Diff for /imach/src/imach.c between versions 1.7 and 1.148

version 1.7, 2001/05/02 17:50:24 version 1.148, 2014/06/17 17:38:48
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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 1.148  2014/06/17 17:38:48  brouard
   individuals from different ages are interviewed on their health status    Summary: Nothing new
   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    Just a new packaging for OS/X version 0.98nS
   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 1.147  2014/06/16 10:33:11  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    *** empty log message ***
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.146  2014/06/16 10:20:28  brouard
   to be observed in state i at the first wave. Therefore the model is:    Summary: Merge
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Author: Brouard
   is a covariate. If you want to have a more complex model than "constant and  
   age", you should modify the program where the markup    Merge, before building revised version.
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
   The advantage that this computer programme claims, comes from that if the    Author: Nicolas Brouard
   delay between waves is not identical for each individual, or if some  
   individual missed an interview, the information is not rounded or lost, but    Lot of changes in order to output the results with some covariates
   taken into account using an interpolation or extrapolation.    After the Edimburgh REVES conference 2014, it seems mandatory to
   hPijx is the probability to be    improve the code.
   observed in state i at age x+h conditional to the observed state i at age    No more memory valgrind error but a lot has to be done in order to
   x. The delay 'h' can be split into an exact number (nh*stepm) of    continue the work of splitting the code into subroutines.
   unobserved intermediate  states. This elementary transition (by month or    Also, decodemodel has been improved. Tricode is still not
   quarter trimester, semester or year) is model as a multinomial logistic.    optimal. nbcode should be improved. Documentation has been added in
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    the source code.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.143  2014/01/26 09:45:38  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   of the life expectancies. It also computes the prevalence limits.  
      * 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).    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.142  2014/01/26 03:57:36  brouard
   from the European Union.    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    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...
 #include <math.h>  
 #include <stdio.h>    Revision 1.140  2011/09/02 10:37:54  brouard
 #include <stdlib.h>    Summary: times.h is ok with mingw32 now.
 #include <unistd.h>  
     Revision 1.139  2010/06/14 07:50:17  brouard
 #define MAXLINE 256    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define FILENAMELENGTH 80    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 /*#define DEBUG*/  
 #define windows    Revision 1.138  2010/04/30 18:19:40  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    *** empty log message ***
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.137  2010/04/29 18:11:38  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): Checking covariates for more complex models
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    than V1+V2. A lot of change to be done. Unstable.
   
 #define NINTERVMAX 8    Revision 1.136  2010/04/26 20:30:53  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): merging some libgsl code. Fixing computation
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    of likelione (using inter/intrapolation if mle = 0) in order to
 #define NCOVMAX 8 /* Maximum number of covariates */    get same likelihood as if mle=1.
 #define MAXN 20000    Some cleaning of code and comments added.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.135  2009/10/29 15:33:14  brouard
 #define AGEBASE 40    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
     Revision 1.134  2009/10/29 13:18:53  brouard
 int nvar;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 static int cptcov;  
 int cptcovn, cptcovage=0, cptcoveff=0;    Revision 1.133  2009/07/06 10:21:25  brouard
 int npar=NPARMAX;    just nforces
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.132  2009/07/06 08:22:05  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Many tings
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.131  2009/06/20 16:22:47  brouard
 int maxwav; /* Maxim number of waves */    Some dimensions resccaled
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.130  2009/05/26 06:44:34  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Max Covariate is now set to 20 instead of 8. A
 double **oldm, **newm, **savm; /* Working pointers to matrices */    lot of cleaning with variables initialized to 0. Trying to make
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Revision 1.129  2007/08/31 13:49:27  lievre
 FILE *ficreseij;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.128  2006/06/30 13:02:05  brouard
   char fileresv[FILENAMELENGTH];    (Module): Clarifications on computing e.j
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 #define NR_END 1    imach-114 because nhstepm was no more computed in the age
 #define FREE_ARG char*    loop. Now we define nhstepma in the age loop.
 #define FTOL 1.0e-10    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 #define NRANSI    and then all the health expectancies with variances or standard
 #define ITMAX 200    deviation (needs data from the Hessian matrices) which slows the
     computation.
 #define TOL 2.0e-4    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.126  2006/04/28 17:23:28  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 #define GOLD 1.618034    loop. Now we define nhstepma in the age loop.
 #define GLIMIT 100.0    Version 0.98h
 #define TINY 1.0e-20  
     Revision 1.125  2006/04/04 15:20:31  lievre
 static double maxarg1,maxarg2;    Errors in calculation of health expectancies. Age was not initialized.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Forecasting file added.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.124  2006/03/22 17:13:53  lievre
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define rint(a) floor(a+0.5)    The log-likelihood is printed in the log file
   
 static double sqrarg;    Revision 1.123  2006/03/20 10:52:43  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * imach.c (Module): <title> changed, corresponds to .htm file
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    name. <head> headers where missing.
   
 int imx;    * imach.c (Module): Weights can have a decimal point as for
 int stepm;    English (a comma might work with a correct LC_NUMERIC environment,
 /* Stepm, step in month: minimum step interpolation*/    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 int m,nb;    1.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Version 0.98g
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij;    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 double *weight;    English (a comma might work with a correct LC_NUMERIC environment,
 int **s; /* Status */    otherwise the weight is truncated).
 double *agedc, **covar, idx;    Modification of warning when the covariates values are not 0 or
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    1.
     Version 0.98g
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    * imach.c (Module): refinements in the computation of lli if
 {    status=-2 in order to have more reliable computation if stepm is
    char *s;                             /* pointer */    not 1 month. Version 0.98f
    int  l1, l2;                         /* length counters */  
     Revision 1.120  2006/03/16 15:10:38  lievre
    l1 = strlen( path );                 /* length of path */    (Module): refinements in the computation of lli if
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    status=-2 in order to have more reliable computation if stepm is
    s = strrchr( path, '\\' );           /* find last / */    not 1 month. Version 0.98f
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.119  2006/03/15 17:42:26  brouard
       extern char       *getwd( );    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.118  2006/03/14 18:20:07  brouard
       extern char       *getcwd( );    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #endif    (Module): Function pstamp added
          return( GLOCK_ERROR_GETCWD );    (Module): Version 0.98d
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.117  2006/03/14 17:16:22  brouard
    } else {                             /* strip direcotry from path */    (Module): varevsij Comments added explaining the second
       s++;                              /* after this, the filename */    table of variances if popbased=1 .
       l2 = strlen( s );                 /* length of filename */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Function pstamp added
       strcpy( name, s );                /* save file name */    (Module): Version 0.98d
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.116  2006/03/06 10:29:27  brouard
    }    (Module): Variance-covariance wrong links and
    l1 = strlen( dirc );                 /* length of directory */    varian-covariance of ej. is needed (Saito).
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */    Revision 1.115  2006/02/27 12:17:45  brouard
 }    (Module): One freematrix added in mlikeli! 0.98c
   
     Revision 1.114  2006/02/26 12:57:58  brouard
 /******************************************/    (Module): Some improvements in processing parameter
     filename with strsep.
 void replace(char *s, char*t)  
 {    Revision 1.113  2006/02/24 14:20:24  brouard
   int i;    (Module): Memory leaks checks with valgrind and:
   int lg=20;    datafile was not closed, some imatrix were not freed and on matrix
   i=0;    allocation too.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.112  2006/01/30 09:55:26  brouard
     (s[i] = t[i]);    (Module): Back to gnuplot.exe instead of wgnuplot.exe
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.111  2006/01/25 20:38:18  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 int nbocc(char *s, char occ)    can be a simple dot '.'.
 {  
   int i,j=0;    Revision 1.110  2006/01/25 00:51:50  brouard
   int lg=20;    (Module): Lots of cleaning and bugs added (Gompertz)
   i=0;  
   lg=strlen(s);    Revision 1.109  2006/01/24 19:37:15  brouard
   for(i=0; i<= lg; i++) {    (Module): Comments (lines starting with a #) are allowed in data.
   if  (s[i] == occ ) j++;  
   }    Revision 1.108  2006/01/19 18:05:42  lievre
   return j;    Gnuplot problem appeared...
 }    To be fixed
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   int i,lg,j,p=0;  
   i=0;    Revision 1.106  2006/01/19 13:24:36  brouard
   for(j=0; j<=strlen(t)-1; j++) {    Some cleaning and links added in html output
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.104  2005/09/30 16:11:43  lievre
     (u[j] = t[j]);    (Module): sump fixed, loop imx fixed, and simplifications.
   }    (Module): If the status is missing at the last wave but we know
      u[p]='\0';    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
    for(j=0; j<= lg; j++) {    contributions to the likelihood is 1 - Prob of dying from last
     if (j>=(p+1))(v[j-p-1] = t[j]);    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   }    the healthy state at last known wave). Version is 0.98
 }  
     Revision 1.103  2005/09/30 15:54:49  lievre
 /********************** nrerror ********************/    (Module): sump fixed, loop imx fixed, and simplifications.
   
 void nrerror(char error_text[])    Revision 1.102  2004/09/15 17:31:30  brouard
 {    Add the possibility to read data file including tab characters.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.101  2004/09/15 10:38:38  brouard
   exit(1);    Fix on curr_time
 }  
 /*********************** vector *******************/    Revision 1.100  2004/07/12 18:29:06  brouard
 double *vector(int nl, int nh)    Add version for Mac OS X. Just define UNIX in Makefile
 {  
   double *v;    Revision 1.99  2004/06/05 08:57:40  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    *** empty log message ***
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.98  2004/05/16 15:05:56  brouard
 }    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 /************************ free vector ******************/    state at each age, but using a Gompertz model: log u =a + b*age .
 void free_vector(double*v, int nl, int nh)    This is the basic analysis of mortality and should be done before any
 {    other analysis, in order to test if the mortality estimated from the
   free((FREE_ARG)(v+nl-NR_END));    cross-longitudinal survey is different from the mortality estimated
 }    from other sources like vital statistic data.
   
 /************************ivector *******************************/    The same imach parameter file can be used but the option for mle should be -3.
 int *ivector(long nl,long nh)  
 {    Agnès, who wrote this part of the code, tried to keep most of the
   int *v;    former routines in order to include the new code within the former code.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    The output is very simple: only an estimate of the intercept and of
   return v-nl+NR_END;    the slope with 95% confident intervals.
 }  
     Current limitations:
 /******************free ivector **************************/    A) Even if you enter covariates, i.e. with the
 void free_ivector(int *v, long nl, long nh)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 {    B) There is no computation of Life Expectancy nor Life Table.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 /******************* imatrix *******************************/    suppressed.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.96  2003/07/15 15:38:55  brouard
 {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    rewritten within the same printf. Workaround: many printfs.
   int **m;  
      Revision 1.95  2003/07/08 07:54:34  brouard
   /* allocate pointers to rows */    * imach.c (Repository):
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Repository): Using imachwizard code to output a more meaningful covariance
   if (!m) nrerror("allocation failure 1 in matrix()");    matrix (cov(a12,c31) instead of numbers.
   m += NR_END;  
   m -= nrl;    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
    
   /* allocate rows and set pointers to them */    Revision 1.93  2003/06/25 16:33:55  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Module): On windows (cygwin) function asctime_r doesn't
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    exist so I changed back to asctime which exists.
   m[nrl] += NR_END;    (Module): Version 0.96b
   m[nrl] -= ncl;  
      Revision 1.92  2003/06/25 16:30:45  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): On windows (cygwin) function asctime_r doesn't
      exist so I changed back to asctime which exists.
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.91  2003/06/25 15:30:29  brouard
 }    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 /****************** free_imatrix *************************/    helps to forecast when convergence will be reached. Elapsed time
 void free_imatrix(m,nrl,nrh,ncl,nch)    is stamped in powell.  We created a new html file for the graphs
       int **m;    concerning matrix of covariance. It has extension -cov.htm.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    mle=-1 a template is output in file "or"mypar.txt with the design
   free((FREE_ARG) (m+nrl-NR_END));    of the covariance matrix to be input.
 }  
     Revision 1.89  2003/06/24 12:30:52  brouard
 /******************* matrix *******************************/    (Module): Some bugs corrected for windows. Also, when
 double **matrix(long nrl, long nrh, long ncl, long nch)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    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.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.87  2003/06/18 12:26:01  brouard
   m += NR_END;    Version 0.96
   m -= nrl;  
     Revision 1.86  2003/06/17 20:04:08  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Change position of html and gnuplot routines and added
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    routine fileappend.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    current date of interview. It may happen when the death was just
   return m;    prior to the death. In this case, dh was negative and likelihood
 }    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 /*************************free matrix ************************/    interview.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    memory allocation. But we also truncated to 8 characters (left
   free((FREE_ARG)(m+nrl-NR_END));    truncation)
 }    (Repository): No more line truncation errors.
   
