit2 possible for memory heap.
 #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);    h Pij x                         | pij_nom  ficrestpij
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 #endif         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       *xmin=x;  
       return fx;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     }         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     ftemp=fu;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
     if (fabs(e) > tol1) {     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       r=(x-w)*(fx-fv);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;    forecasting if prevfcast==1 prevforecast call prevalence()
       q=2.0*(q-r);    health expectancies
       if (q > 0.0) p = -p;    Variance-covariance of DFLE
       q=fabs(q);    prevalence()
       etemp=e;     movingaverage()
       e=d;    varevsij() 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    if popbased==1 varevsij(,popbased)
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    total life expectancies
       else {    Variance of period (stable) prevalence
         d=p/q;   end
         u=x+d;  */
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  
       }  
     } else {   
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #include <math.h>
     }  #include <stdio.h>
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #include <stdlib.h>
     fu=(*f)(u);  #include <string.h>
     if (fu <= fx) {  #include <unistd.h>
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  #include <limits.h>
         SHFT(fv,fw,fx,fu)  #include <sys/types.h>
         } else {  #include <sys/stat.h>
           if (u < x) a=u; else b=u;  #include <errno.h>
           if (fu <= fw || w == x) {  extern int errno;
             v=w;  
             w=u;  #ifdef LINUX
             fv=fw;  #include <time.h>
             fw=fu;  #include "timeval.h"
           } else if (fu <= fv || v == x || v == w) {  #else
             v=u;  #include <sys/time.h>
             fv=fu;  #endif
           }  
         }  #ifdef GSL
   }  #include <gsl/gsl_errno.h>
   nrerror("Too many iterations in brent");  #include <gsl/gsl_multimin.h>
   *xmin=x;  #endif
   return fx;  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 /****************** mnbrak ***********************/  
   #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  #define GNUPLOTPROGRAM "gnuplot"
 {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   double ulim,u,r,q, dum;  #define FILENAMELENGTH 132
   double fu;  
    #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   *fa=(*func)(*ax);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     SHFT(dum,*ax,*bx,dum)  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       SHFT(dum,*fb,*fa,dum)  
       }  #define NINTERVMAX 8
   *cx=(*bx)+GOLD*(*bx-*ax);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   *fc=(*func)(*cx);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   while (*fb > *fc) {  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     r=(*bx-*ax)*(*fb-*fc);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
     q=(*bx-*cx)*(*fb-*fa);  #define MAXN 20000
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define YEARM 12. /**< Number of months per year */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define AGESUP 130
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define AGEBASE 40
     if ((*bx-u)*(u-*cx) > 0.0) {  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
       fu=(*func)(u);  #ifdef UNIX
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define DIRSEPARATOR '/'
       fu=(*func)(u);  #define CHARSEPARATOR "/"
       if (fu < *fc) {  #define ODIRSEPARATOR '\\'
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #else
           SHFT(*fb,*fc,fu,(*func)(u))  #define DIRSEPARATOR '\\'
           }  #define CHARSEPARATOR "\\"
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define ODIRSEPARATOR '/'
       u=ulim;  #endif
       fu=(*func)(u);  
     } else {  <<<<<<< imach.c
       u=(*cx)+GOLD*(*cx-*bx);  /* $Id$ */
       fu=(*func)(u);  =======
     }  /* $Id$ */
     SHFT(*ax,*bx,*cx,u)  >>>>>>> 1.145
       SHFT(*fa,*fb,*fc,fu)  /* $State$ */
       }  
 }  <<<<<<< imach.c
   char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 /*************** linmin ************************/  char fullversion[]="$Revision$ $Date$"; 
   =======
 int ncom;  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 double *pcom,*xicom;  char fullversion[]="$Revision$ $Date$"; 
 double (*nrfunc)(double []);  >>>>>>> 1.145
    char strstart[80];
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double brent(double ax, double bx, double cx,  int nvar=0, nforce=0; /* Number of variables, number of forces */
                double (*f)(double), double tol, double *xmin);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   double f1dim(double x);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
               double *fc, double (*func)(double));  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   int j;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   double xx,xmin,bx,ax;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   double fx,fb,fa;  int cptcoveff=0; /* Total number of covariates to vary for printing results */
    int cptcov=0; /* Working variable */
   ncom=n;  int npar=NPARMAX;
   pcom=vector(1,n);  int nlstate=2; /* Number of live states */
   xicom=vector(1,n);  int ndeath=1; /* Number of dead states */
   nrfunc=func;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for (j=1;j<=n;j++) {  int popbased=0;
     pcom[j]=p[j];  
     xicom[j]=xi[j];  int *wav; /* Number of waves for this individuual 0 is possible */
   }  int maxwav=0; /* Maxim number of waves */
   ax=0.0;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   xx=1.0;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);                     to the likelihood and the sum of weights (done by funcone)*/
 #ifdef DEBUG  int mle=1, weightopt=0;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #endif  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for (j=1;j<=n;j++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     xi[j] *= xmin;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     p[j] += xi[j];  double jmean=1; /* Mean space between 2 waves */
   }  double **matprod2(); /* test */
   free_vector(xicom,1,n);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   free_vector(pcom,1,n);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 }  /*FILE *fic ; */ /* Used in readdata only */
   FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 /*************** powell ************************/  FILE *ficlog, *ficrespow;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  int globpr=0; /* Global variable for printing or not */
             double (*func)(double []))  double fretone; /* Only one call to likelihood */
 {  long ipmx=0; /* Number of contributions */
   void linmin(double p[], double xi[], int n, double *fret,  double sw; /* Sum of weights */
               double (*func)(double []));  char filerespow[FILENAMELENGTH];
   int i,ibig,j;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double del,t,*pt,*ptt,*xit;  FILE *ficresilk;
   double fp,fptt;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   double *xits;  FILE *ficresprobmorprev;
   pt=vector(1,n);  FILE *fichtm, *fichtmcov; /* Html File */
   ptt=vector(1,n);  FILE *ficreseij;
   xit=vector(1,n);  char filerese[FILENAMELENGTH];
   xits=vector(1,n);  FILE *ficresstdeij;
   *fret=(*func)(p);  char fileresstde[FILENAMELENGTH];
   for (j=1;j<=n;j++) pt[j]=p[j];  FILE *ficrescveij;
   for (*iter=1;;++(*iter)) {  char filerescve[FILENAMELENGTH];
     fp=(*fret);  FILE  *ficresvij;
     ibig=0;  char fileresv[FILENAMELENGTH];
     del=0.0;  FILE  *ficresvpl;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char fileresvpl[FILENAMELENGTH];
     for (i=1;i<=n;i++)  char title[MAXLINE];
       printf(" %d %.12f",i, p[i]);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     printf("\n");  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     for (i=1;i<=n;i++) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char command[FILENAMELENGTH];
       fptt=(*fret);  int  outcmd=0;
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #endif  
       printf("%d",i);fflush(stdout);  char filelog[FILENAMELENGTH]; /* Log file */
       linmin(p,xit,n,fret,func);  char filerest[FILENAMELENGTH];
       if (fabs(fptt-(*fret)) > del) {  char fileregp[FILENAMELENGTH];
         del=fabs(fptt-(*fret));  char popfile[FILENAMELENGTH];
         ibig=i;  
       }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       for (j=1;j<=n;j++) {  struct timezone tzp;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  extern int gettimeofday();
         printf(" x(%d)=%.12e",j,xit[j]);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       }  long time_value;
       for(j=1;j<=n;j++)  extern long time();
         printf(" p=%.12e",p[j]);  char strcurr[80], strfor[80];
       printf("\n");  
 #endif  char *endptr;
     }  long lval;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double dval;
 #ifdef DEBUG  
       int k[2],l;  #define NR_END 1
       k[0]=1;  #define FREE_ARG char*
       k[1]=-1;  #define FTOL 1.0e-10
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  #define NRANSI 
         printf(" %.12e",p[j]);  #define ITMAX 200 
       printf("\n");  
       for(l=0;l<=1;l++) {  #define TOL 2.0e-4 
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define CGOLD 0.3819660 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #define ZEPS 1.0e-10 
         }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  #define GOLD 1.618034 
 #endif  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
   
       free_vector(xit,1,n);  static double maxarg1,maxarg2;
       free_vector(xits,1,n);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       free_vector(ptt,1,n);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       free_vector(pt,1,n);    
       return;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     }  #define rint(a) floor(a+0.5)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  static double sqrarg;
       ptt[j]=2.0*p[j]-pt[j];  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       xit[j]=p[j]-pt[j];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       pt[j]=p[j];  int agegomp= AGEGOMP;
     }  
     fptt=(*func)(ptt);  int imx; 
     if (fptt < fp) {  int stepm=1;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /* Stepm, step in month: minimum step interpolation*/
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  int estepm;
         for (j=1;j<=n;j++) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  int m,nb;
         }  long *num;
 #ifdef DEBUG  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         for(j=1;j<=n;j++)  double **pmmij, ***probs;
           printf(" %.12e",xit[j]);  double *ageexmed,*agecens;
         printf("\n");  double dateintmean=0;
 #endif  
       }  double *weight;
     }  int **s; /* Status */
   }  double *agedc;
 }  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                     * covar=matrix(0,NCOVMAX,1,n); 
 /**** Prevalence limit ****************/                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   double  idx; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 {  int *Ndum; /** Freq of modality (tricode */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int **codtab; /**< codtab=imatrix(1,100,1,10); */
      matrix by transitions matrix until convergence is reached */  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double **matprod2();  double ftolhess; /**< Tolerance for computing hessian */
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /**************** split *************************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     for (j=1;j<=nlstate+ndeath;j++){       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    */ 
     }    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
    cov[1]=1.;  
      l1 = strlen(path );                   /* length of path */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     newm=savm;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     /* Covariates have to be included here again */      strcpy( name, path );               /* we got the fullname name because no directory */
      cov[2]=agefin;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       for (k=1; k<=cptcovn;k++) {      /* get current working directory */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      /*    extern  char* getcwd ( char *buf , int len);*/
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       }        return( GLOCK_ERROR_GETCWD );
       for (k=1; k<=cptcovage;k++)      }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      /* got dirc from getcwd*/
       for (k=1; k<=cptcovprod;k++)      printf(" DIRC = %s \n",dirc);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      l2 = strlen( ss );                  /* length of filename */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
     savm=oldm;      printf(" DIRC2 = %s \n",dirc);
     oldm=newm;    }
     maxmax=0.;    /* We add a separator at the end of dirc if not exists */
     for(j=1;j<=nlstate;j++){    l1 = strlen( dirc );                  /* length of directory */
       min=1.;    if( dirc[l1-1] != DIRSEPARATOR ){
       max=0.;      dirc[l1] =  DIRSEPARATOR;
       for(i=1; i<=nlstate; i++) {      dirc[l1+1] = 0; 
         sumnew=0;      printf(" DIRC3 = %s \n",dirc);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    }
         prlim[i][j]= newm[i][j]/(1-sumnew);    ss = strrchr( name, '.' );            /* find last / */
         max=FMAX(max,prlim[i][j]);    if (ss >0){
         min=FMIN(min,prlim[i][j]);      ss++;
       }      strcpy(ext,ss);                     /* save extension */
       maxmin=max-min;      l1= strlen( name);
       maxmax=FMAX(maxmax,maxmin);      l2= strlen(ss)+1;
     }      strncpy( finame, name, l1-l2);
     if(maxmax < ftolpl){      finame[l1-l2]= 0;
       return prlim;    }
     }  
   }    return( 0 );                          /* we're done */
 }  }
   