 /******************* ma3x *******************************/    Revision 1.84  2003/06/13 21:44:43  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    many times. Probs is memory consuming and must be used with
   double ***m;    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.83  2003/06/10 13:39:11  lievre
   m += NR_END;    *** empty log message ***
   m -= nrl;  
     Revision 1.82  2003/06/05 15:57:20  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Add log in  imach.c and  fullversion number is now printed.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  */
   m[nrl] -= ncl;  /*
      Interpolated Markov Chain
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Short summary of the programme:
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    This program computes Healthy Life Expectancies from
   m[nrl][ncl] += NR_END;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m[nrl][ncl] -= nll;    first survey ("cross") where individuals from different ages are
   for (j=ncl+1; j<=nch; j++)    interviewed on their health status or degree of disability (in the
     m[nrl][j]=m[nrl][j-1]+nlay;    case of a health survey which is our main interest) -2- at least a
      second wave of interviews ("longitudinal") which measure each change
   for (i=nrl+1; i<=nrh; i++) {    (if any) in individual health status.  Health expectancies are
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    computed from the time spent in each health state according to a
     for (j=ncl+1; j<=nch; j++)    model. More health states you consider, more time is necessary to reach the
       m[i][j]=m[i][j-1]+nlay;    Maximum Likelihood of the parameters involved in the model.  The
   }    simplest model is the multinomial logistic model where pij is the
   return m;    probability 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: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /*************************free ma3x ************************/    'age' is age and 'sex' is a covariate. If you want to have a more
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    you to do it.  More covariates you add, slower the
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    convergence.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 /***************** f1dim *************************/    identical for each individual. Also, if a individual missed an
 extern int ncom;    intermediate interview, the information is lost, but taken into
 extern double *pcom,*xicom;    account using an interpolation or extrapolation.  
 extern double (*nrfunc)(double []);  
      hPijx is the probability to be observed in state i at age x+h
 double f1dim(double x)    conditional to the observed state i at age x. The delay 'h' can be
 {    split into an exact number (nh*stepm) of unobserved intermediate
   int j;    states. This elementary transition (by month, quarter,
   double f;    semester or year) is modelled as a multinomial logistic.  The hPx
   double *xt;    matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
   xt=vector(1,ncom);    hPijx.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Also this programme outputs the covariance matrix of the parameters but also
   free_vector(xt,1,ncom);    of the life expectancies. It also computes the period (stable) prevalence. 
   return f;    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /*****************brent *************************/    This software have been partly granted by Euro-REVES, a concerted action
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    from the European Union.
 {    It is copyrighted identically to a GNU software product, ie programme and
   int iter;    software can be distributed freely for non commercial use. Latest version
   double a,b,d,etemp;    can be accessed at http://euroreves.ined.fr/imach .
   double fu,fv,fw,fx;  
   double ftemp;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   double p,q,r,tol1,tol2,u,v,w,x,xm;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   double e=0.0;    
      **********************************************************************/
   a=(ax < cx ? ax : cx);  /*
   b=(ax > cx ? ax : cx);    main
   x=w=v=bx;    read parameterfile
   fw=fv=fx=(*f)(x);    read datafile
   for (iter=1;iter<=ITMAX;iter++) {    concatwav
     xm=0.5*(a+b);    freqsummary
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if (mle >= 1)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      mlikeli
     printf(".");fflush(stdout);    print results files
 #ifdef DEBUG    if mle==1 
     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);       computes hessian
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    read end of parameter file: agemin, agemax, bage, fage, estepm
 #endif        begin-prev-date,...
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    open gnuplot file
       *xmin=x;    open html file
       return fx;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
     }     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     ftemp=fu;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     if (fabs(e) > tol1) {      freexexit2 possible for memory heap.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    h Pij x                         | pij_nom  ficrestpij
       p=(x-v)*q-(x-w)*r;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       q=2.0*(q-r);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       if (q > 0.0) p = -p;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       q=fabs(q);  
       etemp=e;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       e=d;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
         d=CGOLD*(e=(x >= xm ? a-x : b-x));     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       else {     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
         d=p/q;  
         u=x+d;    forecasting if prevfcast==1 prevforecast call prevalence()
         if (u-a < tol2 || b-u < tol2)    health expectancies
           d=SIGN(tol1,xm-x);    Variance-covariance of DFLE
       }    prevalence()
     } else {     movingaverage()
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    varevsij() 
     }    if popbased==1 varevsij(,popbased)
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    total life expectancies
     fu=(*f)(u);    Variance of period (stable) prevalence
     if (fu <= fx) {   end
       if (u >= x) a=x; else b=x;  */
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  
         } else {  
           if (u < x) a=u; else b=u;   
           if (fu <= fw || w == x) {  #include <math.h>
             v=w;  #include <stdio.h>
             w=u;  #include <stdlib.h>
             fv=fw;  #include <string.h>
             fw=fu;  #include <unistd.h>
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  #include <limits.h>
             fv=fu;  #include <sys/types.h>
           }  #include <sys/stat.h>
         }  #include <errno.h>
   }  extern int errno;
   nrerror("Too many iterations in brent");  
   *xmin=x;  #ifdef LINUX
   return fx;  #include <time.h>
 }  #include "timeval.h"
   #else
 /****************** mnbrak ***********************/  #include <sys/time.h>
   #endif
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  #ifdef GSL
 {  #include <gsl/gsl_errno.h>
   double ulim,u,r,q, dum;  #include <gsl/gsl_multimin.h>
   double fu;  #endif
    
   *fa=(*func)(*ax);  /* #include <libintl.h> */
   *fb=(*func)(*bx);  /* #define _(String) gettext (String) */
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       SHFT(dum,*fb,*fa,dum)  
       }  #define GNUPLOTPROGRAM "gnuplot"
   *cx=(*bx)+GOLD*(*bx-*ax);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   *fc=(*func)(*cx);  #define FILENAMELENGTH 132
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     q=(*bx-*cx)*(*fb-*fa);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  #define NINTERVMAX 8
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       fu=(*func)(u);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       if (fu < *fc) {  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
           SHFT(*fb,*fc,fu,(*func)(u))  #define MAXN 20000
           }  #define YEARM 12. /**< Number of months per year */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define AGESUP 130
       u=ulim;  #define AGEBASE 40
       fu=(*func)(u);  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
     } else {  #ifdef UNIX
       u=(*cx)+GOLD*(*cx-*bx);  #define DIRSEPARATOR '/'
       fu=(*func)(u);  #define CHARSEPARATOR "/"
     }  #define ODIRSEPARATOR '\\'
     SHFT(*ax,*bx,*cx,u)  #else
       SHFT(*fa,*fb,*fc,fu)  #define DIRSEPARATOR '\\'
       }  #define CHARSEPARATOR "\\"
 }  #define ODIRSEPARATOR '/'
   #endif
 /*************** linmin ************************/  
   /* $Id$ */
 int ncom;  /* $State$ */
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  char version[]="Imach version 0.98nS, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
    char fullversion[]="$Revision$ $Date$"; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char strstart[80];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double brent(double ax, double bx, double cx,  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
                double (*f)(double), double tol, double *xmin);  int nvar=0, nforce=0; /* Number of variables, number of forces */
   double f1dim(double x);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
               double *fc, double (*func)(double));  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   int j;  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   double xx,xmin,bx,ax;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   double fx,fb,fa;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
    int cptcoveff=0; /* Total number of covariates to vary for printing results */
   ncom=n;  int cptcov=0; /* Working variable */
   pcom=vector(1,n);  int npar=NPARMAX;
   xicom=vector(1,n);  int nlstate=2; /* Number of live states */
   nrfunc=func;  int ndeath=1; /* Number of dead states */
   for (j=1;j<=n;j++) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     pcom[j]=p[j];  int popbased=0;
     xicom[j]=xi[j];  
   }  int *wav; /* Number of waves for this individuual 0 is possible */
   ax=0.0;  int maxwav=0; /* Maxim number of waves */
   xx=1.0;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
 #ifdef DEBUG                     to the likelihood and the sum of weights (done by funcone)*/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int mle=1, weightopt=0;
 #endif  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   for (j=1;j<=n;j++) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     xi[j] *= xmin;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     p[j] += xi[j];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   }  double jmean=1; /* Mean space between 2 waves */
   free_vector(xicom,1,n);  double **matprod2(); /* test */
   free_vector(pcom,1,n);  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   /*FILE *fic ; */ /* Used in readdata only */
 /*************** powell ************************/  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  FILE *ficlog, *ficrespow;
             double (*func)(double []))  int globpr=0; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   void linmin(double p[], double xi[], int n, double *fret,  long ipmx=0; /* Number of contributions */
               double (*func)(double []));  double sw; /* Sum of weights */
   int i,ibig,j;  char filerespow[FILENAMELENGTH];
   double del,t,*pt,*ptt,*xit;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double fp,fptt;  FILE *ficresilk;
   double *xits;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   pt=vector(1,n);  FILE *ficresprobmorprev;
   ptt=vector(1,n);  FILE *fichtm, *fichtmcov; /* Html File */
   xit=vector(1,n);  FILE *ficreseij;
   xits=vector(1,n);  char filerese[FILENAMELENGTH];
   *fret=(*func)(p);  FILE *ficresstdeij;
   for (j=1;j<=n;j++) pt[j]=p[j];  char fileresstde[FILENAMELENGTH];
   for (*iter=1;;++(*iter)) {  FILE *ficrescveij;
     fp=(*fret);  char filerescve[FILENAMELENGTH];
     ibig=0;  FILE  *ficresvij;
     del=0.0;  char fileresv[FILENAMELENGTH];
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  FILE  *ficresvpl;
     for (i=1;i<=n;i++)  char fileresvpl[FILENAMELENGTH];
       printf(" %d %.12f",i, p[i]);  char title[MAXLINE];
     printf("\n");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     for (i=1;i<=n;i++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       fptt=(*fret);  char command[FILENAMELENGTH];
 #ifdef DEBUG  int  outcmd=0;
       printf("fret=%lf \n",*fret);  
 #endif  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  char filelog[FILENAMELENGTH]; /* Log file */
       if (fabs(fptt-(*fret)) > del) {  char filerest[FILENAMELENGTH];
         del=fabs(fptt-(*fret));  char fileregp[FILENAMELENGTH];
         ibig=i;  char popfile[FILENAMELENGTH];
       }  
 #ifdef DEBUG  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  struct timezone tzp;
         printf(" x(%d)=%.12e",j,xit[j]);  extern int gettimeofday();
       }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       for(j=1;j<=n;j++)  long time_value;
         printf(" p=%.12e",p[j]);  extern long time();
       printf("\n");  char strcurr[80], strfor[80];
 #endif  
     }  char *endptr;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  long lval;
 #ifdef DEBUG  double dval;
       int k[2],l;  
       k[0]=1;  #define NR_END 1
       k[1]=-1;  #define FREE_ARG char*
       printf("Max: %.12e",(*func)(p));  #define FTOL 1.0e-10
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  #define NRANSI 
       printf("\n");  #define ITMAX 200 
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  #define TOL 2.0e-4 
           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]);  #define CGOLD 0.3819660 
         }  #define ZEPS 1.0e-10 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       }  
 #endif  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   #define TINY 1.0e-20 
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  static double maxarg1,maxarg2;
       free_vector(ptt,1,n);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       free_vector(pt,1,n);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       return;    
     }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define rint(a) floor(a+0.5)
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  static double sqrarg;
       xit[j]=p[j]-pt[j];  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       pt[j]=p[j];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     }  int agegomp= AGEGOMP;
     fptt=(*func)(ptt);  
     if (fptt < fp) {  int imx; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int stepm=1;
       if (t < 0.0) {  /* Stepm, step in month: minimum step interpolation*/
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  int estepm;
           xi[j][ibig]=xi[j][n];  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
           xi[j][n]=xit[j];  
         }  int m,nb;
 #ifdef DEBUG  long *num;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         for(j=1;j<=n;j++)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
           printf(" %.12e",xit[j]);  double **pmmij, ***probs;
         printf("\n");  double *ageexmed,*agecens;
 #endif  double dateintmean=0;
       }  
     }  double *weight;
   }  int **s; /* Status */
 }  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 /**** Prevalence limit ****************/                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double  idx; 
 {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int *Ndum; /** Freq of modality (tricode */
      matrix by transitions matrix until convergence is reached */  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   int i, ii,j,k;  double *lsurv, *lpop, *tpop;
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double **out, cov[NCOVMAX], **pmij();  double ftolhess; /**< Tolerance for computing hessian */
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for (ii=1;ii<=nlstate+ndeath;ii++)  {
     for (j=1;j<=nlstate+ndeath;j++){    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     }    */ 
     char  *ss;                            /* pointer */
    cov[1]=1.;    int   l1, l2;                         /* length counters */
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    l1 = strlen(path );                   /* length of path */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     newm=savm;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     /* Covariates have to be included here again */    if ( ss == NULL ) {                   /* no directory, so determine current directory */
      cov[2]=agefin;      strcpy( name, path );               /* we got the fullname name because no directory */
        /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       for (k=1; k<=cptcovn;k++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      /* get current working directory */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      /*    extern  char* getcwd ( char *buf , int len);*/
       }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       for (k=1; k<=cptcovage;k++)        return( GLOCK_ERROR_GETCWD );
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      }
       for (k=1; k<=cptcovprod;k++)      /* got dirc from getcwd*/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      ss++;                               /* after this, the filename */
       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';
   for(i=1; i<= nlstate; i++){    return s;
      s1=0;  }
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for(j=i+1; j<=nlstate+ndeath; j++)  {
       s1+=exp(ps[i][j]);    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     ps[i][i]=1./(s1+1.);       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     for(j=1; j<i; j++)       gives blocc="abcdef2ghi" and alocc="j".
       ps[i][j]= exp(ps[i][j])*ps[i][i];       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     for(j=i+1; j<=nlstate+ndeath; j++)    */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    char *s, *t, *bl;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    t=in;s=in;
   } /* end i */    while ((*in != occ) && (*in != '\0')){
       *alocc++ = *in++;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    }
     for(jj=1; jj<= nlstate+ndeath; jj++){    if( *in == occ){
       ps[ii][jj]=0;      *(alocc)='\0';
       ps[ii][ii]=1;      s=++in;
     }    }
   }   
     if (s == t) {/* occ not found */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      *(alocc-(in-s))='\0';
     for(jj=1; jj<= nlstate+ndeath; jj++){      in=s;
      printf("%lf ",ps[ii][jj]);    }
    }    while ( *in != '\0'){
     printf("\n ");      *blocc++ = *in++;
     }    }
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*    *blocc='\0';
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    return t;
   goto end;*/  }
     return ps;  char *cutv(char *blocc, char *alocc, char *in, char occ)
 }  {
     /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
 /**************** Product of 2 matrices ******************/       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
 {    */
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    char *s, *t;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    t=in;s=in;
   /* in, b, out are matrice of pointers which should have been initialized    while (*in != '\0'){
      before: only the contents of out is modified. The function returns      while( *in == occ){
      a pointer to pointers identical to out */        *blocc++ = *in++;
   long i, j, k;        s=in;
   for(i=nrl; i<= nrh; i++)      }
     for(k=ncolol; k<=ncoloh; k++)      *blocc++ = *in++;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    }
         out[i][k] +=in[i][j]*b[j][k];    if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
   return out;    else
 }      *(blocc-(in-s)-1)='\0';
     in=s;
     while ( *in != '\0'){
 /************* Higher Matrix Product ***************/      *alocc++ = *in++;
     }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {    *alocc='\0';
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    return s;
      duration (i.e. until  }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  int nbocc(char *s, char occ)
      (typically every 2 years instead of every month which is too big).  {
      Model is determined by parameters x and covariates have to be    int i,j=0;
      included manually here.    int lg=20;
     i=0;
      */    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   int i, j, d, h, k;    if  (s[i] == occ ) j++;
   double **out, cov[NCOVMAX];    }
   double **newm;    return j;
   }
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /* void cutv(char *u,char *v, char*t, char occ) */
     for (j=1;j<=nlstate+ndeath;j++){  /* { */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     }  /*      gives u="abcdef2ghi" and v="j" *\/ */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*   int i,lg,j,p=0; */
   for(h=1; h <=nhstepm; h++){  /*   i=0; */
     for(d=1; d <=hstepm; d++){  /*   lg=strlen(t); */
       newm=savm;  /*   for(j=0; j<=lg-1; j++) { */
       /* Covariates have to be included here again */  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       cov[1]=1.;  /*   } */
       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]]];  /*   for(j=0; j<p; j++) { */
 for (k=1; k<=cptcovage;k++)  /*     (u[j] = t[j]); */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*   } */
    for (k=1; k<=cptcovprod;k++)  /*      u[p]='\0'; */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /*   } */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /* } */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /********************** nrerror ********************/
       savm=oldm;  
       oldm=newm;  void nrerror(char error_text[])
     }  {
     for(i=1; i<=nlstate+ndeath; i++)    fprintf(stderr,"ERREUR ...\n");
       for(j=1;j<=nlstate+ndeath;j++) {    fprintf(stderr,"%s\n",error_text);
         po[i][j][h]=newm[i][j];    exit(EXIT_FAILURE);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  }
          */  /*********************** vector *******************/
       }  double *vector(int nl, int nh)
   } /* end h */  {
   return po;    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /*************** log-likelihood *************/  }
 double func( double *x)  
 {  /************************ free vector ******************/
   int i, ii, j, k, mi, d, kk;  void free_vector(double*v, int nl, int nh)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    free((FREE_ARG)(v+nl-NR_END));
   double sw; /* Sum of weights */  }
   double lli; /* Individual log likelihood */  
   long ipmx;  /************************ivector *******************************/
   /*extern weight */  int *ivector(long nl,long nh)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    int *v;
   /*for(i=1;i<imx;i++)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 printf(" %d\n",s[4][i]);    if (!v) nrerror("allocation failure in ivector");
   */    return v-nl+NR_END;
   cov[1]=1.;  }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /******************free ivector **************************/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  void free_ivector(int *v, long nl, long nh)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
        for(mi=1; mi<= wav[i]-1; mi++){    free((FREE_ARG)(v+nl-NR_END));
       for (ii=1;ii<=nlstate+ndeath;ii++)  }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
             for(d=0; d<dh[mi][i]; d++){  /************************lvector *******************************/
               newm=savm;  long *lvector(long nl,long nh)
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  {
               for (kk=1; kk<=cptcovage;kk++) {    long *v;
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
                  /*printf("%d %d",kk,Tage[kk]);*/    if (!v) nrerror("allocation failure in ivector");
               }    return v-nl+NR_END;
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/  }
               /*cov[3]=pow(cov[2],2)/1000.;*/  
   /******************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;
     m[nrl] -= ncl;
   hess=matrix(1,npar,1,npar);  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   printf("\nCalculation of the hessian matrix. Wait...\n");    return m;
   for (i=1;i<=npar;i++){    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     printf("%d",i);fflush(stdout);  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     hess[i][i]=hessii(p,ftolhess,i,delti);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     /*printf(" %f ",p[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];  }
       }  
     }  /******************* 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;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double ***m;
    
   a=matrix(1,npar,1,npar);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   y=matrix(1,npar,1,npar);    if (!m) nrerror("allocation failure 1 in matrix()");
   x=vector(1,npar);    m += NR_END;
   indx=ivector(1,npar);    m -= nrl;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   ludcmp(a,npar,indx,&pd);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   for (j=1;j<=npar;j++) {    m[nrl] -= ncl;
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       matcov[i][j]=x[i];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
   }    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   printf("\n#Hessian matrix#\n");      m[nrl][j]=m[nrl][j-1]+nlay;
   for (i=1;i<=npar;i++) {    
     for (j=1;j<=npar;j++) {    for (i=nrl+1; i<=nrh; i++) {
       printf("%.3e ",hess[i][j]);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
     printf("\n");        m[i][j]=m[i][j-1]+nlay;
   }    }
     return m; 
   /* Recompute Inverse */    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   for (i=1;i<=npar;i++)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    */
   ludcmp(a,npar,indx,&pd);  }
   