 /*************** transition probabilities ***************/  
   /******************************************/
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  void replace_back_to_slash(char *s, char*t)
   double s1, s2;  {
   /*double t34;*/    int i;
   int i,j,j1, nc, ii, jj;    int lg=0;
     i=0;
     for(i=1; i<= nlstate; i++){    lg=strlen(t);
     for(j=1; j<i;j++){    for(i=0; i<= lg; i++) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      (s[i] = t[i]);
         /*s2 += param[i][j][nc]*cov[nc];*/      if (t[i]== '\\') s[i]='/';
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  }
       }  
       ps[i][j]=s2;  char *trimbb(char *out, char *in)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     }    char *s;
     for(j=i+1; j<=nlstate+ndeath;j++){    s=out;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    while (*in != '\0'){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        in++;
       }      }
       ps[i][j]=(s2);      *out++ = *in++;
     }    }
   }    *out='\0';
     /*ps[3][2]=1;*/    return s;
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for(j=1; j<i; j++)  {
       s1+=exp(ps[i][j]);    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     for(j=i+1; j<=nlstate+ndeath; j++)       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       s1+=exp(ps[i][j]);       gives blocc="abcdef2ghi" and alocc="j".
     ps[i][i]=1./(s1+1.);       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     for(j=1; j<i; j++)    */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    char *s, *t, *bl;
     for(j=i+1; j<=nlstate+ndeath; j++)    t=in;s=in;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    while ((*in != occ) && (*in != '\0')){
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      *alocc++ = *in++;
   } /* end i */    }
     if( *in == occ){
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      *(alocc)='\0';
     for(jj=1; jj<= nlstate+ndeath; jj++){      s=++in;
       ps[ii][jj]=0;    }
       ps[ii][ii]=1;   
     }    if (s == t) {/* occ not found */
   }      *(alocc-(in-s))='\0';
       in=s;
     }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    while ( *in != '\0'){
     for(jj=1; jj<= nlstate+ndeath; jj++){      *blocc++ = *in++;
      printf("%lf ",ps[ii][jj]);    }
    }  
     printf("\n ");    *blocc='\0';
     }    return t;
     printf("\n ");printf("%lf ",cov[2]);*/  }
 /*  char *cutv(char *blocc, char *alocc, char *in, char occ)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  {
   goto end;*/    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     return ps;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 }       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
 /**************** Product of 2 matrices ******************/    */
     char *s, *t;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    t=in;s=in;
 {    while (*in != '\0'){
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      while( *in == occ){
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        *blocc++ = *in++;
   /* in, b, out are matrice of pointers which should have been initialized        s=in;
      before: only the contents of out is modified. The function returns      }
      a pointer to pointers identical to out */      *blocc++ = *in++;
   long i, j, k;    }
   for(i=nrl; i<= nrh; i++)    if (s == t) /* occ not found */
     for(k=ncolol; k<=ncoloh; k++)      *(blocc-(in-s))='\0';
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    else
         out[i][k] +=in[i][j]*b[j][k];      *(blocc-(in-s)-1)='\0';
     in=s;
   return out;    while ( *in != '\0'){
 }      *alocc++ = *in++;
     }
   
 /************* Higher Matrix Product ***************/    *alocc='\0';
     return s;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  }
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  int nbocc(char *s, char occ)
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    int i,j=0;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    int lg=20;
      (typically every 2 years instead of every month which is too big).    i=0;
      Model is determined by parameters x and covariates have to be    lg=strlen(s);
      included manually here.    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
      */    }
     return j;
   int i, j, d, h, k;  }
   double **out, cov[NCOVMAX];  
   double **newm;  /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
   /* Hstepm could be zero and should return the unit matrix */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   for (i=1;i<=nlstate+ndeath;i++)  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     for (j=1;j<=nlstate+ndeath;j++){  /*      gives u="abcdef2ghi" and v="j" *\/ */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /*   int i,lg,j,p=0; */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*   i=0; */
     }  /*   lg=strlen(t); */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*   for(j=0; j<=lg-1; j++) { */
   for(h=1; h <=nhstepm; h++){  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     for(d=1; d <=hstepm; d++){  /*   } */
       newm=savm;  
       /* Covariates have to be included here again */  /*   for(j=0; j<p; j++) { */
       cov[1]=1.;  /*     (u[j] = t[j]); */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*   } */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*      u[p]='\0'; */
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*    for(j=0; j<= lg; j++) { */
       for (k=1; k<=cptcovprod;k++)  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*   } */
   /* } */
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /********************** nrerror ********************/
       /*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,  void nrerror(char error_text[])
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    fprintf(stderr,"ERREUR ...\n");
       oldm=newm;    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  /*********************** vector *******************/
         po[i][j][h]=newm[i][j];  double *vector(int nl, int nh)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    double *v;
       }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   } /* end h */    if (!v) nrerror("allocation failure in vector");
   return po;    return v-nl+NR_END;
 }  }
   
   /************************ free vector ******************/
 /*************** log-likelihood *************/  void free_vector(double*v, int nl, int nh)
 double func( double *x)  {
 {    free((FREE_ARG)(v+nl-NR_END));
   int i, ii, j, k, mi, d, kk;  }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  /************************ivector *******************************/
   double sw; /* Sum of weights */  int *ivector(long nl,long nh)
   double lli; /* Individual log likelihood */  {
   long ipmx;    int *v;
   /*extern weight */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* We are differentiating ll according to initial status */    if (!v) nrerror("allocation failure in ivector");
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    return v-nl+NR_END;
   /*for(i=1;i<imx;i++)  }
     printf(" %d\n",s[4][i]);  
   */  /******************free ivector **************************/
   cov[1]=1.;  void free_ivector(int *v, long nl, long nh)
   {
   for(k=1; k<=nlstate; k++) ll[k]=0.;    free((FREE_ARG)(v+nl-NR_END));
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  }
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){  /************************lvector *******************************/
       for (ii=1;ii<=nlstate+ndeath;ii++)  long *lvector(long nl,long nh)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
       for(d=0; d<dh[mi][i]; d++){    long *v;
         newm=savm;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    if (!v) nrerror("allocation failure in ivector");
         for (kk=1; kk<=cptcovage;kk++) {    return v-nl+NR_END;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  }
         }  
          /******************free lvector **************************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  void free_lvector(long *v, long nl, long nh)
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  {
         savm=oldm;    free((FREE_ARG)(v+nl-NR_END));
         oldm=newm;  }
          
          /******************* imatrix *******************************/
       } /* end mult */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
             /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       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]]);*/    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       ipmx +=1;    int **m; 
       sw += weight[i];    
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    /* allocate pointers to rows */ 
     } /* end of wave */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   } /* end of individual */    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    m -= nrl; 
   /* 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 */    
   return -l;    /* 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()"); 
     m[nrl] += NR_END; 
 /*********** Maximum Likelihood Estimation ***************/    m[nrl] -= ncl; 
     
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 {    
   int i,j, iter;    /* return pointer to array of pointers to rows */ 
   double **xi,*delti;    return m; 
   double fret;  } 
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  /****************** free_imatrix *************************/
     for (j=1;j<=npar;j++)  void free_imatrix(m,nrl,nrh,ncl,nch)
       xi[i][j]=(i==j ? 1.0 : 0.0);        int **m;
   printf("Powell\n");        long nch,ncl,nrh,nrl; 
   powell(p,xi,npar,ftol,&iter,&fret,func);       /* free an int matrix allocated by imatrix() */ 
   { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 }  
   /******************* matrix *******************************/
 /**** Computes Hessian and covariance matrix ***/  double **matrix(long nrl, long nrh, long ncl, long nch)
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double  **a,**y,*x,pd;    double **m;
   double **hess;  
   int i, j,jk;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   int *indx;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   double hessii(double p[], double delta, int theta, double delti[]);    m -= nrl;
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   void ludcmp(double **a, int npar, int *indx, double *d) ;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   hess=matrix(1,npar,1,npar);    m[nrl] -= ncl;
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (i=1;i<=npar;i++){    return m;
     printf("%d",i);fflush(stdout);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     hess[i][i]=hessii(p,ftolhess,i,delti);  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     /*printf(" %f ",p[i]);*/  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     /*printf(" %lf ",hess[i][i]);*/     */
   }  }
    
   for (i=1;i<=npar;i++) {  /*************************free matrix ************************/
     for (j=1;j<=npar;j++)  {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       if (j>i) {  {
         printf(".%d%d",i,j);fflush(stdout);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         hess[i][j]=hessij(p,delti,i,j);    free((FREE_ARG)(m+nrl-NR_END));
         hess[j][i]=hess[i][j];      }
         /*printf(" %lf ",hess[i][j]);*/  
       }  /******************* ma3x *******************************/
     }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   }  {
   printf("\n");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
      m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   a=matrix(1,npar,1,npar);    if (!m) nrerror("allocation failure 1 in matrix()");
   y=matrix(1,npar,1,npar);    m += NR_END;
   x=vector(1,npar);    m -= nrl;
   indx=ivector(1,npar);  
   for (i=1;i<=npar;i++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   ludcmp(a,npar,indx,&pd);    m[nrl] += NR_END;
     m[nrl] -= ncl;
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     x[j]=1;  
     lubksb(a,npar,indx,x);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for (i=1;i<=npar;i++){    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       matcov[i][j]=x[i];    m[nrl][ncl] += NR_END;
     }    m[nrl][ncl] -= nll;
   }    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
   printf("\n#Hessian matrix#\n");    
   for (i=1;i<=npar;i++) {    for (i=nrl+1; i<=nrh; i++) {
     for (j=1;j<=npar;j++) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       printf("%.3e ",hess[i][j]);      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
     printf("\n");    }
   }    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   /* Recompute Inverse */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   for (i=1;i<=npar;i++)    */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /*************************free ma3x ************************/
   /*  printf("\n#Hessian matrix recomputed#\n");  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
   for (j=1;j<=npar;j++) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for (i=1;i<=npar;i++) x[i]=0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     x[j]=1;    free((FREE_ARG)(m+nrl-NR_END));
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /*************** function subdirf ***********/
       printf("%.3e ",y[i][j]);  char *subdirf(char fileres[])
     }  {
     printf("\n");    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
   */    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
   free_matrix(a,1,npar,1,npar);    return tmpout;
   free_matrix(y,1,npar,1,npar);  }
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  /*************** function subdirf2 ***********/
   free_matrix(hess,1,npar,1,npar);  char *subdirf2(char fileres[], char *preop)
   {
     
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 /*************** hessian matrix ****************/    strcat(tmpout,"/");
 double hessii( double x[], double delta, int theta, double delti[])    strcat(tmpout,preop);
 {    strcat(tmpout,fileres);
   int i;    return tmpout;
   int l=1, lmax=20;  }
   double k1,k2;  
   double p2[NPARMAX+1];  /*************** function subdirf3 ***********/
   double res;  char *subdirf3(char fileres[], char *preop, char *preop2)
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  {
   double fx;    
   int k=0,kmax=10;    /* Caution optionfilefiname is hidden */
   double l1;    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   fx=func(x);    strcat(tmpout,preop);
   for (i=1;i<=npar;i++) p2[i]=x[i];    strcat(tmpout,preop2);
   for(l=0 ; l <=lmax; l++){    strcat(tmpout,fileres);
     l1=pow(10,l);    return tmpout;
     delts=delt;  }
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  /***************** f1dim *************************/
       p2[theta]=x[theta] +delt;  extern int ncom; 
       k1=func(p2)-fx;  extern double *pcom,*xicom;
       p2[theta]=x[theta]-delt;  extern double (*nrfunc)(double []); 
       k2=func(p2)-fx;   
       /*res= (k1-2.0*fx+k2)/delt/delt; */  double f1dim(double x) 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  { 
          int j; 
 #ifdef DEBUG    double f;
       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);    double *xt; 
 #endif   
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    xt=vector(1,ncom); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         k=kmax;    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    return f; 
         k=kmax; l=lmax*10.;  } 
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  /*****************brent *************************/
         delts=delt;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       }  { 
     }    int iter; 
   }    double a,b,d,etemp;
   delti[theta]=delts;    double fu,fv,fw,fx;
   return res;    double ftemp;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
 }    double e=0.0; 
    
 double hessij( double x[], double delti[], int thetai,int thetaj)    a=(ax < cx ? ax : cx); 
 {    b=(ax > cx ? ax : cx); 
   int i;    x=w=v=bx; 
   int l=1, l1, lmax=20;    fw=fv=fx=(*f)(x); 
   double k1,k2,k3,k4,res,fx;    for (iter=1;iter<=ITMAX;iter++) { 
   double p2[NPARMAX+1];      xm=0.5*(a+b); 
   int k;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   fx=func(x);      printf(".");fflush(stdout);
   for (k=1; k<=2; k++) {      fprintf(ficlog,".");fflush(ficlog);
     for (i=1;i<=npar;i++) p2[i]=x[i];  #ifdef DEBUG
     p2[thetai]=x[thetai]+delti[thetai]/k;      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);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      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);
     k1=func(p2)-fx;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
    #endif
     p2[thetai]=x[thetai]+delti[thetai]/k;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        *xmin=x; 
     k2=func(p2)-fx;        return fx; 
        } 
     p2[thetai]=x[thetai]-delti[thetai]/k;      ftemp=fu;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      if (fabs(e) > tol1) { 
     k3=func(p2)-fx;        r=(x-w)*(fx-fv); 
          q=(x-v)*(fx-fw); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        p=(x-v)*q-(x-w)*r; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        q=2.0*(q-r); 
     k4=func(p2)-fx;        if (q > 0.0) p = -p; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        q=fabs(q); 
 #ifdef DEBUG        etemp=e; 
     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);        e=d; 
 #endif        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   return res;        else { 
 }          d=p/q; 
           u=x+d; 
 /************** Inverse of matrix **************/          if (u-a < tol2 || b-u < tol2) 
 void ludcmp(double **a, int n, int *indx, double *d)            d=SIGN(tol1,xm-x); 
 {        } 
   int i,imax,j,k;      } else { 
   double big,dum,sum,temp;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double *vv;      } 
        u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   vv=vector(1,n);      fu=(*f)(u); 
   *d=1.0;      if (fu <= fx) { 
   for (i=1;i<=n;i++) {        if (u >= x) a=x; else b=x; 
     big=0.0;        SHFT(v,w,x,u) 
     for (j=1;j<=n;j++)          SHFT(fv,fw,fx,fu) 
       if ((temp=fabs(a[i][j])) > big) big=temp;          } else { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            if (u < x) a=u; else b=u; 
     vv[i]=1.0/big;            if (fu <= fw || w == x) { 
   }              v=w; 
   for (j=1;j<=n;j++) {              w=u; 
     for (i=1;i<j;i++) {              fv=fw; 
       sum=a[i][j];              fw=fu; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            } else if (fu <= fv || v == x || v == w) { 
       a[i][j]=sum;              v=u; 
     }              fv=fu; 
     big=0.0;            } 
     for (i=j;i<=n;i++) {          } 
       sum=a[i][j];    } 
       for (k=1;k<j;k++)    nrerror("Too many iterations in brent"); 
         sum -= a[i][k]*a[k][j];    *xmin=x; 
       a[i][j]=sum;    return fx; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  } 
         big=dum;  
         imax=i;  /****************** mnbrak ***********************/
       }  
     }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     if (j != imax) {              double (*func)(double)) 
       for (k=1;k<=n;k++) {  { 
         dum=a[imax][k];    double ulim,u,r,q, dum;
         a[imax][k]=a[j][k];    double fu; 
         a[j][k]=dum;   
       }    *fa=(*func)(*ax); 
       *d = -(*d);    *fb=(*func)(*bx); 
       vv[imax]=vv[j];    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
     indx[j]=imax;        SHFT(dum,*fb,*fa,dum) 
     if (a[j][j] == 0.0) a[j][j]=TINY;        } 
     if (j != n) {    *cx=(*bx)+GOLD*(*bx-*ax); 
       dum=1.0/(a[j][j]);    *fc=(*func)(*cx); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    while (*fb > *fc) { 
     }      r=(*bx-*ax)*(*fb-*fc); 
   }      q=(*bx-*cx)*(*fb-*fa); 
   free_vector(vv,1,n);  /* Doesn't work */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 ;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 void lubksb(double **a, int n, int *indx, double b[])        fu=(*func)(u); 
 {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   int i,ii=0,ip,j;        fu=(*func)(u); 
   double sum;        if (fu < *fc) { 
            SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   for (i=1;i<=n;i++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
     ip=indx[i];            } 
     sum=b[ip];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     b[ip]=b[i];        u=ulim; 
     if (ii)        fu=(*func)(u); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      } else { 
     else if (sum) ii=i;        u=(*cx)+GOLD*(*cx-*bx); 
     b[i]=sum;        fu=(*func)(u); 
   }      } 
   for (i=n;i>=1;i--) {      SHFT(*ax,*bx,*cx,u) 
     sum=b[i];        SHFT(*fa,*fb,*fc,fu) 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        } 
     b[i]=sum/a[i][i];  } 
   }  
 }  /*************** linmin ************************/
   
 /************ Frequencies ********************/  int ncom; 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  double *pcom,*xicom;
 {  /* Some frequencies */  double (*nrfunc)(double []); 
     
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double ***freq; /* Frequencies */  { 
   double *pp;    double brent(double ax, double bx, double cx, 
   double pos;                 double (*f)(double), double tol, double *xmin); 
   FILE *ficresp;    double f1dim(double x); 
   char fileresp[FILENAMELENGTH];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   pp=vector(1,nlstate);    int j; 
  probs= ma3x(1,130 ,1,8, 1,8);    double xx,xmin,bx,ax; 
   strcpy(fileresp,"p");    double fx,fb,fa;
   strcat(fileresp,fileres);   
   if((ficresp=fopen(fileresp,"w"))==NULL) {    ncom=n; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    pcom=vector(1,n); 
     exit(0);    xicom=vector(1,n); 
   }    nrfunc=func; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for (j=1;j<=n;j++) { 
   j1=0;      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   j=cptcoveff;    } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    ax=0.0; 
     xx=1.0; 
   for(k1=1; k1<=j;k1++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
    for(i1=1; i1<=ncodemax[k1];i1++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
        j1++;  #ifdef DEBUG
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
          scanf("%d", i);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for (i=-1; i<=nlstate+ndeath; i++)    #endif
          for (jk=-1; jk<=nlstate+ndeath; jk++)      for (j=1;j<=n;j++) { 
            for(m=agemin; m <= agemax+3; m++)      xi[j] *= xmin; 
              freq[i][jk][m]=0;      p[j] += xi[j]; 
            } 
        for (i=1; i<=imx; i++) {    free_vector(xicom,1,n); 
          bool=1;    free_vector(pcom,1,n); 
          if  (cptcovn>0) {  } 
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  char *asc_diff_time(long time_sec, char ascdiff[])
                bool=0;  {
          }    long sec_left, days, hours, minutes;
           if (bool==1) {    days = (time_sec) / (60*60*24);
            for(m=firstpass; m<=lastpass-1; m++){    sec_left = (time_sec) % (60*60*24);
              if(agev[m][i]==0) agev[m][i]=agemax+1;    hours = (sec_left) / (60*60) ;
              if(agev[m][i]==1) agev[m][i]=agemax+2;    sec_left = (sec_left) %(60*60);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    minutes = (sec_left) /60;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    sec_left = (sec_left) % (60);
            }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
          }    return ascdiff;
        }  }
         if  (cptcovn>0) {  
          fprintf(ficresp, "\n#********** Variable ");  /*************** powell ************************/
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
        fprintf(ficresp, "**********\n#");              double (*func)(double [])) 
         }  { 
        for(i=1; i<=nlstate;i++)    void linmin(double p[], double xi[], int n, double *fret, 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);                double (*func)(double [])); 
        fprintf(ficresp, "\n");    int i,ibig,j; 
            double del,t,*pt,*ptt,*xit;
   for(i=(int)agemin; i <= (int)agemax+3; i++){    double fp,fptt;
     if(i==(int)agemax+3)    double *xits;
       printf("Total");    int niterf, itmp;
     else  
       printf("Age %d", i);    pt=vector(1,n); 
     for(jk=1; jk <=nlstate ; jk++){    ptt=vector(1,n); 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    xit=vector(1,n); 
         pp[jk] += freq[jk][m][i];    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     for(jk=1; jk <=nlstate ; jk++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       for(m=-1, pos=0; m <=0 ; m++)    for (*iter=1;;++(*iter)) { 
         pos += freq[jk][m][i];      fp=(*fret); 
       if(pp[jk]>=1.e-10)      ibig=0; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      del=0.0; 
       else      last_time=curr_time;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      (void) gettimeofday(&curr_time,&tzp);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
         pp[jk] += freq[jk][m][i];     for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     for(jk=1,pos=0; jk <=nlstate ; jk++)        fprintf(ficlog," %d %.12lf",i, p[i]);
       pos += pp[jk];        fprintf(ficrespow," %.12lf", p[i]);
     for(jk=1; jk <=nlstate ; jk++){      }
       if(pos>=1.e-5)      printf("\n");
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      fprintf(ficlog,"\n");
       else      fprintf(ficrespow,"\n");fflush(ficrespow);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      if(*iter <=3){
       if( i <= (int) agemax){        tm = *localtime(&curr_time.tv_sec);
         if(pos>=1.e-5){        strcpy(strcurr,asctime(&tm));
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /*       asctime_r(&tm,strcurr); */
           probs[i][jk][j1]= pp[jk]/pos;        forecast_time=curr_time; 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        itmp = strlen(strcurr);
         }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       else          strcurr[itmp-1]='\0';
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     }        for(niterf=10;niterf<=30;niterf+=10){
     for(jk=-1; jk <=nlstate+ndeath; jk++)          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       for(m=-1; m <=nlstate+ndeath; m++)          tmf = *localtime(&forecast_time.tv_sec);
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /*      asctime_r(&tmf,strfor); */
     if(i <= (int) agemax)          strcpy(strfor,asctime(&tmf));
       fprintf(ficresp,"\n");          itmp = strlen(strfor);
     printf("\n");          if(strfor[itmp-1]=='\n')
     }          strfor[itmp-1]='\0';
     }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
  }          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);
          }
   fclose(ficresp);      }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1;i<=n;i++) { 
   free_vector(pp,1,nlstate);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
 }  /* End of Freq */  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 /************* Waves Concatenation ***************/        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        printf("%d",i);fflush(stdout);
 {        fprintf(ficlog,"%d",i);fflush(ficlog);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        linmin(p,xit,n,fret,func); 
      Death is a valid wave (if date is known).        if (fabs(fptt-(*fret)) > del) { 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          del=fabs(fptt-(*fret)); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          ibig=i; 
      and mw[mi+1][i]. dh depends on stepm.        } 
      */  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   int i, mi, m;        fprintf(ficlog,"%d %.12e",i,(*fret));
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (j=1;j<=n;j++) {
      double sum=0., jmean=0.;*/          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   int j, k=0,jk, ju, jl;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double sum=0.;        }
   jmin=1e+5;        for(j=1;j<=n;j++) {
   jmax=-1;          printf(" p=%.12e",p[j]);
   jmean=0.;          fprintf(ficlog," p=%.12e",p[j]);
   for(i=1; i<=imx; i++){        }
     mi=0;        printf("\n");
     m=firstpass;        fprintf(ficlog,"\n");
     while(s[m][i] <= nlstate){  #endif
       if(s[m][i]>=1)      } 
         mw[++mi][i]=m;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       if(m >=lastpass)  #ifdef DEBUG
         break;        int k[2],l;
       else        k[0]=1;
         m++;        k[1]=-1;
     }/* end while */        printf("Max: %.12e",(*func)(p));
     if (s[m][i] > nlstate){        fprintf(ficlog,"Max: %.12e",(*func)(p));
       mi++;     /* Death is another wave */        for (j=1;j<=n;j++) {
       /* if(mi==0)  never been interviewed correctly before death */          printf(" %.12e",p[j]);
          /* Only death is a correct wave */          fprintf(ficlog," %.12e",p[j]);
       mw[mi][i]=m;        }
     }        printf("\n");
         fprintf(ficlog,"\n");
     wav[i]=mi;        for(l=0;l<=1;l++) {
     if(mi==0)          for (j=1;j<=n;j++) {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for(i=1; i<=imx; i++){          }
     for(mi=1; mi<wav[i];mi++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if (stepm <=0)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         dh[mi][i]=1;        }
       else{  #endif
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        free_vector(xit,1,n); 
           if(j==0) j=1;  /* Survives at least one month after exam */        free_vector(xits,1,n); 
           k=k+1;        free_vector(ptt,1,n); 
           if (j >= jmax) jmax=j;        free_vector(pt,1,n); 
           if (j <= jmin) jmin=j;        return; 
           sum=sum+j;      } 
           /* if (j<10) printf("j=%d num=%d ",j,i); */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           }      for (j=1;j<=n;j++) { 
         }        ptt[j]=2.0*p[j]-pt[j]; 
         else{        xit[j]=p[j]-pt[j]; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        pt[j]=p[j]; 
           k=k+1;      } 
           if (j >= jmax) jmax=j;      fptt=(*func)(ptt); 
           else if (j <= jmin)jmin=j;      if (fptt < fp) { 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
           sum=sum+j;        if (t < 0.0) { 
         }          linmin(p,xit,n,fret,func); 
         jk= j/stepm;          for (j=1;j<=n;j++) { 
         jl= j -jk*stepm;            xi[j][ibig]=xi[j][n]; 
         ju= j -(jk+1)*stepm;            xi[j][n]=xit[j]; 
         if(jl <= -ju)          }
           dh[mi][i]=jk;  #ifdef DEBUG
         else          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           dh[mi][i]=jk+1;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         if(dh[mi][i]==0)          for(j=1;j<=n;j++){
           dh[mi][i]=1; /* At least one step */            printf(" %.12e",xit[j]);
       }            fprintf(ficlog," %.12e",xit[j]);
     }          }
   }          printf("\n");
   jmean=sum/k;          fprintf(ficlog,"\n");
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  #endif
  }        }
 /*********** Tricode ****************************/      } 
 void tricode(int *Tvar, int **nbcode, int imx)    } 
 {  } 
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;  /**** Prevalence limit (stable or period prevalence)  ****************/
   cptcoveff=0;  
    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (k=0; k<19; k++) Ndum[k]=0;  {
   for (k=1; k<=7; k++) ncodemax[k]=0;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {    int i, ii,j,k;
       ij=(int)(covar[Tvar[j]][i]);    double min, max, maxmin, maxmax,sumnew=0.;
       Ndum[ij]++;    /* double **matprod2(); */ /* test */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    double **out, cov[NCOVMAX+1], **pmij();
       if (ij > cptcode) cptcode=ij;    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
     for (i=0; i<=cptcode; i++) {    for (ii=1;ii<=nlstate+ndeath;ii++)
       if(Ndum[i]!=0) ncodemax[j]++;      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     ij=1;      }
   