   /*  printf("\n#Hessian matrix recomputed#\n");  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   for (j=1;j<=npar;j++) {  {
     for (i=1;i<=npar;i++) x[i]=0;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     x[j]=1;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     lubksb(a,npar,indx,x);    free((FREE_ARG)(m+nrl-NR_END));
     for (i=1;i<=npar;i++){  }
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  /*************** function subdirf ***********/
     }  char *subdirf(char fileres[])
     printf("\n");  {
   }    /* Caution optionfilefiname is hidden */
   */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   free_matrix(a,1,npar,1,npar);    strcat(tmpout,fileres);
   free_matrix(y,1,npar,1,npar);    return tmpout;
   free_vector(x,1,npar);  }
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
   {
 }    
     /* Caution optionfilefiname is hidden */
 /*************** hessian matrix ****************/    strcpy(tmpout,optionfilefiname);
 double hessii( double x[], double delta, int theta, double delti[])    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   int i;    strcat(tmpout,fileres);
   int l=1, lmax=20;    return tmpout;
   double k1,k2;  }
   double p2[NPARMAX+1];  
   double res;  /*************** function subdirf3 ***********/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  char *subdirf3(char fileres[], char *preop, char *preop2)
   double fx;  {
   int k=0,kmax=10;    
   double l1;    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   fx=func(x);    strcat(tmpout,"/");
   for (i=1;i<=npar;i++) p2[i]=x[i];    strcat(tmpout,preop);
   for(l=0 ; l <=lmax; l++){    strcat(tmpout,preop2);
     l1=pow(10,l);    strcat(tmpout,fileres);
     delts=delt;    return tmpout;
     for(k=1 ; k <kmax; k=k+1){  }
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  /***************** f1dim *************************/
       k1=func(p2)-fx;  extern int ncom; 
       p2[theta]=x[theta]-delt;  extern double *pcom,*xicom;
       k2=func(p2)-fx;  extern double (*nrfunc)(double []); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */   
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  double f1dim(double x) 
        { 
 #ifdef DEBUG    int j; 
       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 f;
 #endif    double *xt; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */   
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    xt=vector(1,ncom); 
         k=kmax;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    free_vector(xt,1,ncom); 
         k=kmax; l=lmax*10.;    return f; 
       }  } 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /*****************brent *************************/
       }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
   }    int iter; 
   delti[theta]=delts;    double a,b,d,etemp;
   return res;    double fu,fv,fw,fx;
      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); 
   int i;    b=(ax > cx ? ax : cx); 
   int l=1, l1, lmax=20;    x=w=v=bx; 
   double k1,k2,k3,k4,res,fx;    fw=fv=fx=(*f)(x); 
   double p2[NPARMAX+1];    for (iter=1;iter<=ITMAX;iter++) { 
   int k;      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   fx=func(x);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   for (k=1; k<=2; k++) {      printf(".");fflush(stdout);
     for (i=1;i<=npar;i++) p2[i]=x[i];      fprintf(ficlog,".");fflush(ficlog);
     p2[thetai]=x[thetai]+delti[thetai]/k;  #ifdef DEBUG
     p2[thetaj]=x[thetaj]+delti[thetaj]/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);
     k1=func(p2)-fx;      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);
        /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     p2[thetai]=x[thetai]+delti[thetai]/k;  #endif
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     k2=func(p2)-fx;        *xmin=x; 
          return fx; 
     p2[thetai]=x[thetai]-delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      ftemp=fu;
     k3=func(p2)-fx;      if (fabs(e) > tol1) { 
          r=(x-w)*(fx-fv); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        q=(x-v)*(fx-fw); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        p=(x-v)*q-(x-w)*r; 
     k4=func(p2)-fx;        q=2.0*(q-r); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        if (q > 0.0) p = -p; 
 #ifdef DEBUG        q=fabs(q); 
     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);        etemp=e; 
 #endif        e=d; 
   }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   return res;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 }        else { 
           d=p/q; 
 /************** Inverse of matrix **************/          u=x+d; 
 void ludcmp(double **a, int n, int *indx, double *d)          if (u-a < tol2 || b-u < tol2) 
 {            d=SIGN(tol1,xm-x); 
   int i,imax,j,k;        } 
   double big,dum,sum,temp;      } else { 
   double *vv;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
        } 
   vv=vector(1,n);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   *d=1.0;      fu=(*f)(u); 
   for (i=1;i<=n;i++) {      if (fu <= fx) { 
     big=0.0;        if (u >= x) a=x; else b=x; 
     for (j=1;j<=n;j++)        SHFT(v,w,x,u) 
       if ((temp=fabs(a[i][j])) > big) big=temp;          SHFT(fv,fw,fx,fu) 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          } else { 
     vv[i]=1.0/big;            if (u < x) a=u; else b=u; 
   }            if (fu <= fw || w == x) { 
   for (j=1;j<=n;j++) {              v=w; 
     for (i=1;i<j;i++) {              w=u; 
       sum=a[i][j];              fv=fw; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              fw=fu; 
       a[i][j]=sum;            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     big=0.0;              fv=fu; 
     for (i=j;i<=n;i++) {            } 
       sum=a[i][j];          } 
       for (k=1;k<j;k++)    } 
         sum -= a[i][k]*a[k][j];    nrerror("Too many iterations in brent"); 
       a[i][j]=sum;    *xmin=x; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    return fx; 
         big=dum;  } 
         imax=i;  
       }  /****************** mnbrak ***********************/
     }  
     if (j != imax) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       for (k=1;k<=n;k++) {              double (*func)(double)) 
         dum=a[imax][k];  { 
         a[imax][k]=a[j][k];    double ulim,u,r,q, dum;
         a[j][k]=dum;    double fu; 
       }   
       *d = -(*d);    *fa=(*func)(*ax); 
       vv[imax]=vv[j];    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
     indx[j]=imax;      SHFT(dum,*ax,*bx,dum) 
     if (a[j][j] == 0.0) a[j][j]=TINY;        SHFT(dum,*fb,*fa,dum) 
     if (j != n) {        } 
       dum=1.0/(a[j][j]);    *cx=(*bx)+GOLD*(*bx-*ax); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { 
   }      r=(*bx-*ax)*(*fb-*fc); 
   free_vector(vv,1,n);  /* Doesn't work */      q=(*bx-*cx)*(*fb-*fa); 
 ;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void lubksb(double **a, int n, int *indx, double b[])      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   int i,ii=0,ip,j;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double sum;        fu=(*func)(u); 
          if (fu < *fc) { 
   for (i=1;i<=n;i++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     ip=indx[i];            SHFT(*fb,*fc,fu,(*func)(u)) 
     sum=b[ip];            } 
     b[ip]=b[i];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     if (ii)        u=ulim; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        fu=(*func)(u); 
     else if (sum) ii=i;      } else { 
     b[i]=sum;        u=(*cx)+GOLD*(*cx-*bx); 
   }        fu=(*func)(u); 
   for (i=n;i>=1;i--) {      } 
     sum=b[i];      SHFT(*ax,*bx,*cx,u) 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        SHFT(*fa,*fb,*fc,fu) 
     b[i]=sum/a[i][i];        } 
   }  } 
 }  
   /*************** linmin ************************/
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  int ncom; 
 {  /* Some frequencies */  double *pcom,*xicom;
    double (*nrfunc)(double []); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;   
   double ***freq; /* Frequencies */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double *pp;  { 
   double pos;    double brent(double ax, double bx, double cx, 
   FILE *ficresp;                 double (*f)(double), double tol, double *xmin); 
   char fileresp[FILENAMELENGTH];    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   pp=vector(1,nlstate);                double *fc, double (*func)(double)); 
     int j; 
   strcpy(fileresp,"p");    double xx,xmin,bx,ax; 
   strcat(fileresp,fileres);    double fx,fb,fa;
   if((ficresp=fopen(fileresp,"w"))==NULL) {   
     printf("Problem with prevalence resultfile: %s\n", fileresp);    ncom=n; 
     exit(0);    pcom=vector(1,n); 
   }    xicom=vector(1,n); 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    nrfunc=func; 
   j1=0;    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   j=cptcoveff;      xicom[j]=xi[j]; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    } 
     ax=0.0; 
   for(k1=1; k1<=j;k1++){    xx=1.0; 
    for(i1=1; i1<=ncodemax[k1];i1++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
        j1++;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
         for (i=-1; i<=nlstate+ndeath; i++)      printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
          for (jk=-1; jk<=nlstate+ndeath; jk++)      fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
            for(m=agemin; m <= agemax+3; m++)  #endif
              freq[i][jk][m]=0;    for (j=1;j<=n;j++) { 
              xi[j] *= xmin; 
        for (i=1; i<=imx; i++) {      p[j] += xi[j]; 
          bool=1;    } 
          if  (cptcovn>0) {    free_vector(xicom,1,n); 
            for (z1=1; z1<=cptcoveff; z1++)    free_vector(pcom,1,n); 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;  } 
          }  
           if (bool==1) {  char *asc_diff_time(long time_sec, char ascdiff[])
            for(m=firstpass; m<=lastpass-1; m++){  {
              if(agev[m][i]==0) agev[m][i]=agemax+1;    long sec_left, days, hours, minutes;
              if(agev[m][i]==1) agev[m][i]=agemax+2;    days = (time_sec) / (60*60*24);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    sec_left = (time_sec) % (60*60*24);
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    hours = (sec_left) / (60*60) ;
            }    sec_left = (sec_left) %(60*60);
          }    minutes = (sec_left) /60;
        }    sec_left = (sec_left) % (60);
         if  (cptcovn>0) {    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
          fprintf(ficresp, "\n#********** Variable ");    return ascdiff;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
        }  
        fprintf(ficresp, "**********\n#");  /*************** powell ************************/
        for(i=1; i<=nlstate;i++)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              double (*func)(double [])) 
        fprintf(ficresp, "\n");  { 
            void linmin(double p[], double xi[], int n, double *fret, 
   for(i=(int)agemin; i <= (int)agemax+3; i++){                double (*func)(double [])); 
     if(i==(int)agemax+3)    int i,ibig,j; 
       printf("Total");    double del,t,*pt,*ptt,*xit;
     else    double fp,fptt;
       printf("Age %d", i);    double *xits;
     for(jk=1; jk <=nlstate ; jk++){    int niterf, itmp;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
         pp[jk] += freq[jk][m][i];    pt=vector(1,n); 
     }    ptt=vector(1,n); 
     for(jk=1; jk <=nlstate ; jk++){    xit=vector(1,n); 
       for(m=-1, pos=0; m <=0 ; m++)    xits=vector(1,n); 
         pos += freq[jk][m][i];    *fret=(*func)(p); 
       if(pp[jk]>=1.e-10)    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for (*iter=1;;++(*iter)) { 
       else      fp=(*fret); 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      ibig=0; 
     }      del=0.0; 
     for(jk=1; jk <=nlstate ; jk++){      last_time=curr_time;
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)      (void) gettimeofday(&curr_time,&tzp);
         pp[jk] += freq[jk][m][i];      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
     for(jk=1,pos=0; jk <=nlstate ; jk++)  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       pos += pp[jk];     for (i=1;i<=n;i++) {
     for(jk=1; jk <=nlstate ; jk++){        printf(" %d %.12f",i, p[i]);
       if(pos>=1.e-5)        fprintf(ficlog," %d %.12lf",i, p[i]);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        fprintf(ficrespow," %.12lf", p[i]);
       else      }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      printf("\n");
       if( i <= (int) agemax){      fprintf(ficlog,"\n");
         if(pos>=1.e-5)      fprintf(ficrespow,"\n");fflush(ficrespow);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      if(*iter <=3){
       else        tm = *localtime(&curr_time.tv_sec);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        strcpy(strcurr,asctime(&tm));
       }  /*       asctime_r(&tm,strcurr); */
     }        forecast_time=curr_time; 
     for(jk=-1; jk <=nlstate+ndeath; jk++)        itmp = strlen(strcurr);
       for(m=-1; m <=nlstate+ndeath; m++)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          strcurr[itmp-1]='\0';
     if(i <= (int) agemax)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       fprintf(ficresp,"\n");        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     printf("\n");        for(niterf=10;niterf<=30;niterf+=10){
     }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     }          tmf = *localtime(&forecast_time.tv_sec);
  }  /*      asctime_r(&tmf,strfor); */
            strcpy(strfor,asctime(&tmf));
   fclose(ficresp);          itmp = strlen(strfor);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          if(strfor[itmp-1]=='\n')
   free_vector(pp,1,nlstate);          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);
 }  /* End of Freq */          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);
         }
 /************* Waves Concatenation ***************/      }
       for (i=1;i<=n;i++) { 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 {        fptt=(*fret); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  #ifdef DEBUG
      Death is a valid wave (if date is known).        printf("fret=%lf \n",*fret);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        fprintf(ficlog,"fret=%lf \n",*fret);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  #endif
      and mw[mi+1][i]. dh depends on stepm.        printf("%d",i);fflush(stdout);
      */        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
   int i, mi, m;        if (fabs(fptt-(*fret)) > del) { 
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          del=fabs(fptt-(*fret)); 
 float sum=0.;          ibig=i; 
         } 
   for(i=1; i<=imx; i++){  #ifdef DEBUG
     mi=0;        printf("%d %.12e",i,(*fret));
     m=firstpass;        fprintf(ficlog,"%d %.12e",i,(*fret));
     while(s[m][i] <= nlstate){        for (j=1;j<=n;j++) {
       if(s[m][i]>=1)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         mw[++mi][i]=m;          printf(" x(%d)=%.12e",j,xit[j]);
       if(m >=lastpass)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         break;        }
       else        for(j=1;j<=n;j++) {
         m++;          printf(" p=%.12e",p[j]);
     }/* end while */          fprintf(ficlog," p=%.12e",p[j]);
     if (s[m][i] > nlstate){        }
       mi++;     /* Death is another wave */        printf("\n");
       /* if(mi==0)  never been interviewed correctly before death */        fprintf(ficlog,"\n");
          /* Only death is a correct wave */  #endif
       mw[mi][i]=m;      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
     wav[i]=mi;        int k[2],l;
     if(mi==0)        k[0]=1;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        k[1]=-1;
   }        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   for(i=1; i<=imx; i++){        for (j=1;j<=n;j++) {
     for(mi=1; mi<wav[i];mi++){          printf(" %.12e",p[j]);
       if (stepm <=0)          fprintf(ficlog," %.12e",p[j]);
         dh[mi][i]=1;        }
       else{        printf("\n");
         if (s[mw[mi+1][i]][i] > nlstate) {        fprintf(ficlog,"\n");
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for(l=0;l<=1;l++) {
           if(j=0) j=1;  /* Survives at least one month after exam */          for (j=1;j<=n;j++) {
         }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         else{            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           k=k+1;          }
           if (j >= jmax) jmax=j;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           else if (j <= jmin)jmin=j;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           sum=sum+j;        }
         }  #endif
         jk= j/stepm;  
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;        free_vector(xit,1,n); 
         if(jl <= -ju)        free_vector(xits,1,n); 
           dh[mi][i]=jk;        free_vector(ptt,1,n); 
         else        free_vector(pt,1,n); 
           dh[mi][i]=jk+1;        return; 
         if(dh[mi][i]==0)      } 
           dh[mi][i]=1; /* At least one step */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       }      for (j=1;j<=n;j++) { 
     }        ptt[j]=2.0*p[j]-pt[j]; 
   }        xit[j]=p[j]-pt[j]; 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);        pt[j]=p[j]; 
 }      } 
 /*********** Tricode ****************************/      fptt=(*func)(ptt); 
 void tricode(int *Tvar, int **nbcode, int imx)      if (fptt < fp) { 
 {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   int Ndum[20],ij=1, k, j, i;        if (t < 0.0) { 
   int cptcode=0;          linmin(p,xit,n,fret,func); 
   cptcoveff=0;          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; 
   for (k=0; k<19; k++) Ndum[k]=0;            xi[j][n]=xit[j]; 
   for (k=1; k<=7; k++) ncodemax[k]=0;          }
   #ifdef DEBUG
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (i=1; i<=imx; i++) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       ij=(int)(covar[Tvar[j]][i]);          for(j=1;j<=n;j++){
       Ndum[ij]++;            printf(" %.12e",xit[j]);
       if (ij > cptcode) cptcode=ij;            fprintf(ficlog," %.12e",xit[j]);
     }          }
           printf("\n");
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/          fprintf(ficlog,"\n");
     for (i=0; i<=cptcode; i++) {  #endif
       if(Ndum[i]!=0) ncodemax[j]++;        }
     }      } 
     ij=1;    } 
   } 
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  /**** Prevalence limit (stable or period prevalence)  ****************/
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/  {
           ij++;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         }       matrix by transitions matrix until convergence is reached */
         if (ij > ncodemax[j]) break;  
       }      int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
   }      /* double **matprod2(); */ /* test */
  for (i=1; i<=10; i++) {    double **out, cov[NCOVMAX+1], **pmij();
       ij=Tvar[i];    double **newm;
       Ndum[ij]++;    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
  ij=1;    for (ii=1;ii<=nlstate+ndeath;ii++)
  for (i=1; i<=cptcovn; i++) {      for (j=1;j<=nlstate+ndeath;j++){
    if((Ndum[i]!=0) && (i<=ncov)){        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      Tvaraff[i]=ij;      }
    ij++;  
    }     cov[1]=1.;
  }   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];      newm=savm;
    /*printf("j=%d %d\n",j,Tvar[j]);*/      /* Covariates have to be included here again */
  }      cov[2]=agefin;
        