      cov[1]=1.;
     for (i=1; i<=ncodemax[j]; i++) {   
       for (k=0; k<=19; k++) {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         if (Ndum[k] != 0) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           nbcode[Tvar[j]][ij]=k;      newm=savm;
           ij++;      /* Covariates have to be included here again */
         }      cov[2]=agefin;
         if (ij > ncodemax[j]) break;      
       }        for (k=1; k<=cptcovn;k++) {
     }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   }          /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       }
  for (k=0; k<19; k++) Ndum[k]=0;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
  for (i=1; i<=ncovmodel-2; i++) {      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       ij=Tvar[i];      
       Ndum[ij]++;      /*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]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
  ij=1;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
  for (i=1; i<=10; i++) {      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
    if((Ndum[i]!=0) && (i<=ncov)){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      Tvaraff[ij]=i;      
      ij++;      savm=oldm;
    }      oldm=newm;
  }      maxmax=0.;
        for(j=1;j<=nlstate;j++){
     cptcoveff=ij-1;        min=1.;
 }        max=0.;
         for(i=1; i<=nlstate; i++) {
 /*********** Health Expectancies ****************/          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          prlim[i][j]= newm[i][j]/(1-sumnew);
 {          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   /* Health expectancies */          max=FMAX(max,prlim[i][j]);
   int i, j, nhstepm, hstepm, h;          min=FMIN(min,prlim[i][j]);
   double age, agelim,hf;        }
   double ***p3mat;        maxmin=max-min;
          maxmax=FMAX(maxmax,maxmin);
   fprintf(ficreseij,"# Health expectancies\n");      }
   fprintf(ficreseij,"# Age");      if(maxmax < ftolpl){
   for(i=1; i<=nlstate;i++)        return prlim;
     for(j=1; j<=nlstate;j++)      }
       fprintf(ficreseij," %1d-%1d",i,j);    }
   fprintf(ficreseij,"\n");  }
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */  /*************** transition probabilities ***************/ 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   agelim=AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* According to parameters values stored in x and the covariate's values stored in cov,
     /* nhstepm age range expressed in number of stepm */       computes the probability to be observed in state j being in state i by appying the
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);       model to the ncovmodel covariates (including constant and age).
     /* Typically if 20 years = 20*12/6=40 stepm */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
     if (stepm >= YEARM) hstepm=1;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */       ncth covariate in the global vector x is given by the formula:
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     /* Computed by stepm unit matrices, product of hstepm matrices, stored       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);         sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
        Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     for(i=1; i<=nlstate;i++)    */
       for(j=1; j<=nlstate;j++)    double s1, lnpijopii;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    /*double t34;*/
           eij[i][j][(int)age] +=p3mat[i][j][h];    int i,j,j1, nc, ii, jj;
         }  
          for(i=1; i<= nlstate; i++){
     hf=1;        for(j=1; j<i;j++){
     if (stepm >= YEARM) hf=stepm/YEARM;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     fprintf(ficreseij,"%.0f",age );            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     for(i=1; i<=nlstate;i++)            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       for(j=1; j<=nlstate;j++){  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          }
       }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     fprintf(ficreseij,"\n");  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   }        for(j=i+1; j<=nlstate+ndeath;j++){
 }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
 /************ Variance ******************/            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 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)  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
 {          }
   /* Variance of health expectancies */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   /*  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, h;      for(i=1; i<= nlstate; i++){
   int k, cptcode;        s1=0;
   double *xp;        for(j=1; j<i; j++){
   double **gp, **gm;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   double ***gradg, ***trgradg;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   double ***p3mat;        }
   double age,agelim;        for(j=i+1; j<=nlstate+ndeath; j++){
   int theta;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
    fprintf(ficresvij,"# Covariances of life expectancies\n");        }
   fprintf(ficresvij,"# Age");        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   for(i=1; i<=nlstate;i++)        ps[i][i]=1./(s1+1.);
     for(j=1; j<=nlstate;j++)        /* Computing other pijs */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        for(j=1; j<i; j++)
   fprintf(ficresvij,"\n");          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
   xp=vector(1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   dnewm=matrix(1,nlstate,1,npar);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   doldm=matrix(1,nlstate,1,nlstate);      } /* end i */
        
   hstepm=1*YEARM; /* Every year of age */      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for(jj=1; jj<= nlstate+ndeath; jj++){
   agelim = AGESUP;          ps[ii][jj]=0;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ps[ii][ii]=1;
     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 */      
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     gp=matrix(0,nhstepm,1,nlstate);      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     gm=matrix(0,nhstepm,1,nlstate);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       /*   } */
     for(theta=1; theta <=npar; theta++){      /*   printf("\n "); */
       for(i=1; i<=npar; i++){ /* Computes gradient */      /* } */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /* printf("\n ");printf("%lf ",cov[2]);*/
       }      /*
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(i=1; i<= npar; i++) printf("%f ",x[i]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        goto end;*/
       for(j=1; j<= nlstate; j++){      return ps;
         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];  /**************** Product of 2 matrices ******************/
         }  
       }  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
      {
       for(i=1; i<=npar; i++) /* Computes gradient */    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* in, b, out are matrice of pointers which should have been initialized 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       before: only the contents of out is modified. The function returns
       for(j=1; j<= nlstate; j++){       a pointer to pointers identical to out */
         for(h=0; h<=nhstepm; h++){    int i, j, k;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    for(i=nrl; i<= nrh; i++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      for(k=ncolol; k<=ncoloh; k++){
         }        out[i][k]=0.;
       }        for(j=ncl; j<=nch; j++)
       for(j=1; j<= nlstate; j++)          out[i][k] +=in[i][j]*b[j][k];
         for(h=0; h<=nhstepm; h++){      }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    return out;
         }  }
     } /* End theta */  
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  /************* Higher Matrix Product ***************/
   
     for(h=0; h<=nhstepm; h++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       for(j=1; j<=nlstate;j++)  {
         for(theta=1; theta <=npar; theta++)    /* Computes the transition matrix starting at age 'age' over 
           trgradg[h][j][theta]=gradg[h][theta][j];       'nhstepm*hstepm*stepm' months (i.e. until
        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 
         vareij[i][j][(int)age] =0.;       (typically every 2 years instead of every month which is too big 
     for(h=0;h<=nhstepm;h++){       for the memory).
       for(k=0;k<=nhstepm;k++){       Model is determined by parameters x and covariates have to be 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);       included manually here. 
         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];    int i, j, d, h, k;
       }    double **out, cov[NCOVMAX+1];
     }    double **newm;
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;    /* Hstepm could be zero and should return the unit matrix */
     fprintf(ficresvij,"%.0f ",age );    for (i=1;i<=nlstate+ndeath;i++)
     for(i=1; i<=nlstate;i++)      for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<=nlstate;j++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }      }
     fprintf(ficresvij,"\n");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     free_matrix(gp,0,nhstepm,1,nlstate);    for(h=1; h <=nhstepm; h++){
     free_matrix(gm,0,nhstepm,1,nlstate);      for(d=1; d <=hstepm; d++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        newm=savm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        /* Covariates have to be included here again */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        cov[1]=1.;
   } /* End age */        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          for (k=1; k<=cptcovn;k++) 
   free_vector(xp,1,npar);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   free_matrix(doldm,1,nlstate,1,npar);        for (k=1; k<=cptcovage;k++)
   free_matrix(dnewm,1,nlstate,1,nlstate);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 /************ 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)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   /* Variance of prevalence limit */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **newm;        savm=oldm;
   double **dnewm,**doldm;        oldm=newm;
   int i, j, nhstepm, hstepm;      }
   int k, cptcode;      for(i=1; i<=nlstate+ndeath; i++)
   double *xp;        for(j=1;j<=nlstate+ndeath;j++) {
   double *gp, *gm;          po[i][j][h]=newm[i][j];
   double **gradg, **trgradg;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   double age,agelim;        }
   int theta;      /*printf("h=%d ",h);*/
        } /* end h */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  /*     printf("\n H=%d \n",h); */
   fprintf(ficresvpl,"# Age");    return po;
   for(i=1; i<=nlstate;i++)  }
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");  
   /*************** log-likelihood *************/
   xp=vector(1,npar);  double func( double *x)
   dnewm=matrix(1,nlstate,1,npar);  {
   doldm=matrix(1,nlstate,1,nlstate);    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   hstepm=1*YEARM; /* Every year of age */    double **out;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double sw; /* Sum of weights */
   agelim = AGESUP;    double lli; /* Individual log likelihood */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int s1, s2;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double bbh, survp;
     if (stepm >= YEARM) hstepm=1;    long ipmx;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /*extern weight */
     gradg=matrix(1,npar,1,nlstate);    /* We are differentiating ll according to initial status */
     gp=vector(1,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     gm=vector(1,nlstate);    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     for(theta=1; theta <=npar; theta++){    */
       for(i=1; i<=npar; i++){ /* Computes gradient */    cov[1]=1.;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    if(mle==1){
         gp[i] = prlim[i][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            /* Computes the values of the ncovmodel covariates of the model
       for(i=1; i<=npar; i++) /* Computes gradient */           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           to be observed in j being in i according to the model.
       for(i=1;i<=nlstate;i++)         */
         gm[i] = prlim[i][i];        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+k]=covar[Tvar[k]][i];
       for(i=1;i<=nlstate;i++)        }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     } /* End theta */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
            has been calculated etc */
     trgradg =matrix(1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<=nlstate;j++)            for (j=1;j<=nlstate+ndeath;j++){
       for(theta=1; theta <=npar; theta++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         trgradg[j][theta]=gradg[theta][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for(i=1;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
       varpl[i][(int)age] =0.;            newm=savm;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            for (kk=1; kk<=cptcovage;kk++) {
     for(i=1;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficresvpl,"%.0f ",age );                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)            savm=oldm;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            oldm=newm;
     fprintf(ficresvpl,"\n");          } /* end mult */
     free_vector(gp,1,nlstate);        
     free_vector(gm,1,nlstate);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     free_matrix(gradg,1,npar,1,nlstate);          /* But now since version 0.9 we anticipate for bias at large stepm.
     free_matrix(trgradg,1,nlstate,1,npar);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   } /* End age */           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
   free_vector(xp,1,npar);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   free_matrix(doldm,1,nlstate,1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   free_matrix(dnewm,1,nlstate,1,nlstate);           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
 /************ Variance of one-step probabilities  ******************/           * For stepm > 1 the results are less biased than in previous versions. 
 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;          /* bias bh is positive if real duration
   double *xp;           * is higher than the multiple of stepm and negative otherwise.
   double *gp, *gm;           */
   double **gradg, **trgradg;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double age,agelim, cov[NCOVMAX];          if( s2 > nlstate){ 
   int theta;            /* i.e. if s2 is a death state and if the date of death is known 
   char fileresprob[FILENAMELENGTH];               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
   strcpy(fileresprob,"prob");               which is also equal to probability to die before dh 
   strcat(fileresprob,fileres);               minus probability to die before dh-stepm . 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {               In version up to 0.92 likelihood was computed
     printf("Problem with resultfile: %s\n", fileresprob);          as if date of death was unknown. Death was treated as any other
   }          health state: the date of the interview describes the actual state
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          and not the date of a change in health state. The former idea was
            to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
   xp=vector(1,npar);          introduced the exact date of death then we should have modified
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          the contribution of an exact death to the likelihood. This new
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          contribution is smaller and very dependent of the step unit
            stepm. It is no more the probability to die between last interview
   cov[1]=1;          and month of death but the probability to survive from last
   for (age=bage; age<=fage; age ++){          interview up to one month before death multiplied by the
     cov[2]=age;          probability to die within a month. Thanks to Chris
     gradg=matrix(1,npar,1,9);          Jackson for correcting this bug.  Former versions increased
     trgradg=matrix(1,9,1,npar);          mortality artificially. The bad side is that we add another loop
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          which slows down the processing. The difference can be up to 10%
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          lower mortality.
                */
     for(theta=1; theta <=npar; theta++){            lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
                } else if  (s2==-2) {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            for (j=1,survp=0. ; j<=nlstate; j++) 
                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       k=0;            /*survp += out[s1][j]; */
       for(i=1; i<= (nlstate+ndeath); i++){            lli= log(survp);
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;          
           gp[k]=pmmij[i][j];          else if  (s2==-4) { 
         }            for (j=3,survp=0. ; j<=nlstate; j++)  
       }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
       for(i=1; i<=npar; i++)          } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
              else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       k=0;            lli= log(survp); 
       for(i=1; i<=(nlstate+ndeath); i++){          } 
         for(j=1; j<=(nlstate+ndeath);j++){          
           k=k+1;          else{
           gm[k]=pmmij[i][j];            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 */
       }          } 
                /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          /*if(lli ==000.0)*/
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            /*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); */
     }          ipmx +=1;
           sw += weight[i];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(theta=1; theta <=npar; theta++)        } /* end of wave */
       trgradg[j][theta]=gradg[theta][j];      } /* end of individual */
      }  else if(mle==2){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
      pmij(pmmij,cov,ncovmodel,x,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
             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];
      /*printf("\n%d ",(int)age);            }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            oldm=newm;
      }*/          } /* end mult */
         