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);      for (k=1; k<=cptcovn;k++) {
     scanf("%d",i);*/        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]]);*/
       }
 /*********** Health Expectancies ****************/      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
 {      
   /* Health expectancies */      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   int i, j, nhstepm, hstepm, h;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double age, agelim,hf;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double ***p3mat;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
        /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   fprintf(ficreseij,"# Health expectancies\n");      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   fprintf(ficreseij,"# Age");      
   for(i=1; i<=nlstate;i++)      savm=oldm;
     for(j=1; j<=nlstate;j++)      oldm=newm;
       fprintf(ficreseij," %1d-%1d",i,j);      maxmax=0.;
   fprintf(ficreseij,"\n");      for(j=1;j<=nlstate;j++){
         min=1.;
   hstepm=1*YEARM; /*  Every j years of age (in month) */        max=0.;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   agelim=AGESUP;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          prlim[i][j]= newm[i][j]/(1-sumnew);
     /* nhstepm age range expressed in number of stepm */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          max=FMAX(max,prlim[i][j]);
     /* Typically if 20 years = 20*12/6=40 stepm */          min=FMIN(min,prlim[i][j]);
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        maxmin=max-min;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        maxmax=FMAX(maxmax,maxmin);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      if(maxmax < ftolpl){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          return prlim;
       }
     }
     for(i=1; i<=nlstate;i++)  }
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  /*************** transition probabilities ***************/ 
           eij[i][j][(int)age] +=p3mat[i][j][h];  
         }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      {
     hf=1;    /* According to parameters values stored in x and the covariate's values stored in cov,
     if (stepm >= YEARM) hf=stepm/YEARM;       computes the probability to be observed in state j being in state i by appying the
     fprintf(ficreseij,"%.0f",age );       model to the ncovmodel covariates (including constant and age).
     for(i=1; i<=nlstate;i++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
       for(j=1; j<=nlstate;j++){       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);       ncth covariate in the global vector x is given by the formula:
       }       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     fprintf(ficreseij,"\n");       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   }       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
 }       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]
 /************ Variance ******************/    */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    double s1, lnpijopii;
 {    /*double t34;*/
   /* Variance of health expectancies */    int i,j,j1, nc, ii, jj;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;      for(i=1; i<= nlstate; i++){
   double **dnewm,**doldm;        for(j=1; j<i;j++){
   int i, j, nhstepm, hstepm, h;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   int k, cptcode;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
    double *xp;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   double **gp, **gm;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   double ***gradg, ***trgradg;          }
   double ***p3mat;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   double age,agelim;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   int theta;        }
         for(j=i+1; j<=nlstate+ndeath;j++){
    fprintf(ficresvij,"# Covariances of life expectancies\n");          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   fprintf(ficresvij,"# Age");            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   for(i=1; i<=nlstate;i++)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     for(j=1; j<=nlstate;j++)  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }
   fprintf(ficresvij,"\n");          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate,1,npar);      
   doldm=matrix(1,nlstate,1,nlstate);      for(i=1; i<= nlstate; i++){
          s1=0;
   hstepm=1*YEARM; /* Every year of age */        for(j=1; j<i; j++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   agelim = AGESUP;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(j=i+1; j<=nlstate+ndeath; j++){
     if (stepm >= YEARM) hstepm=1;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     gp=matrix(0,nhstepm,1,nlstate);        ps[i][i]=1./(s1+1.);
     gm=matrix(0,nhstepm,1,nlstate);        /* Computing other pijs */
         for(j=1; j<i; j++)
     for(theta=1; theta <=npar; theta++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(j=i+1; j<=nlstate+ndeath; j++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          ps[i][j]= exp(ps[i][j])*ps[i][i];
       }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } /* end i */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      
       for(j=1; j<= nlstate; j++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(h=0; h<=nhstepm; h++){        for(jj=1; jj<= nlstate+ndeath; jj++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          ps[ii][jj]=0;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          ps[ii][ii]=1;
         }        }
       }      }
          
       for(i=1; i<=npar; i++) /* Computes gradient */      
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       for(j=1; j<= nlstate; j++){      /*   } */
         for(h=0; h<=nhstepm; h++){      /*   printf("\n "); */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      /* } */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      /* printf("\n ");printf("%lf ",cov[2]);*/
         }      /*
       }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for(j=1; j<= nlstate; j++)        goto end;*/
         for(h=0; h<=nhstepm; h++){      return ps;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  
     } /* End theta */  /**************** Product of 2 matrices ******************/
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   {
     for(h=0; h<=nhstepm; h++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for(j=1; j<=nlstate;j++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         for(theta=1; theta <=npar; theta++)    /* in, b, out are matrice of pointers which should have been initialized 
           trgradg[h][j][theta]=gradg[h][theta][j];       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     for(i=1;i<=nlstate;i++)    int i, j, k;
       for(j=1;j<=nlstate;j++)    for(i=nrl; i<= nrh; i++)
         vareij[i][j][(int)age] =0.;      for(k=ncolol; k<=ncoloh; k++){
     for(h=0;h<=nhstepm;h++){        out[i][k]=0.;
       for(k=0;k<=nhstepm;k++){        for(j=ncl; j<=nch; j++)
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          out[i][k] +=in[i][j]*b[j][k];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      }
         for(i=1;i<=nlstate;i++)    return out;
           for(j=1;j<=nlstate;j++)  }
             vareij[i][j][(int)age] += doldm[i][j];  
       }  
     }  /************* Higher Matrix Product ***************/
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     fprintf(ficresvij,"%.0f ",age );  {
     for(i=1; i<=nlstate;i++)    /* Computes the transition matrix starting at age 'age' over 
       for(j=1; j<=nlstate;j++){       'nhstepm*hstepm*stepm' months (i.e. until
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       }       nhstepm*hstepm matrices. 
     fprintf(ficresvij,"\n");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     free_matrix(gp,0,nhstepm,1,nlstate);       (typically every 2 years instead of every month which is too big 
     free_matrix(gm,0,nhstepm,1,nlstate);       for the memory).
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);       Model is determined by parameters x and covariates have to be 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);       included manually here. 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */       */
    
   free_vector(xp,1,npar);    int i, j, d, h, k;
   free_matrix(doldm,1,nlstate,1,npar);    double **out, cov[NCOVMAX+1];
   free_matrix(dnewm,1,nlstate,1,nlstate);    double **newm;
   