   fprintf(ficresprob,"\n%d ",(int)age);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          bbh=(double)bh[mi][i]/(double)stepm; 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          ipmx +=1;
   }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        } /* end of wave */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      } /* end of individual */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }  else if(mle==3){  /* exponential inter-extrapolation */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  free_vector(xp,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
 fclose(ficresprob);          for (ii=1;ii<=nlstate+ndeath;ii++)
  exit(0);            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);
 /***********************************************/            }
 /**************** Main Program *****************/          for(d=0; d<dh[mi][i]; d++){
 /***********************************************/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /*int main(int argc, char *argv[])*/            for (kk=1; kk<=cptcovage;kk++) {
 int main()              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double agedeb, agefin,hf;            savm=oldm;
   double agemin=1.e20, agemax=-1.e20;            oldm=newm;
           } /* end mult */
   double fret;        
   double **xi,tmp,delta;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   double dum; /* Dummy variable */          bbh=(double)bh[mi][i]/(double)stepm; 
   double ***p3mat;          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 */
   int *indx;          ipmx +=1;
   char line[MAXLINE], linepar[MAXLINE];          sw += weight[i];
   char title[MAXLINE];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];        } /* end of wave */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      } /* end of individual */
   char filerest[FILENAMELENGTH];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   char fileregp[FILENAMELENGTH];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int firstobs=1, lastobs=10;        for(mi=1; mi<= wav[i]-1; mi++){
   int sdeb, sfin; /* Status at beginning and end */          for (ii=1;ii<=nlstate+ndeath;ii++)
   int c,  h , cpt,l;            for (j=1;j<=nlstate+ndeath;j++){
   int ju,jl, mi;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            }
            for(d=0; d<dh[mi][i]; d++){
   int hstepm, nhstepm;            newm=savm;
   double bage, fage, age, agelim, agebase;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ftolpl=FTOL;            for (kk=1; kk<=cptcovage;kk++) {
   double **prlim;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *severity;            }
   double ***param; /* Matrix of parameters */          
   double  *p;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **matcov; /* Matrix of covariance */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***delti3; /* Scale */            savm=oldm;
   double *delti; /* Scale */            oldm=newm;
   double ***eij, ***vareij;          } /* end mult */
   double **varpl; /* Variances of prevalence limits by age */        
   double *epj, vepp;          s1=s[mw[mi][i]][i];
   double kk1;          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";            lli=log(out[s1][s2] - savm[s1][s2]);
   char *alph[]={"a","a","b","c","d","e"}, str[4];          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
   char z[1]="c", occ;          ipmx +=1;
 #include <sys/time.h>          sw += weight[i];
 #include <time.h>          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  /*      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]); */
   /* long total_usecs;        } /* end of wave */
   struct timeval start_time, end_time;      } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   printf("\nIMACH, Version 0.64b");          for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("\nEnter the parameter file name: ");            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #ifdef windows              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   scanf("%s",pathtot);            }
   getcwd(pathcd, size);          for(d=0; d<dh[mi][i]; d++){
   /*cygwin_split_path(pathtot,path,optionfile);            newm=savm;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* cutv(path,optionfile,pathtot,'\\');*/            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 split(pathtot, path,optionfile);            }
   chdir(path);          
   replace(pathc,path);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #endif                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #ifdef unix            savm=oldm;
   scanf("%s",optionfile);            oldm=newm;
 #endif          } /* end mult */
         
 /*-------- arguments in the command line --------*/          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   strcpy(fileres,"r");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   strcat(fileres, optionfile);          ipmx +=1;
           sw += weight[i];
   /*---------arguments file --------*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        } /* end of wave */
     printf("Problem with optionfile %s\n",optionfile);      } /* end of individual */
     goto end;    } /* End of if */
   }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   strcpy(filereso,"o");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   strcat(filereso,fileres);    return -l;
   if((ficparo=fopen(filereso,"w"))==NULL) {  }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }  /*************** log-likelihood *************/
   double funcone( double *x)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    /* Same as likeli but slower because of a lot of printf and if */
     ungetc(c,ficpar);    int i, ii, j, k, mi, d, kk;
     fgets(line, MAXLINE, ficpar);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     puts(line);    double **out;
     fputs(line,ficparo);    double lli; /* Individual log likelihood */
   }    double llt;
   ungetc(c,ficpar);    int s1, s2;
     double bbh, survp;
   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);    /*extern weight */
   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);    /* We are differentiating ll according to initial status */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   covar=matrix(0,NCOVMAX,1,n);      printf(" %d\n",s[4][i]);
   cptcovn=0;    */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    cov[1]=1.;
   
   ncovmodel=2+cptcovn;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Read guess parameters */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* Reads comments: lines beginning with '#' */      for(mi=1; mi<= wav[i]-1; mi++){
   while((c=getc(ficpar))=='#' && c!= EOF){        for (ii=1;ii<=nlstate+ndeath;ii++)
     ungetc(c,ficpar);          for (j=1;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     puts(line);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fputs(line,ficparo);          }
   }        for(d=0; d<dh[mi][i]; d++){
   ungetc(c,ficpar);          newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for (kk=1; kk<=cptcovage;kk++) {
     for(i=1; i <=nlstate; i++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j <=nlstate+ndeath-1; j++){          }
       fscanf(ficpar,"%1d%1d",&i1,&j1);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       fprintf(ficparo,"%1d%1d",i1,j1);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       printf("%1d%1d",i,j);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(k=1; k<=ncovmodel;k++){          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         fscanf(ficpar," %lf",&param[i][j][k]);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         printf(" %lf",param[i][j][k]);          savm=oldm;
         fprintf(ficparo," %lf",param[i][j][k]);          oldm=newm;
       }        } /* end mult */
       fscanf(ficpar,"\n");        
       printf("\n");        s1=s[mw[mi][i]][i];
       fprintf(ficparo,"\n");        s2=s[mw[mi+1][i]][i];
     }        bbh=(double)bh[mi][i]/(double)stepm; 
          /* bias is positive if real duration
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;         * is higher than the multiple of stepm and negative otherwise.
          */
   p=param[1][1];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
            lli=log(out[s1][s2] - savm[s1][s2]);
   /* Reads comments: lines beginning with '#' */        } else if  (s2==-2) {
   while((c=getc(ficpar))=='#' && c!= EOF){          for (j=1,survp=0. ; j<=nlstate; j++) 
     ungetc(c,ficpar);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     fgets(line, MAXLINE, ficpar);          lli= log(survp);
     puts(line);        }else if (mle==1){
     fputs(line,ficparo);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }        } else if(mle==2){
   ungetc(c,ficpar);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          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 */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for(i=1; i <=nlstate; i++){          lli=log(out[s1][s2]); /* Original formula */
     for(j=1; j <=nlstate+ndeath-1; j++){        } else{  /* mle=0 back to 1 */
       fscanf(ficpar,"%1d%1d",&i1,&j1);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       printf("%1d%1d",i,j);          /*lli=log(out[s1][s2]); */ /* Original formula */
       fprintf(ficparo,"%1d%1d",i1,j1);        } /* End of if */
       for(k=1; k<=ncovmodel;k++){        ipmx +=1;
         fscanf(ficpar,"%le",&delti3[i][j][k]);        sw += weight[i];
         printf(" %le",delti3[i][j][k]);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficparo," %le",delti3[i][j][k]);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        if(globpr){
       fscanf(ficpar,"\n");          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       printf("\n");   %11.6f %11.6f %11.6f ", \
       fprintf(ficparo,"\n");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   delti=delti3[1][1];            llt +=ll[k]*gipmx/gsw;
              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresilk," %10.6f\n", -llt);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      } /* end of wave */
     puts(line);    } /* end of individual */
     fputs(line,ficparo);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   ungetc(c,ficpar);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      if(globpr==0){ /* First time we count the contributions and weights */
   matcov=matrix(1,npar,1,npar);      gipmx=ipmx;
   for(i=1; i <=npar; i++){      gsw=sw;
     fscanf(ficpar,"%s",&str);    }
     printf("%s",str);    return -l;
     fprintf(ficparo,"%s",str);  }
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);  /*************** function likelione ***********/
       fprintf(ficparo," %.5le",matcov[i][j]);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     }  {
     fscanf(ficpar,"\n");    /* This routine should help understanding what is done with 
     printf("\n");       the selection of individuals/waves and
     fprintf(ficparo,"\n");       to check the exact contribution to the likelihood.
   }       Plotting could be done.
   for(i=1; i <=npar; i++)     */
     for(j=i+1;j<=npar;j++)    int k;
       matcov[i][j]=matcov[j][i];  
        if(*globpri !=0){ /* Just counts and sums, no printings */
   printf("\n");      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     /*-------- data file ----------*/        printf("Problem with resultfile: %s\n", fileresilk);
     if((ficres =fopen(fileres,"w"))==NULL) {        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       printf("Problem with resultfile: %s\n", fileres);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(ficres,"#%s\n",version);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
          /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     if((fic=fopen(datafile,"r"))==NULL)    {      for(k=1; k<=nlstate; k++) 
       printf("Problem with datafile: %s\n", datafile);goto end;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     n= lastobs;  
     severity = vector(1,maxwav);    *fretone=(*funcone)(p);
     outcome=imatrix(1,maxwav+1,1,n);    if(*globpri !=0){
     num=ivector(1,n);      fclose(ficresilk);
     moisnais=vector(1,n);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     annais=vector(1,n);      fflush(fichtm); 
     moisdc=vector(1,n);    } 
     andc=vector(1,n);    return;
     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 */  /*********** Maximum Likelihood Estimation ***************/
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     s=imatrix(1,maxwav+1,1,n);  {
     adl=imatrix(1,maxwav+1,1,n);        int i,j, iter;
     tab=ivector(1,NCOVMAX);    double **xi;
     ncodemax=ivector(1,8);    double fret;
     double fretone; /* Only one call to likelihood */
     i=1;    /*  char filerespow[FILENAMELENGTH];*/
     while (fgets(line, MAXLINE, fic) != NULL)    {    xi=matrix(1,npar,1,npar);
       if ((i >= firstobs) && (i <=lastobs)) {    for (i=1;i<=npar;i++)
              for (j=1;j<=npar;j++)
         for (j=maxwav;j>=1;j--){        xi[i][j]=(i==j ? 1.0 : 0.0);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           strcpy(line,stra);    strcpy(filerespow,"pow"); 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    strcat(filerespow,fileres);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", filerespow);
              fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(j=1;j<=nlstate+ndeath;j++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncov;j>=1;j--){    powell(p,xi,npar,ftol,&iter,&fret,func);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    free_matrix(xi,1,npar,1,npar);
         num[i]=atol(stra);    fclose(ficrespow);
            printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           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;}*/    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
         i=i+1;  }
       }  
     }  /**** Computes Hessian and covariance matrix ***/
     /* printf("ii=%d", ij);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
        scanf("%d",i);*/  {
   imx=i-1; /* Number of individuals */    double  **a,**y,*x,pd;
     double **hess;
   /* for (i=1; i<=imx; i++){    int i, j,jk;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    int *indx;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
   /* Calculation of the number of parameter from char model*/    double gompertz(double p[]);
   Tvar=ivector(1,15);    hess=matrix(1,npar,1,npar);
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    printf("\nCalculation of the hessian matrix. Wait...\n");
   Tvard=imatrix(1,15,1,2);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   Tage=ivector(1,15);          for (i=1;i<=npar;i++){
          printf("%d",i);fflush(stdout);
   if (strlen(model) >1){      fprintf(ficlog,"%d",i);fflush(ficlog);
     j=0, j1=0, k1=1, k2=1;     
     j=nbocc(model,'+');       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     j1=nbocc(model,'*');      
     cptcovn=j+1;      /*  printf(" %f ",p[i]);
     cptcovprod=j1;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
        }
        