 }    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
 /************ Variance of prevlim ******************/      for (j=1;j<=nlstate+ndeath;j++){
 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)        oldm[i][j]=(i==j ? 1.0 : 0.0);
 {        po[i][j][0]=(i==j ? 1.0 : 0.0);
   /* Variance of prevalence limit */      }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double **newm;    for(h=1; h <=nhstepm; h++){
   double **dnewm,**doldm;      for(d=1; d <=hstepm; d++){
   int i, j, nhstepm, hstepm;        newm=savm;
   int k, cptcode;        /* Covariates have to be included here again */
   double *xp;        cov[1]=1.;
   double *gp, *gm;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double **gradg, **trgradg;        for (k=1; k<=cptcovn;k++) 
   double age,agelim;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int theta;        for (k=1; k<=cptcovage;k++)
              cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   fprintf(ficresvpl,"# Age");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   xp=vector(1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   dnewm=matrix(1,nlstate,1,npar);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   doldm=matrix(1,nlstate,1,nlstate);        savm=oldm;
          oldm=newm;
   hstepm=1*YEARM; /* Every year of age */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(i=1; i<=nlstate+ndeath; i++)
   agelim = AGESUP;        for(j=1;j<=nlstate+ndeath;j++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          po[i][j][h]=newm[i][j];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /*printf("h=%d ",h);*/
     gradg=matrix(1,npar,1,nlstate);    } /* end h */
     gp=vector(1,nlstate);  /*     printf("\n H=%d \n",h); */
     gm=vector(1,nlstate);    return po;
   }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*************** log-likelihood *************/
       }  double func( double *x)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    int i, ii, j, k, mi, d, kk;
         gp[i] = prlim[i][i];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
        double **out;
       for(i=1; i<=npar; i++) /* Computes gradient */    double sw; /* Sum of weights */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double lli; /* Individual log likelihood */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int s1, s2;
       for(i=1;i<=nlstate;i++)    double bbh, survp;
         gm[i] = prlim[i][i];    long ipmx;
     /*extern weight */
       for(i=1;i<=nlstate;i++)    /* We are differentiating ll according to initial status */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     } /* End theta */    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     trgradg =matrix(1,nlstate,1,npar);    */
     cov[1]=1.;
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         trgradg[j][theta]=gradg[theta][j];  
     if(mle==1){
     for(i=1;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       varpl[i][(int)age] =0.;        /* Computes the values of the ncovmodel covariates of the model
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
     for(i=1;i<=nlstate;i++)           to be observed in j being in i according to the model.
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */         */
         for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     fprintf(ficresvpl,"%.0f ",age );          cov[2+k]=covar[Tvar[k]][i];
     for(i=1; i<=nlstate;i++)        }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     fprintf(ficresvpl,"\n");           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     free_vector(gp,1,nlstate);           has been calculated etc */
     free_vector(gm,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
     free_matrix(gradg,1,npar,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_matrix(trgradg,1,nlstate,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   } /* End age */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);            }
   free_matrix(doldm,1,nlstate,1,npar);          for(d=0; d<dh[mi][i]; d++){
   free_matrix(dnewm,1,nlstate,1,nlstate);            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]; /* Tage[kk] gives the data-covariate associated with age */
             }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /***********************************************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /**************** Main Program *****************/            savm=oldm;
 /***********************************************/            oldm=newm;
           } /* end mult */
 /*int main(int argc, char *argv[])*/        
 int main()          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 {          /* But now since version 0.9 we anticipate for bias at large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double agedeb, agefin,hf;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double agemin=1.e20, agemax=-1.e20;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double fret;           * probability in order to take into account the bias as a fraction of the way
   double **xi,tmp,delta;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   double dum; /* Dummy variable */           * For stepm=1 the results are the same as for previous versions of Imach.
   double ***p3mat;           * For stepm > 1 the results are less biased than in previous versions. 
   int *indx;           */
   char line[MAXLINE], linepar[MAXLINE];          s1=s[mw[mi][i]][i];
   char title[MAXLINE];          s2=s[mw[mi+1][i]][i];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          bbh=(double)bh[mi][i]/(double)stepm; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];          /* bias bh is positive if real duration
   char filerest[FILENAMELENGTH];           * is higher than the multiple of stepm and negative otherwise.
   char fileregp[FILENAMELENGTH];           */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int firstobs=1, lastobs=10;          if( s2 > nlstate){ 
   int sdeb, sfin; /* Status at beginning and end */            /* i.e. if s2 is a death state and if the date of death is known 
   int c,  h , cpt,l;               then the contribution to the likelihood is the probability to 
   int ju,jl, mi;               die between last step unit time and current  step unit time, 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;               which is also equal to probability to die before dh 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;               minus probability to die before dh-stepm . 
                 In version up to 0.92 likelihood was computed
   int hstepm, nhstepm;          as if date of death was unknown. Death was treated as any other
   double bage, fage, age, agelim, agebase;          health state: the date of the interview describes the actual state
   double ftolpl=FTOL;          and not the date of a change in health state. The former idea was
   double **prlim;          to consider that at each interview the state was recorded
   double *severity;          (healthy, disable or death) and IMaCh was corrected; but when we
   double ***param; /* Matrix of parameters */          introduced the exact date of death then we should have modified
   double  *p;          the contribution of an exact death to the likelihood. This new
   double **matcov; /* Matrix of covariance */          contribution is smaller and very dependent of the step unit
   double ***delti3; /* Scale */          stepm. It is no more the probability to die between last interview
   double *delti; /* Scale */          and month of death but the probability to survive from last
   double ***eij, ***vareij;          interview up to one month before death multiplied by the
   double **varpl; /* Variances of prevalence limits by age */          probability to die within a month. Thanks to Chris
   double *epj, vepp;          Jackson for correcting this bug.  Former versions increased
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";          mortality artificially. The bad side is that we add another loop
   char *alph[]={"a","a","b","c","d","e"}, str[4];          which slows down the processing. The difference can be up to 10%
           lower mortality.
   char z[1]="c", occ;            */
 #include <sys/time.h>            lli=log(out[s1][s2] - savm[s1][s2]);
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
   /* long total_usecs;          } else if  (s2==-2) {
   struct timeval start_time, end_time;            for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            /*survp += out[s1][j]; */
             lli= log(survp);
           }
   printf("\nIMACH, Version 0.64a");          
   printf("\nEnter the parameter file name: ");          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
 #ifdef windows              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   scanf("%s",pathtot);            lli= log(survp); 
   getcwd(pathcd, size);          } 
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          else if  (s2==-5) { 
   /* cutv(path,optionfile,pathtot,'\\');*/            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 split(pathtot, path,optionfile);            lli= log(survp); 
   chdir(path);          } 
   replace(pathc,path);          
 #endif          else{
 #ifdef unix            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   scanf("%s",optionfile);            /*  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 */
 #endif          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 /*-------- arguments in the command line --------*/          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   strcpy(fileres,"r");          ipmx +=1;
   strcat(fileres, optionfile);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*---------arguments file --------*/        } /* end of wave */
       } /* end of individual */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }  else if(mle==2){
     printf("Problem with optionfile %s\n",optionfile);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     goto end;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   strcpy(filereso,"o");            for (j=1;j<=nlstate+ndeath;j++){
   strcat(filereso,fileres);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficparo=fopen(filereso,"w"))==NULL) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            }
   }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
   /* Reads comments: lines beginning with '#' */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   while((c=getc(ficpar))=='#' && c!= EOF){            for (kk=1; kk<=cptcovage;kk++) {
     ungetc(c,ficpar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fgets(line, MAXLINE, ficpar);            }
     puts(line);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fputs(line,ficparo);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   ungetc(c,ficpar);            oldm=newm;
           } /* end mult */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          s1=s[mw[mi][i]][i];
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   covar=matrix(0,NCOVMAX,1,n);              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 (strlen(model)<=1) cptcovn=0;          ipmx +=1;
   else {          sw += weight[i];
     j=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     j=nbocc(model,'+');        } /* end of wave */
     cptcovn=j+1;      } /* end of individual */
   }    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   ncovmodel=2+cptcovn;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Read guess parameters */            for (j=1;j<=nlstate+ndeath;j++){
   /* Reads comments: lines beginning with '#' */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   while((c=getc(ficpar))=='#' && c!= EOF){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          for(d=0; d<dh[mi][i]; d++){
     puts(line);            newm=savm;
     fputs(line,ficparo);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   ungetc(c,ficpar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=1; i <=nlstate; i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(j=1; j <=nlstate+ndeath-1; j++){            savm=oldm;
       fscanf(ficpar,"%1d%1d",&i1,&j1);            oldm=newm;
       fprintf(ficparo,"%1d%1d",i1,j1);          } /* end mult */
       printf("%1d%1d",i,j);        
       for(k=1; k<=ncovmodel;k++){          s1=s[mw[mi][i]][i];
         fscanf(ficpar," %lf",&param[i][j][k]);          s2=s[mw[mi+1][i]][i];
         printf(" %lf",param[i][j][k]);          bbh=(double)bh[mi][i]/(double)stepm; 
         fprintf(ficparo," %lf",param[i][j][k]);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       }          ipmx +=1;
       fscanf(ficpar,"\n");          sw += weight[i];
       printf("\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficparo,"\n");        } /* end of wave */
     }      } /* end of individual */
      }else if (mle==4){  /* ml=4 no inter-extrapolation */
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   p=param[1][1];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   /* Reads comments: lines beginning with '#' */          for (ii=1;ii<=nlstate+ndeath;ii++)
   while((c=getc(ficpar))=='#' && c!= EOF){            for (j=1;j<=nlstate+ndeath;j++){
     ungetc(c,ficpar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fgets(line, MAXLINE, ficpar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     puts(line);            }
     fputs(line,ficparo);          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   ungetc(c,ficpar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            }
   for(i=1; i <=nlstate; i++){          
     for(j=1; j <=nlstate+ndeath-1; j++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fscanf(ficpar,"%1d%1d",&i1,&j1);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       printf("%1d%1d",i,j);            savm=oldm;
       fprintf(ficparo,"%1d%1d",i1,j1);            oldm=newm;
       for(k=1; k<=ncovmodel;k++){          } /* end mult */
         fscanf(ficpar,"%le",&delti3[i][j][k]);        
         printf(" %le",delti3[i][j][k]);          s1=s[mw[mi][i]][i];
         fprintf(ficparo," %le",delti3[i][j][k]);          s2=s[mw[mi+1][i]][i];
       }          if( s2 > nlstate){ 
       fscanf(ficpar,"\n");            lli=log(out[s1][s2] - savm[s1][s2]);
       printf("\n");          }else{
       fprintf(ficparo,"\n");            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     }          }
   }          ipmx +=1;
   delti=delti3[1][1];          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Reads comments: lines beginning with '#' */  /*      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]); */
   while((c=getc(ficpar))=='#' && c!= EOF){        } /* end of wave */
     ungetc(c,ficpar);      } /* end of individual */
     fgets(line, MAXLINE, ficpar);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     puts(line);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fputs(line,ficparo);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   ungetc(c,ficpar);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   matcov=matrix(1,npar,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i <=npar; i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fscanf(ficpar,"%s",&str);            }
     printf("%s",str);          for(d=0; d<dh[mi][i]; d++){
     fprintf(ficparo,"%s",str);            newm=savm;
     for(j=1; j <=i; j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fscanf(ficpar," %le",&matcov[i][j]);            for (kk=1; kk<=cptcovage;kk++) {
       printf(" %.5le",matcov[i][j]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fprintf(ficparo," %.5le",matcov[i][j]);            }
     }          
     fscanf(ficpar,"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     printf("\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficparo,"\n");            savm=oldm;
   }            oldm=newm;
   for(i=1; i <=npar; i++)          } /* end mult */
     for(j=i+1;j<=npar;j++)        
       matcov[i][j]=matcov[j][i];          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
   printf("\n");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
           sw += weight[i];
     /*-------- data file ----------*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if((ficres =fopen(fileres,"w"))==NULL) {          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       printf("Problem with resultfile: %s\n", fileres);goto end;        } /* end of wave */
     }      } /* end of individual */
     fprintf(ficres,"#%s\n",version);    } /* End of if */
        for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     if((fic=fopen(datafile,"r"))==NULL)    {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       printf("Problem with datafile: %s\n", datafile);goto end;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
   }
     n= lastobs;  
     severity = vector(1,maxwav);  /*************** log-likelihood *************/
     outcome=imatrix(1,maxwav+1,1,n);  double funcone( double *x)
     num=ivector(1,n);  {
     moisnais=vector(1,n);    /* Same as likeli but slower because of a lot of printf and if */
     annais=vector(1,n);    int i, ii, j, k, mi, d, kk;
     moisdc=vector(1,n);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     andc=vector(1,n);    double **out;
     agedc=vector(1,n);    double lli; /* Individual log likelihood */
     cod=ivector(1,n);    double llt;
     weight=vector(1,n);    int s1, s2;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double bbh, survp;
     mint=matrix(1,maxwav,1,n);    /*extern weight */
     anint=matrix(1,maxwav,1,n);    /* We are differentiating ll according to initial status */
     s=imatrix(1,maxwav+1,1,n);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     adl=imatrix(1,maxwav+1,1,n);        /*for(i=1;i<imx;i++) 
     tab=ivector(1,NCOVMAX);      printf(" %d\n",s[4][i]);
     ncodemax=ivector(1,8);    */
     cov[1]=1.;
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {    for(k=1; k<=nlstate; k++) ll[k]=0.;
       if ((i >= firstobs) && (i <=lastobs)) {  
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (j=maxwav;j>=1;j--){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      for(mi=1; mi<= wav[i]-1; mi++){
           strcpy(line,stra);        for (ii=1;ii<=nlstate+ndeath;ii++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (j=1;j<=nlstate+ndeath;j++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                  }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(d=0; d<dh[mi][i]; d++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          for (kk=1; kk<=cptcovage;kk++) {
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         for (j=ncov;j>=1;j--){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         num[i]=atol(stra);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
         /*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]));*/          oldm=newm;
         } /* end mult */
         i=i+1;        
       }        s1=s[mw[mi][i]][i];
     }        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
     /*scanf("%d",i);*/        /* bias is positive if real duration
   imx=i-1; /* Number of individuals */         * is higher than the multiple of stepm and negative otherwise.
          */
   /* Calculation of the number of parameter from char model*/        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   Tvar=ivector(1,15);          lli=log(out[s1][s2] - savm[s1][s2]);
   Tprod=ivector(1,15);        } else if  (s2==-2) {
   Tvaraff=ivector(1,15);          for (j=1,survp=0. ; j<=nlstate; j++) 
   Tvard=imatrix(1,15,1,2);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   Tage=ivector(1,15);                lli= log(survp);
            }else if (mle==1){
   if (strlen(model) >1){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     j=0, j1=0, k1=1, k2=1;        } else if(mle==2){
     j=nbocc(model,'+');          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 */
     j1=nbocc(model,'*');        } else if(mle==3){  /* exponential inter-extrapolation */
     cptcovn=j+1;          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 */
     cptcovprod=j1;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
              lli=log(out[s1][s2]); /* Original formula */
     strcpy(modelsav,model);        } else{  /* mle=0 back to 1 */
    if (j==0) {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       if (j1==0){          /*lli=log(out[s1][s2]); */ /* Original formula */
         cutv(stra,strb,modelsav,'V');        } /* End of if */
         Tvar[1]=atoi(strb);        ipmx +=1;
       }        sw += weight[i];
       else if (j1==1) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         cutv(stra,strb,modelsav,'*');        /*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]); */
         Tage[1]=1; cptcovage++;        if(globpr){
         if (strcmp(stra,"age")==0) {          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
           cptcovprod--;   %11.6f %11.6f %11.6f ", \
           cutv(strd,strc,strb,'V');                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           Tvar[1]=atoi(strc);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         else if (strcmp(strb,"age")==0) {            llt +=ll[k]*gipmx/gsw;
           cptcovprod--;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           cutv(strd,strc,stra,'V');          }
           Tvar[1]=atoi(strc);          fprintf(ficresilk," %10.6f\n", -llt);
         }        }
         else {      } /* end of wave */
           cutv(strd,strc,strb,'V');    } /* end of individual */
           cutv(stre,strd,stra,'V');    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           Tvar[1]=ncov+1;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           for (k=1; k<=lastobs;k++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];    if(globpr==0){ /* First time we count the contributions and weights */
         }      gipmx=ipmx;
         /*printf("%s %s %s\n", stra,strb,modelsav);      gsw=sw;
 printf("%d ",Tvar[1]);    }
 scanf("%d",i);*/    return -l;
       }  }
     }  
    else {  
       for(i=j; i>=1;i--){  /*************** function likelione ***********/
         cutv(stra,strb,modelsav,'+');  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         /*printf("%s %s %s\n", stra,strb,modelsav);  {
           scanf("%d",i);*/    /* This routine should help understanding what is done with 
         if (strchr(strb,'*')) {       the selection of individuals/waves and
           cutv(strd,strc,strb,'*');       to check the exact contribution to the likelihood.
           if (strcmp(strc,"age")==0) {       Plotting could be done.
             cptcovprod--;     */
             cutv(strb,stre,strd,'V');    int k;
             Tvar[i+1]=atoi(stre);  
             cptcovage++;    if(*globpri !=0){ /* Just counts and sums, no printings */
             Tage[cptcovage]=i+1;      strcpy(fileresilk,"ilk"); 
             printf("stre=%s ", stre);      strcat(fileresilk,fileres);
           }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           else if (strcmp(strd,"age")==0) {        printf("Problem with resultfile: %s\n", fileresilk);
             cptcovprod--;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
             cutv(strb,stre,strc,'V');      }
             Tvar[i+1]=atoi(stre);      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");
             cptcovage++;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
             Tage[cptcovage]=i+1;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
           }      for(k=1; k<=nlstate; k++) 
           else {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
             cutv(strb,stre,strc,'V');      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
             Tvar[i+1]=ncov+k1;    }
             cutv(strb,strc,strd,'V');  
             Tprod[k1]=i+1;    *fretone=(*funcone)(p);
             Tvard[k1][1]=atoi(strc);    if(*globpri !=0){
             Tvard[k1][2]=atoi(stre);      fclose(ficresilk);
             Tvar[cptcovn+k2]=Tvard[k1][1];      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
             Tvar[cptcovn+k2+1]=Tvard[k1][2];      fflush(fichtm); 
             for (k=1; k<=lastobs;k++)    } 
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    return;
             k1++;  }
             k2=k2+2;  
           }  
         }  /*********** Maximum Likelihood Estimation ***************/
         else {  
           cutv(strd,strc,strb,'V');  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           /* printf("%s %s %s", strd,strc,strb);*/  {
           Tvar[i+1]=atoi(strc);    int i,j, iter;
         }    double **xi;
         strcpy(modelsav,stra);      double fret;
       }    double fretone; /* Only one call to likelihood */
       cutv(strd,strc,stra,'V');    /*  char filerespow[FILENAMELENGTH];*/
       Tvar[1]=atoi(strc);    xi=matrix(1,npar,1,npar);
     }    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++)
   /* for (i=1; i<=5; i++)        xi[i][j]=(i==j ? 1.0 : 0.0);
      printf("i=%d %d ",i,Tvar[i]);*/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/    strcpy(filerespow,"pow"); 
  /*printf("cptcovprod=%d ", cptcovprod);*/    strcat(filerespow,fileres);
   /*  scanf("%d ",i);*/    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     fclose(fic);      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     /*  if(mle==1){*/    }
     if (weightopt != 1) { /* Maximisation without weights*/    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       for(i=1;i<=n;i++) weight[i]=1.0;    for (i=1;i<=nlstate;i++)
     }      for(j=1;j<=nlstate+ndeath;j++)
     /*-calculation of age at interview from date of interview and age at death -*/        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     agev=matrix(1,maxwav,1,imx);    fprintf(ficrespow,"\n");
      