     strcpy(modelsav,model);    for (i=1;i<=npar;i++) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      for (j=1;j<=npar;j++)  {
       printf("Error. Non available option model=%s ",model);        if (j>i) { 
       goto end;          printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
              hess[i][j]=hessij(p,delti,i,j,func,npar);
     for(i=(j+1); i>=1;i--){          
       cutv(stra,strb,modelsav,'+');          hess[j][i]=hess[i][j];    
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          /*printf(" %lf ",hess[i][j]);*/
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        }
       /*scanf("%d",i);*/      }
       if (strchr(strb,'*')) {    }
         cutv(strd,strc,strb,'*');    printf("\n");
         if (strcmp(strc,"age")==0) {    fprintf(ficlog,"\n");
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           Tvar[i]=atoi(stre);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           cptcovage++;    
             Tage[cptcovage]=i;    a=matrix(1,npar,1,npar);
             /*printf("stre=%s ", stre);*/    y=matrix(1,npar,1,npar);
         }    x=vector(1,npar);
         else if (strcmp(strd,"age")==0) {    indx=ivector(1,npar);
           cptcovprod--;    for (i=1;i<=npar;i++)
           cutv(strb,stre,strc,'V');      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           Tvar[i]=atoi(stre);    ludcmp(a,npar,indx,&pd);
           cptcovage++;  
           Tage[cptcovage]=i;    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
         else {      x[j]=1;
           cutv(strb,stre,strc,'V');      lubksb(a,npar,indx,x);
           Tvar[i]=ncov+k1;      for (i=1;i<=npar;i++){ 
           cutv(strb,strc,strd,'V');        matcov[i][j]=x[i];
           Tprod[k1]=i;      }
           Tvard[k1][1]=atoi(strc);    }
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];    printf("\n#Hessian matrix#\n");
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    fprintf(ficlog,"\n#Hessian matrix#\n");
           for (k=1; k<=lastobs;k++)    for (i=1;i<=npar;i++) { 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for (j=1;j<=npar;j++) { 
           k1++;        printf("%.3e ",hess[i][j]);
           k2=k2+2;        fprintf(ficlog,"%.3e ",hess[i][j]);
         }      }
       }      printf("\n");
       else {      fprintf(ficlog,"\n");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    }
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    /* Recompute Inverse */
       Tvar[i]=atoi(strc);    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       strcpy(modelsav,stra);      ludcmp(a,npar,indx,&pd);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/    /*  printf("\n#Hessian matrix recomputed#\n");
     }  
 }    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      x[j]=1;
   printf("cptcovprod=%d ", cptcovprod);      lubksb(a,npar,indx,x);
   scanf("%d ",i);*/      for (i=1;i<=npar;i++){ 
     fclose(fic);        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
     /*  if(mle==1){*/        fprintf(ficlog,"%.3e ",y[i][j]);
     if (weightopt != 1) { /* Maximisation without weights*/      }
       for(i=1;i<=n;i++) weight[i]=1.0;      printf("\n");
     }      fprintf(ficlog,"\n");
     /*-calculation of age at interview from date of interview and age at death -*/    }
     agev=matrix(1,maxwav,1,imx);    */
   
    for (i=1; i<=imx; i++)    free_matrix(a,1,npar,1,npar);
      for(m=2; (m<= maxwav); m++)    free_matrix(y,1,npar,1,npar);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    free_vector(x,1,npar);
          anint[m][i]=9999;    free_ivector(indx,1,npar);
          s[m][i]=-1;    free_matrix(hess,1,npar,1,npar);
        }  
      
     for (i=1; i<=imx; i++)  {  }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  /*************** hessian matrix ****************/
         if(s[m][i] >0){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           if (s[m][i] == nlstate+1) {  {
             if(agedc[i]>0)    int i;
               if(moisdc[i]!=99 && andc[i]!=9999)    int l=1, lmax=20;
               agev[m][i]=agedc[i];    double k1,k2;
             else {    double p2[MAXPARM+1]; /* identical to x */
               if (andc[i]!=9999){    double res;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
               agev[m][i]=-1;    double fx;
               }    int k=0,kmax=10;
             }    double l1;
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    fx=func(x);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    for (i=1;i<=npar;i++) p2[i]=x[i];
             if(mint[m][i]==99 || anint[m][i]==9999)    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
               agev[m][i]=1;      l1=pow(10,l);
             else if(agev[m][i] <agemin){      delts=delt;
               agemin=agev[m][i];      for(k=1 ; k <kmax; k=k+1){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        delt = delta*(l1*k);
             }        p2[theta]=x[theta] +delt;
             else if(agev[m][i] >agemax){        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
               agemax=agev[m][i];        p2[theta]=x[theta]-delt;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        k2=func(p2)-fx;
             }        /*res= (k1-2.0*fx+k2)/delt/delt; */
             /*agev[m][i]=anint[m][i]-annais[i];*/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
             /*   agev[m][i] = age[i]+2*m;*/        
           }  #ifdef DEBUGHESS
           else { /* =9 */        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);
             agev[m][i]=1;        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             s[m][i]=-1;  #endif
           }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         else /*= 0 Unknown */          k=kmax;
           agev[m][i]=1;        }
       }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
              k=kmax; l=lmax*10.;
     }        }
     for (i=1; i<=imx; i++)  {        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(m=1; (m<= maxwav); m++){          delts=delt;
         if (s[m][i] > (nlstate+ndeath)) {        }
           printf("Error: Wrong value in nlstate or ndeath\n");        }
           goto end;    }
         }    delti[theta]=delts;
       }    return res; 
     }    
   }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     free_vector(severity,1,maxwav);  {
     free_imatrix(outcome,1,maxwav+1,1,n);    int i;
     free_vector(moisnais,1,n);    int l=1, l1, lmax=20;
     free_vector(annais,1,n);    double k1,k2,k3,k4,res,fx;
     free_matrix(mint,1,maxwav,1,n);    double p2[MAXPARM+1];
     free_matrix(anint,1,maxwav,1,n);    int k;
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);    fx=func(x);
     for (k=1; k<=2; k++) {
          for (i=1;i<=npar;i++) p2[i]=x[i];
     wav=ivector(1,imx);      p2[thetai]=x[thetai]+delti[thetai]/k;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      k1=func(p2)-fx;
        