     for (i=1; i<=imx; i++)  {    powell(p,xi,npar,ftol,&iter,&fret,func);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){    free_matrix(xi,1,npar,1,npar);
         if(s[m][i] >0){    fclose(ficrespow);
           if (s[m][i] == nlstate+1) {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
             if(agedc[i]>0)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
               agev[m][i]=agedc[i];  
             else{  }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;  /**** Computes Hessian and covariance matrix ***/
             }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           }  {
           else if(s[m][i] !=9){ /* Should no more exist */    double  **a,**y,*x,pd;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    double **hess;
             if(mint[m][i]==99 || anint[m][i]==9999)    int i, j,jk;
               agev[m][i]=1;    int *indx;
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
             }    void lubksb(double **a, int npar, int *indx, double b[]) ;
             else if(agev[m][i] >agemax){    void ludcmp(double **a, int npar, int *indx, double *d) ;
               agemax=agev[m][i];    double gompertz(double p[]);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    hess=matrix(1,npar,1,npar);
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/    printf("\nCalculation of the hessian matrix. Wait...\n");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           }    for (i=1;i<=npar;i++){
           else { /* =9 */      printf("%d",i);fflush(stdout);
             agev[m][i]=1;      fprintf(ficlog,"%d",i);fflush(ficlog);
             s[m][i]=-1;     
           }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         }      
         else /*= 0 Unknown */      /*  printf(" %f ",p[i]);
           agev[m][i]=1;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       }    }
        
     }    for (i=1;i<=npar;i++) {
     for (i=1; i<=imx; i++)  {      for (j=1;j<=npar;j++)  {
       for(m=1; (m<= maxwav); m++){        if (j>i) { 
         if (s[m][i] > (nlstate+ndeath)) {          printf(".%d%d",i,j);fflush(stdout);
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           goto end;          hess[i][j]=hessij(p,delti,i,j,func,npar);
         }          
       }          hess[j][i]=hess[i][j];    
     }          /*printf(" %lf ",hess[i][j]);*/
         }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      }
     }
     free_vector(severity,1,maxwav);    printf("\n");
     free_imatrix(outcome,1,maxwav+1,1,n);    fprintf(ficlog,"\n");
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_matrix(mint,1,maxwav,1,n);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_matrix(anint,1,maxwav,1,n);    
     free_vector(moisdc,1,n);    a=matrix(1,npar,1,npar);
     free_vector(andc,1,n);    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
        indx=ivector(1,npar);
     wav=ivector(1,imx);    for (i=1;i<=npar;i++)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    ludcmp(a,npar,indx,&pd);
      