     /* Concatenates waves */      p2[thetai]=x[thetai]+delti[thetai]/k;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     
       Tcode=ivector(1,100);      p2[thetai]=x[thetai]-delti[thetai]/k;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       ncodemax[1]=1;      k3=func(p2)-fx;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    
            p2[thetai]=x[thetai]-delti[thetai]/k;
    codtab=imatrix(1,100,1,10);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
    h=0;      k4=func(p2)-fx;
    m=pow(2,cptcoveff);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
    for(k=1;k<=cptcoveff; k++){      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);
      for(i=1; i <=(m/pow(2,k));i++){      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);
        for(j=1; j <= ncodemax[k]; j++){  #endif
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    }
            h++;    return res;
            if (h>m) h=1;codtab[h][k]=j;  }
          }  
        }  /************** Inverse of matrix **************/
      }  void ludcmp(double **a, int n, int *indx, double *d) 
    }  { 
     int i,imax,j,k; 
     double big,dum,sum,temp; 
    /*for(i=1; i <=m ;i++){    double *vv; 
      for(k=1; k <=cptcovn; k++){   
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    vv=vector(1,n); 
      }    *d=1.0; 
      printf("\n");    for (i=1;i<=n;i++) { 
    }      big=0.0; 
    scanf("%d",i);*/      for (j=1;j<=n;j++) 
            if ((temp=fabs(a[i][j])) > big) big=temp; 
    /* Calculates basic frequencies. Computes observed prevalence at single age      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        and prints on file fileres'p'. */      vv[i]=1.0/big; 
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    } 
     for (j=1;j<=n;j++) { 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (i=1;i<j;i++) { 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        sum=a[i][j]; 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        a[i][j]=sum; 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      } 
            big=0.0; 
     /* For Powell, parameters are in a vector p[] starting at p[1]      for (i=j;i<=n;i++) { 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        sum=a[i][j]; 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
     if(mle==1){        a[i][j]=sum; 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     }          big=dum; 
              imax=i; 
     /*--------- 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);      } 
          if (j != imax) { 
    jk=1;        for (k=1;k<=n;k++) { 
    fprintf(ficres,"# Parameters\n");          dum=a[imax][k]; 
    printf("# Parameters\n");          a[imax][k]=a[j][k]; 
    for(i=1,jk=1; i <=nlstate; i++){          a[j][k]=dum; 
      for(k=1; k <=(nlstate+ndeath); k++){        } 
        if (k != i)        *d = -(*d); 
          {        vv[imax]=vv[j]; 
            printf("%d%d ",i,k);      } 
            fprintf(ficres,"%1d%1d ",i,k);      indx[j]=imax; 
            for(j=1; j <=ncovmodel; j++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
              printf("%f ",p[jk]);      if (j != n) { 
              fprintf(ficres,"%f ",p[jk]);        dum=1.0/(a[j][j]); 
              jk++;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
            }      } 
            printf("\n");    } 
            fprintf(ficres,"\n");    free_vector(vv,1,n);  /* Doesn't work */
          }  ;
      }  } 
    }  
  if(mle==1){  void lubksb(double **a, int n, int *indx, double b[]) 
     /* Computing hessian and covariance matrix */  { 
     ftolhess=ftol; /* Usually correct */    int i,ii=0,ip,j; 
     hesscov(matcov, p, npar, delti, ftolhess, func);    double sum; 
  }   
     fprintf(ficres,"# Scales\n");    for (i=1;i<=n;i++) { 
     printf("# Scales\n");      ip=indx[i]; 
      for(i=1,jk=1; i <=nlstate; i++){      sum=b[ip]; 
       for(j=1; j <=nlstate+ndeath; j++){      b[ip]=b[i]; 
         if (j!=i) {      if (ii) 
           fprintf(ficres,"%1d%1d",i,j);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           printf("%1d%1d",i,j);      else if (sum) ii=i; 
           for(k=1; k<=ncovmodel;k++){      b[i]=sum; 
             printf(" %.5e",delti[jk]);    } 
             fprintf(ficres," %.5e",delti[jk]);    for (i=n;i>=1;i--) { 
             jk++;      sum=b[i]; 
           }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           printf("\n");      b[i]=sum/a[i][i]; 
           fprintf(ficres,"\n");    } 
         }  } 
       }  
       }  void pstamp(FILE *fichier)
      {
     k=1;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     fprintf(ficres,"# Covariance\n");  }
     printf("# Covariance\n");  
     for(i=1;i<=npar;i++){  /************ Frequencies ********************/
       /*  if (k>nlstate) k=1;  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[])
       i1=(i-1)/(ncovmodel*nlstate)+1;  {  /* Some frequencies */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    
       printf("%s%d%d",alph[k],i1,tab[i]);*/    int i, m, jk, k1,i1, j1, bool, z1,j;
       fprintf(ficres,"%3d",i);    int first;
       printf("%3d",i);    double ***freq; /* Frequencies */
       for(j=1; j<=i;j++){    double *pp, **prop;
         fprintf(ficres," %.5e",matcov[i][j]);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         printf(" %.5e",matcov[i][j]);    char fileresp[FILENAMELENGTH];
       }    
       fprintf(ficres,"\n");    pp=vector(1,nlstate);
       printf("\n");    prop=matrix(1,nlstate,iagemin,iagemax+3);
       k++;    strcpy(fileresp,"p");
     }    strcat(fileresp,fileres);
        if((ficresp=fopen(fileresp,"w"))==NULL) {
     while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with prevalence resultfile: %s\n", fileresp);
       ungetc(c,ficpar);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fgets(line, MAXLINE, ficpar);      exit(0);
       puts(line);    }
       fputs(line,ficparo);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     }    j1=0;
     ungetc(c,ficpar);    
      j=cptcoveff;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
     if (fage <= 2) {    first=1;
       bage = agemin;  
       fage = agemax;    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
     }    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
     /*    j1++;
     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\n",agemin,agemax,bage,fage);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
              scanf("%d", i);*/
 /*------------ gnuplot -------------*/        for (i=-5; i<=nlstate+ndeath; i++)  
 chdir(pathcd);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   if((ficgp=fopen("graph.plt","w"))==NULL) {            for(m=iagemin; m <= iagemax+3; m++)
     printf("Problem with file graph.gp");goto end;              freq[i][jk][m]=0;
   }        
 #ifdef windows        for (i=1; i<=nlstate; i++)  
   fprintf(ficgp,"cd \"%s\" \n",pathc);          for(m=iagemin; m <= iagemax+3; m++)
 #endif            prop[i][m]=0;
 m=pow(2,cptcoveff);        
          dateintsum=0;
  /* 1eme*/        k2cpt=0;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for (i=1; i<=imx; i++) {
    for (k1=1; k1<= m ; k1 ++) {          bool=1;
           if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
 #ifdef windows            for (z1=1; z1<=cptcoveff; z1++)       
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
 #endif                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
 #ifdef unix                bool=0;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
 #endif                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
 for (i=1; i<= nlstate ; i ++) {                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }   
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          if (bool==1){
     for (i=1; i<= nlstate ; i ++) {            for(m=firstpass; m<=lastpass; m++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              k2=anint[m][i]+(mint[m][i]/12.);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
      for (i=1; i<= nlstate ; i ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                if (m<lastpass) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 }                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                }
 #ifdef unix                
 fprintf(ficgp,"\nset ter gif small size 400,300");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 #endif                  dateintsum=dateintsum+k2;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                  k2cpt++;
    }                }
   }                /*}*/
   /*2 eme*/            }
           }
   for (k1=1; k1<= m ; k1 ++) {        } /* end i */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);         
            /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     for (i=1; i<= nlstate+1 ; i ++) {        pstamp(ficresp);
       k=2*i;        if  (cptcovn>0) {
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficresp, "\n#********** Variable "); 
       for (j=1; j<= nlstate+1 ; j ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresp, "**********\n#");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficlog, "\n#********** Variable "); 
 }            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          fprintf(ficlog, "**********\n#");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(i=1; i<=nlstate;i++) 
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficresp, "\n");
         else fprintf(ficgp," \%%*lf (\%%*lf)");        
 }          for(i=iagemin; i <= iagemax+3; i++){
       fprintf(ficgp,"\" t\"\" w l 0,");          if(i==iagemax+3){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            fprintf(ficlog,"Total");
       for (j=1; j<= nlstate+1 ; j ++) {          }else{
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            if(first==1){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              first=0;
 }                printf("See log file for details...\n");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            }
       else fprintf(ficgp,"\" t\"\" w l 0,");            fprintf(ficlog,"Age %d", i);
     }          }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
   /*3eme*/          }
           for(jk=1; jk <=nlstate ; jk++){
   for (k1=1; k1<= m ; k1 ++) {            for(m=-1, pos=0; m <=0 ; m++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {              pos += freq[jk][m][i];
       k=2+nlstate*(cpt-1);            if(pp[jk]>=1.e-10){
       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);              if(first==1){
       for (i=1; i< nlstate ; i ++) {                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         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);              }
       }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            }else{
     }              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /* CV preval stat */            }
   for (k1=1; k1<= m ; k1 ++) {          }
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;          for(jk=1; jk <=nlstate ; jk++){
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for (i=1; i< nlstate ; i ++)              pp[jk] += freq[jk][m][i];
         fprintf(ficgp,"+$%d",k+i+1);          }       
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                  pos += pp[jk];
       l=3+(nlstate+ndeath)*cpt;            posprop += prop[jk][i];
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          }
       for (i=1; i< nlstate ; i ++) {          for(jk=1; jk <=nlstate ; jk++){
         l=3+(nlstate+ndeath)*cpt;            if(pos>=1.e-5){
         fprintf(ficgp,"+$%d",l+i+1);              if(first==1)
       }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            }else{
     }              if(first==1)
   }                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /* proba elementaires */            }
    for(i=1,jk=1; i <=nlstate; i++){            if( i <= iagemax){
     for(k=1; k <=(nlstate+ndeath); k++){              if(pos>=1.e-5){
       if (k != i) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
         for(j=1; j <=ncovmodel; j++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           /*fprintf(ficgp,"%s",alph[1]);*/              }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              else
           jk++;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           fprintf(ficgp,"\n");            }
         }          }
       }          
     }          for(jk=-1; jk <=nlstate+ndeath; jk++)
     }            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   for(jk=1; jk <=m; jk++) {              if(first==1)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
    i=1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
    for(k2=1; k2<=nlstate; k2++) {              }
      k3=i;          if(i <= iagemax)
      for(k=1; k<=(nlstate+ndeath); k++) {            fprintf(ficresp,"\n");
        if (k != k2){          if(first==1)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            printf("Others in log...\n");
 ij=1;          fprintf(ficlog,"\n");
         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++;    dateintmean=dateintsum/k2cpt; 
           }   
           else    fclose(ficresp);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         }    free_vector(pp,1,nlstate);
           fprintf(ficgp,")/(1");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
            /* End of Freq */
         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;  /************ Prevalence ********************/
           for(j=3; j <=ncovmodel; j++){  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)
           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]]]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             ij++;       in each health status at the date of interview (if between dateprev1 and dateprev2).
           }       We still use firstpass and lastpass as another selection.
           else    */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   
           }    int i, m, jk, k1, i1, j1, bool, z1,j;
           fprintf(ficgp,")");    double ***freq; /* Frequencies */
         }    double *pp, **prop;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double pos,posprop; 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double  y2; /* in fractional years */
         i=i+ncovmodel;    int iagemin, iagemax;
        }    int first; /** to stop verbosity which is redirected to log file */
      }  
    }    iagemin= (int) agemin;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    iagemax= (int) agemax;
   }    /*pp=vector(1,nlstate);*/
        prop=matrix(1,nlstate,iagemin,iagemax+3); 
   fclose(ficgp);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        j1=0;
 chdir(path);    
     free_matrix(agev,1,maxwav,1,imx);    /*j=cptcoveff;*/
     free_ivector(wav,1,imx);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    first=1;
        for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
     free_imatrix(s,1,maxwav+1,1,n);      /*for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;*/
            
     free_ivector(num,1,n);        for (i=1; i<=nlstate; i++)  
     free_vector(agedc,1,n);          for(m=iagemin; m <= iagemax+3; m++)
     free_vector(weight,1,n);            prop[i][m]=0.0;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/       
     fclose(ficparo);        for (i=1; i<=imx; i++) { /* Each individual */
     fclose(ficres);          bool=1;
     /*  }*/          if  (cptcovn>0) {
                for (z1=1; z1<=cptcoveff; z1++) 
    /*________fin mle=1_________*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
           } 
            if (bool==1) { 
     /* No more information from the sample is required now */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   /* Reads comments: lines beginning with '#' */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   while((c=getc(ficpar))=='#' && c!= EOF){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     ungetc(c,ficpar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fgets(line, MAXLINE, ficpar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     puts(line);                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); 
     fputs(line,ficparo);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   }                  /*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]]);*/
   ungetc(c,ficpar);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    prop[s[m][i]][iagemax+3] += weight[i]; 
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                } 
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            } /* end selection of waves */
 /*--------- index.htm --------*/          }
         }
   strcpy(optionfilehtm,optionfile);        for(i=iagemin; i <= iagemax+3; i++){  
   strcat(optionfilehtm,".htm");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            posprop += prop[jk][i]; 
     printf("Problem with %s \n",optionfilehtm);goto end;          } 
   }          
           for(jk=1; jk <=nlstate ; jk++){     
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">            if( i <=  iagemax){ 
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>              if(posprop>=1.e-5){ 
 Total number of observations=%d <br>                probs[i][jk][j1]= prop[jk][i]/posprop;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>              } else{
 <hr  size=\"2\" color=\"#EC5E5E\">                if(first==1){
 <li>Outputs files<br><br>\n                  first=0;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
 - 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>              }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            } 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          }/* end jk */ 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        }/* end i */ 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      /*} *//* end i1 */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    } /* end j1 */
         - 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);    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
  fprintf(fichtm," <li>Graphs</li><p>");    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
  m=cptcoveff;  }  /* End of prevalence */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   /************* Waves Concatenation ***************/
  j1=0;  
  for(k1=1; k1<=m;k1++){  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)
    for(i1=1; i1<=ncodemax[k1];i1++){  {
        j1++;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        if (cptcovn > 0) {       Death is a valid wave (if date is known).
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
          for (cpt=1; cpt<=cptcoveff;cpt++)       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);       and mw[mi+1][i]. dh depends on stepm.
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       */
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    int i, mi, m;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        for(cpt=1; cpt<nlstate;cpt++){       double sum=0., jmean=0.;*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    int first;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    int j, k=0,jk, ju, jl;
        }    double sum=0.;
     for(cpt=1; cpt<=nlstate;cpt++) {    first=0;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    jmin=1e+5;
 interval) in state (%d): v%s%d%d.gif <br>    jmax=-1;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      jmean=0.;
      }    for(i=1; i<=imx; i++){
      for(cpt=1; cpt<=nlstate;cpt++) {      mi=0;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      m=firstpass;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      while(s[m][i] <= nlstate){
      }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          mw[++mi][i]=m;
 health expectancies in states (1) and (2): e%s%d.gif<br>        if(m >=lastpass)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          break;
 fprintf(fichtm,"\n</body>");        else
    }          m++;
  }      }/* end while */
 fclose(fichtm);      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
   /*--------------- Prevalence limit --------------*/        /* if(mi==0)  never been interviewed correctly before death */
             /* Only death is a correct wave */
   strcpy(filerespl,"pl");        mw[mi][i]=m;
   strcat(filerespl,fileres);      }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      wav[i]=mi;
   }      if(mi==0){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        nbwarn++;
   fprintf(ficrespl,"#Prevalence limit\n");        if(first==0){
   fprintf(ficrespl,"#Age ");          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          first=1;
   fprintf(ficrespl,"\n");        }
          if(first==1){
   prlim=matrix(1,nlstate,1,nlstate);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      } /* end mi==0 */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    } /* End individuals */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    for(i=1; i<=imx; i++){
   k=0;      for(mi=1; mi<wav[i];mi++){
   agebase=agemin;        if (stepm <=0)
   agelim=agemax;          dh[mi][i]=1;
   ftolpl=1.e-10;        else{
   i1=cptcoveff;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   if (cptcovn < 1){i1=1;}            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   for(cptcov=1;cptcov<=i1;cptcov++){              if(j==0) j=1;  /* Survives at least one month after exam */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              else if(j<0){
         k=k+1;                nberr++;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                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]);
         fprintf(ficrespl,"\n#******");                j=1; /* Temporary Dangerous patch */
         for(j=1;j<=cptcoveff;j++)                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                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(ficrespl,"******\n");                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                      }
         for (age=agebase; age<=agelim; age++){              k=k+1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              if (j >= jmax){
           fprintf(ficrespl,"%.0f",age );                jmax=j;
           for(i=1; i<=nlstate;i++)                ijmax=i;
           fprintf(ficrespl," %.5f", prlim[i][i]);              }
           fprintf(ficrespl,"\n");              if (j <= jmin){
         }                jmin=j;
       }                ijmin=i;
     }              }
   fclose(ficrespl);              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   /*------------- h Pij x at various ages ------------*/              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          else{
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   }  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   printf("Computing pij: result on file '%s' \n", filerespij);  
              k=k+1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;            if (j >= jmax) {
   /*if (stepm<=24) stepsize=2;*/              jmax=j;
               ijmax=i;
   agelim=AGESUP;            }
   hstepm=stepsize*YEARM; /* Every year of age */            else if (j <= jmin){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              jmin=j;
                ijmin=i;
   k=0;            }
   for(cptcov=1;cptcov<=i1;cptcov++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            /*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]);*/
       k=k+1;            if(j<0){
         fprintf(ficrespij,"\n#****** ");              nberr++;
         for(j=1;j<=cptcoveff;j++)              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              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]);
         fprintf(ficrespij,"******\n");            }
                    sum=sum+j;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          jk= j/stepm;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          jl= j -jk*stepm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ju= j -(jk+1)*stepm;
           oldm=oldms;savm=savms;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              if(jl==0){
           fprintf(ficrespij,"# Age");              dh[mi][i]=jk;
           for(i=1; i<=nlstate;i++)              bh[mi][i]=0;
             for(j=1; j<=nlstate+ndeath;j++)            }else{ /* We want a negative bias in order to only have interpolation ie
               fprintf(ficrespij," %1d-%1d",i,j);                    * to avoid the price of an extra matrix product in likelihood */
           fprintf(ficrespij,"\n");              dh[mi][i]=jk+1;
           for (h=0; h<=nhstepm; h++){              bh[mi][i]=ju;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            }
             for(i=1; i<=nlstate;i++)          }else{
               for(j=1; j<=nlstate+ndeath;j++)            if(jl <= -ju){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              dh[mi][i]=jk;
             fprintf(ficrespij,"\n");              bh[mi][i]=jl;       /* bias is positive if real duration
           }                                   * is higher than the multiple of stepm and negative otherwise.
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                   */
           fprintf(ficrespij,"\n");            }
         }            else{
     }              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
             }
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
   fclose(ficrespij);              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);*/
   exit(0);            }
   /*---------- Forecasting ------------------*/          } /* end if mle */
         }
   strcpy(fileresf,"f");      } /* end wave */
   strcat(fileresf,fileres);    }
   if((ficresf=fopen(fileresf,"w"))==NULL) {    jmean=sum/k;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   }    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   printf("Computing forecasting: result on file '%s' \n", fileresf);   }
   
   /* Mobile average */  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   /* for (agedeb=bage; agedeb<=fage; agedeb++)  {
     for (i=1; i<=nlstate;i++)    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++)    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       printf("%f %d i=%d j1=%d\n", probs[(int)agedeb][i][cptcod],(int) agedeb,i,cptcod);*/    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /* nbcode[Tvar[j]][1]= 
     */
   mobaverage= ma3x(1,130 ,1,8, 1,8);  
   for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     for (i=1; i<=nlstate;i++)    int modmaxcovj=0; /* Modality max of covariates j */
       for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    int cptcode=0; /* Modality max of covariates j */
         mobaverage[(int)agedeb][i][cptcod]=0.;    int modmincovj=0; /* Modality min of covariates j */
    
   for (agedeb=bage+4; agedeb<=fage; agedeb++){  
     for (i=1; i<=nlstate;i++){    cptcoveff=0; 
       for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   
         for (cpt=0;cpt<=4;cpt++){    for (k=-1; k < maxncov; k++) Ndum[k]=0;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    /* Loop on covariates without age and products */
       }    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     }      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   }                                 modality of this covariate Vj*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual 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);*/                                      * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   if (stepm<=24) stepsize=2;                                        modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
   agelim=AGESUP;          modmaxcovj=ij; 
   hstepm=stepsize*YEARM; /* Every year of age */        else if (ij < modmincovj) 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          modmincovj=ij; 
   hstepm=12;        if ((ij < -1) && (ij > NCOVMAX)){
    k=0;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   for(cptcov=1;cptcov<=i1;cptcov++){          exit(1);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }else
       k=k+1;        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       fprintf(ficresf,"\n#****** ");        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       for(j=1;j<=cptcoveff;j++) {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* getting the maximum value of the modality of the covariate
       }           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                 female is 1, then modmaxcovj=1.*/
       fprintf(ficresf,"******\n");      }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");      cptcode=modmaxcovj;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
      /*for (i=0; i<=cptcode; i++) {*/
       for (agedeb=fage; agedeb>=bage; agedeb--){      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
         for(j=1; j<=nlstate;j++)        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           fprintf(ficresf,"%.3f ",mobaverage[(int)agedeb][j][cptcod]);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
       }        }
       for(j=1; j<=ndeath;j++) fprintf(ficresf,"0.");        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       for (cpt=1; cpt<=8;cpt++)        } /* Ndum[-1] number of undefined modalities */
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
              /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
         /*printf("stepm=%d hstepm=%d nhstepm=%d \n",stepm,hstepm,nhstepm);*/         modmincovj=3; modmaxcovj = 7;
          There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
         oldm=oldms;savm=savms;         variables V1_1 and V1_2.
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           nbcode[Tvar[j]][ij]=k;
                         nbcode[Tvar[j]][1]=0;
         for (h=0; h<=nhstepm; h++){         nbcode[Tvar[j]][2]=1;
                 nbcode[Tvar[j]][3]=2;
           if (h*hstepm/YEARM*stepm==cpt)      */
  fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);      ij=1; /* ij is similar to i but can jumps over null modalities */
                for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
           for(j=1; j<=nlstate+ndeath;j++) {        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
             kk1=0.;          /*recode from 0 */
             for(i=1; i<=nlstate;i++) {                  if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
               /*   kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];*/            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];                                       k is a modality. If we have model=V1+V1*sex 
             }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                        ij++;
             if (h*hstepm/YEARM*stepm==cpt)          }
               fprintf(ficresf," %.5f ", kk1);          if (ij > ncodemax[j]) break; 
           }        }  /* end of loop on */
           }      } /* end of loop on modality */ 
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
         }    
       }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     }    
   fclose(ficresf);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   /*---------- Health expectancies and variances ------------*/     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; 
   strcpy(filerest,"t");   } 
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {   ij=1;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   }     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   printf("Computing Total LEs with variances: file '%s' \n", filerest);     if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
   strcpy(filerese,"e");       ij++;
   strcat(filerese,fileres);     }else
   if((ficreseij=fopen(filerese,"w"))==NULL) {         Tvaraff[ij]=0;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);   }
   }   ij--;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);   cptcoveff=ij; /*Number of total covariates*/
   
  strcpy(fileresv,"v");  }
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  /*********** Health Expectancies ****************/
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
   k=0;  {
   for(cptcov=1;cptcov<=i1;cptcov++){    /* Health expectancies, no variances */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       k=k+1;    int nhstepma, nstepma; /* Decreasing with age */
       fprintf(ficrest,"\n#****** ");    double age, agelim, hf;
       for(j=1;j<=cptcoveff;j++)    double ***p3mat;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double eip;
       fprintf(ficrest,"******\n");  
     pstamp(ficreseij);
       fprintf(ficreseij,"\n#****** ");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       for(j=1;j<=cptcoveff;j++)    fprintf(ficreseij,"# Age");
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    for(i=1; i<=nlstate;i++){
       fprintf(ficreseij,"******\n");      for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       fprintf(ficresvij,"\n#****** ");      }
       for(j=1;j<=cptcoveff;j++)      fprintf(ficreseij," e%1d. ",i);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }
       fprintf(ficresvij,"******\n");    fprintf(ficreseij,"\n");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    
       oldm=oldms;savm=savms;    if(estepm < stepm){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        printf ("Problem %d lower than %d\n",estepm, stepm);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;    else  hstepm=estepm;   
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /* We compute the life expectancy from trapezoids spaced every estepm months
           * This is mainly to measure the difference between two models: for example
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");     * if stepm=24 months pijx are given only every 2 years and by summing them
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficrest,"\n");     * progression in between and thus overestimating or underestimating according
             * to the curvature of the survival function. If, for the same date, we 
       hf=1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       if (stepm >= YEARM) hf=stepm/YEARM;     * to compare the new estimate of Life expectancy with the same linear 
       epj=vector(1,nlstate+1);     * hypothesis. A more precise result, taking into account a more precise
       for(age=bage; age <=fage ;age++){     * curvature will be obtained if estepm is as small as stepm. */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         fprintf(ficrest," %.0f",age);    /* For example we decided to compute the life expectancy with the smallest unit */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       nhstepm is the number of hstepm from age to agelim 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];       nstepm is the number of stepm from age to agelin. 
           }       Look at hpijx to understand the reason of that which relies in memory size
           epj[nlstate+1] +=epj[j];       and note for a fixed period like estepm months */
         }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         for(i=1, vepp=0.;i <=nlstate;i++)       survival function given by stepm (the optimization length). Unfortunately it
           for(j=1;j <=nlstate;j++)       means that if the survival funtion is printed only each two years of age and if
             vepp += vareij[i][j][(int)age];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));       results. So we changed our mind and took the option of the best precision.
         for(j=1;j <=nlstate;j++){    */
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         }  
         fprintf(ficrest,"\n");    agelim=AGESUP;
       }    /* If stepm=6 months */
     }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
              
          /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  fclose(ficreseij);    /* if (stepm >= YEARM) hstepm=1;*/
  fclose(ficresvij);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fclose(ficrest);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    for (age=bage; age<=fage; age ++){ 
   /*  scanf("%d ",i); */      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /*------- Variance limit prevalence------*/        /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
 strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);      /* If stepm=6 months */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     exit(0);      
   }      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  k=0;      
  for(cptcov=1;cptcov<=i1;cptcov++){      printf("%d|",(int)age);fflush(stdout);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      k=k+1;      
      fprintf(ficresvpl,"\n#****** ");      /* Computing expectancies */
      for(j=1;j<=cptcoveff;j++)      for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate;j++)
      fprintf(ficresvpl,"******\n");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);            
      oldm=oldms;savm=savms;            /* 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]);*/
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }          }
  }  
       fprintf(ficreseij,"%3.0f",age );
   fclose(ficresvpl);      for(i=1; i<=nlstate;i++){
         eip=0;
   /*---------- End : free ----------------*/        for(j=1; j<=nlstate;j++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          eip +=eij[i][j][(int)age];
            fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        fprintf(ficreseij,"%9.4f", eip );
        }
        fprintf(ficreseij,"\n");
   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_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    printf("\n");
      fprintf(ficlog,"\n");
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);  }
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  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[] )
   
   printf("End of Imach\n");  {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /* Covariances of health expectancies eij and of total life expectancies according
       to initial status i, ei. .
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    */
   /*printf("Total time was %d uSec.\n", total_usecs);*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   /*------ End -----------*/    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
  end:    double **dnewm,**doldm;
 #ifdef windows    double *xp, *xm;
  chdir(pathcd);    double **gp, **gm;
 #endif    double ***gradg, ***trgradg;
      int theta;
  system("..\\gp37mgw\\wgnuplot graph.plt");  
     double eip, vip;
 #ifdef windows  
   while (z[0] != 'q') {    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     chdir(pathcd);    xp=vector(1,npar);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    xm=vector(1,npar);
     scanf("%s",z);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     if (z[0] == 'c') system("./imach");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     else if (z[0] == 'e') {    
       chdir(path);    pstamp(ficresstdeij);
       system(optionfilehtm);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     }    fprintf(ficresstdeij,"# Age");
     else if (z[0] == 'q') exit(0);    for(i=1; i<=nlstate;i++){
   }      for(j=1; j<=nlstate;j++)
 #endif        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
 }      fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 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, first2;
     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+1];
     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; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*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#");    
         }
         
         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 (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           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]]];
           
       
           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);
   
           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++;
               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++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 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 */
         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);
         
         /* 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;first2=2;
         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) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d 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. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d 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. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* 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 size 320, 240");
                       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=pow(2,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%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.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%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.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=pow(2,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 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        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 size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 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 lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 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 size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 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 lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 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 size 320, 240\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 size 320, 240\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");
           }
         }
       }
      }
     /*goto avoid;*/
      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 size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      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 size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* 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]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(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 */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; 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--;
             cutl(stre,strb,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 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,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 */
             cutl(strc,strb,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*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=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 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* 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);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     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) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     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 guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* 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,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* 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;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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);  
           /*
            */
           /* goto endfree; */
    
           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; /* Segmentation fault */
             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,NCOVMAX,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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.13  
changed lines
  Added in v.1.146


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