     /* Concatenates waves */    for (j=1;j<=npar;j++) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       lubksb(a,npar,indx,x);
       Tcode=ivector(1,100);      for (i=1;i<=npar;i++){ 
       nbcode=imatrix(1,nvar,1,8);        matcov[i][j]=x[i];
       ncodemax[1]=1;      }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    }
        
    codtab=imatrix(1,100,1,10);    printf("\n#Hessian matrix#\n");
    h=0;    fprintf(ficlog,"\n#Hessian matrix#\n");
    m=pow(2,cptcoveff);    for (i=1;i<=npar;i++) { 
        for (j=1;j<=npar;j++) { 
    for(k=1;k<=cptcoveff; k++){        printf("%.3e ",hess[i][j]);
      for(i=1; i <=(m/pow(2,k));i++){        fprintf(ficlog,"%.3e ",hess[i][j]);
        for(j=1; j <= ncodemax[k]; j++){      }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      printf("\n");
            h++;      fprintf(ficlog,"\n");
            if (h>m) h=1;codtab[h][k]=j;    }
          }  
        }    /* Recompute Inverse */
      }    for (i=1;i<=npar;i++)
    }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   
    /*for(i=1; i <=m ;i++){    /*  printf("\n#Hessian matrix recomputed#\n");
      for(k=1; k <=cptcovn; k++){  
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    for (j=1;j<=npar;j++) {
      }      for (i=1;i<=npar;i++) x[i]=0;
      printf("\n");      x[j]=1;
    }      lubksb(a,npar,indx,x);
    scanf("%d",i);*/      for (i=1;i<=npar;i++){ 
            y[i][j]=x[i];
    /* Calculates basic frequencies. Computes observed prevalence at single age        printf("%.3e ",y[i][j]);
        and prints on file fileres'p'. */        fprintf(ficlog,"%.3e ",y[i][j]);
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);      }
       printf("\n");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"\n");
     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 */    free_matrix(a,1,npar,1,npar);
        free_matrix(y,1,npar,1,npar);
     /* For Powell, parameters are in a vector p[] starting at p[1]    free_vector(x,1,npar);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    free_ivector(indx,1,npar);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    free_matrix(hess,1,npar,1,npar);
   
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  }
     }  
      /*************** hessian matrix ****************/
     /*--------- results files --------------*/  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     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);  {
        int i;
    jk=1;    int l=1, lmax=20;
    fprintf(ficres,"# Parameters\n");    double k1,k2;
    printf("# Parameters\n");    double p2[MAXPARM+1]; /* identical to x */
    for(i=1,jk=1; i <=nlstate; i++){    double res;
      for(k=1; k <=(nlstate+ndeath); k++){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        if (k != i)    double fx;
          {    int k=0,kmax=10;
            printf("%d%d ",i,k);    double l1;
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    fx=func(x);
              printf("%f ",p[jk]);    for (i=1;i<=npar;i++) p2[i]=x[i];
              fprintf(ficres,"%f ",p[jk]);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
              jk++;      l1=pow(10,l);
            }      delts=delt;
            printf("\n");      for(k=1 ; k <kmax; k=k+1){
            fprintf(ficres,"\n");        delt = delta*(l1*k);
          }        p2[theta]=x[theta] +delt;
      }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
    }        p2[theta]=x[theta]-delt;
  if(mle==1){        k2=func(p2)-fx;
     /* Computing hessian and covariance matrix */        /*res= (k1-2.0*fx+k2)/delt/delt; */
     ftolhess=ftol; /* Usually correct */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     hesscov(matcov, p, npar, delti, ftolhess, func);        
  }  #ifdef DEBUGHESS
     fprintf(ficres,"# Scales\n");        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     printf("# Scales\n");        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);
      for(i=1,jk=1; i <=nlstate; i++){  #endif
       for(j=1; j <=nlstate+ndeath; j++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if (j!=i) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           fprintf(ficres,"%1d%1d",i,j);          k=kmax;
           printf("%1d%1d",i,j);        }
           for(k=1; k<=ncovmodel;k++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             printf(" %.5e",delti[jk]);          k=kmax; l=lmax*10.;
             fprintf(ficres," %.5e",delti[jk]);        }
             jk++;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           }          delts=delt;
           printf("\n");        }
           fprintf(ficres,"\n");      }
         }    }
       }    delti[theta]=delts;
       }    return res; 
        
     k=1;  }
     fprintf(ficres,"# Covariance\n");  
     printf("# Covariance\n");  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(i=1;i<=npar;i++){  {
       /*  if (k>nlstate) k=1;    int i;
       i1=(i-1)/(ncovmodel*nlstate)+1;    int l=1, l1, lmax=20;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double k1,k2,k3,k4,res,fx;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    double p2[MAXPARM+1];
       fprintf(ficres,"%3d",i);    int k;
       printf("%3d",i);  
       for(j=1; j<=i;j++){    fx=func(x);
         fprintf(ficres," %.5e",matcov[i][j]);    for (k=1; k<=2; k++) {
         printf(" %.5e",matcov[i][j]);      for (i=1;i<=npar;i++) p2[i]=x[i];
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
       fprintf(ficres,"\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       printf("\n");      k1=func(p2)-fx;
       k++;    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     while((c=getc(ficpar))=='#' && c!= EOF){      k2=func(p2)-fx;
       ungetc(c,ficpar);    
       fgets(line, MAXLINE, ficpar);      p2[thetai]=x[thetai]-delti[thetai]/k;
       puts(line);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fputs(line,ficparo);      k3=func(p2)-fx;
     }    
     ungetc(c,ficpar);      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      k4=func(p2)-fx;
          res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     if (fage <= 2) {  #ifdef DEBUG
       bage = agemin;      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);
       fage = agemax;      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);
     }  #endif
     }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    return res;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  }
   
      /************** Inverse of matrix **************/
 /*------------ gnuplot -------------*/  void ludcmp(double **a, int n, int *indx, double *d) 
 chdir(pathcd);  { 
   if((ficgp=fopen("graph.plt","w"))==NULL) {    int i,imax,j,k; 
     printf("Problem with file graph.gp");goto end;    double big,dum,sum,temp; 
   }    double *vv; 
 #ifdef windows   
   fprintf(ficgp,"cd \"%s\" \n",pathc);    vv=vector(1,n); 
 #endif    *d=1.0; 
 m=pow(2,cptcoveff);    for (i=1;i<=n;i++) { 
        big=0.0; 
  /* 1eme*/      for (j=1;j<=n;j++) 
   for (cpt=1; cpt<= nlstate ; cpt ++) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
    for (k1=1; k1<= m ; k1 ++) {      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
 #ifdef windows    } 
     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);    for (j=1;j<=n;j++) { 
 #endif      for (i=1;i<j;i++) { 
 #ifdef unix        sum=a[i][j]; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 #endif        a[i][j]=sum; 
       } 
 for (i=1; i<= nlstate ; i ++) {      big=0.0; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (i=j;i<=n;i++) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        sum=a[i][j]; 
 }        for (k=1;k<j;k++) 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          sum -= a[i][k]*a[k][j]; 
     for (i=1; i<= nlstate ; i ++) {        a[i][j]=sum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          big=dum; 
 }          imax=i; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        } 
      for (i=1; i<= nlstate ; i ++) {      } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      if (j != imax) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (k=1;k<=n;k++) { 
 }            dum=a[imax][k]; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          a[imax][k]=a[j][k]; 
 #ifdef unix          a[j][k]=dum; 
 fprintf(ficgp,"\nset ter gif small size 400,300");        } 
 #endif        *d = -(*d); 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        vv[imax]=vv[j]; 
    }      } 
   }      indx[j]=imax; 
   /*2 eme*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   for (k1=1; k1<= m ; k1 ++) {        dum=1.0/(a[j][j]); 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          } 
     for (i=1; i<= nlstate+1 ; i ++) {    } 
       k=2*i;    free_vector(vv,1,n);  /* Doesn't work */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  ;
       for (j=1; j<= nlstate+1 ; j ++) {  } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void lubksb(double **a, int n, int *indx, double b[]) 
 }    { 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    int i,ii=0,ip,j; 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double sum; 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);   
       for (j=1; j<= nlstate+1 ; j ++) {    for (i=1;i<=n;i++) { 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      ip=indx[i]; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");      sum=b[ip]; 
 }        b[ip]=b[i]; 
       fprintf(ficgp,"\" t\"\" w l 0,");      if (ii) 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for (j=1; j<= nlstate+1 ; j ++) {      else if (sum) ii=i; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      b[i]=sum; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } 
 }      for (i=n;i>=1;i--) { 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      sum=b[i]; 
       else fprintf(ficgp,"\" t\"\" w l 0,");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     }      b[i]=sum/a[i][i]; 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    } 
   }  } 
    
   /*3eme*/  void pstamp(FILE *fichier)
   {
   for (k1=1; k1<= m ; k1 ++) {    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     for (cpt=1; cpt<= nlstate ; cpt ++) {  }
       k=2+nlstate*(cpt-1);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  /************ Frequencies ********************/
       for (i=1; i< nlstate ; i ++) {  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
         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);  {  /* Some frequencies */
       }    
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int i, m, jk, k1,i1, j1, bool, z1,j;
     }    int first;
   }    double ***freq; /* Frequencies */
      double *pp, **prop;
   /* CV preval stat */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   for (k1=1; k1<= m ; k1 ++) {    char fileresp[FILENAMELENGTH];
     for (cpt=1; cpt<nlstate ; cpt ++) {    
       k=3;    pp=vector(1,nlstate);
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    prop=matrix(1,nlstate,iagemin,iagemax+3);
       for (i=1; i< nlstate ; i ++)    strcpy(fileresp,"p");
         fprintf(ficgp,"+$%d",k+i+1);    strcat(fileresp,fileres);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    if((ficresp=fopen(fileresp,"w"))==NULL) {
            printf("Problem with prevalence resultfile: %s\n", fileresp);
       l=3+(nlstate+ndeath)*cpt;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      exit(0);
       for (i=1; i< nlstate ; i ++) {    }
         l=3+(nlstate+ndeath)*cpt;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         fprintf(ficgp,"+$%d",l+i+1);    j1=0;
       }    
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      j=cptcoveff;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }  
   }    first=1;
   
   /* proba elementaires */    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
    for(i=1,jk=1; i <=nlstate; i++){    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
     for(k=1; k <=(nlstate+ndeath); k++){    /*    j1++;
       if (k != i) {  */
         for(j=1; j <=ncovmodel; j++){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           /*fprintf(ficgp,"%s",alph[1]);*/          scanf("%d", i);*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        for (i=-5; i<=nlstate+ndeath; i++)  
           jk++;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           fprintf(ficgp,"\n");            for(m=iagemin; m <= iagemax+3; m++)
         }              freq[i][jk][m]=0;
       }        
     }        for (i=1; i<=nlstate; i++)  
     }          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
   for(jk=1; jk <=m; jk++) {        
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        dateintsum=0;
    i=1;        k2cpt=0;
    for(k2=1; k2<=nlstate; k2++) {        for (i=1; i<=imx; i++) {
      k3=i;          bool=1;
      for(k=1; k<=(nlstate+ndeath); k++) {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
        if (k != k2){            for (z1=1; z1<=cptcoveff; z1++)       
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
 ij=1;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
         for(j=3; j <=ncovmodel; j++) {                bool=0;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                /* 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", 
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
             ij++;                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
           }                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
           else              } 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
         }   
           fprintf(ficgp,")/(1");          if (bool==1){
                    for(m=firstpass; m<=lastpass; m++){
         for(k1=1; k1 <=nlstate; k1++){                k2=anint[m][i]+(mint[m][i]/12.);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 ij=1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           for(j=3; j <=ncovmodel; j++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if (m<lastpass) {
             ij++;                  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];
           else                }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                
           }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           fprintf(ficgp,")");                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                /*}*/
         i=i+ncovmodel;            }
        }          }
      }        } /* end i */
    }         
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   }        pstamp(ficresp);
            if  (cptcovn>0) {
   fclose(ficgp);          fprintf(ficresp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 chdir(path);          fprintf(ficresp, "**********\n#");
     free_matrix(agev,1,maxwav,1,imx);          fprintf(ficlog, "\n#********** Variable "); 
     free_ivector(wav,1,imx);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(ficlog, "**********\n#");
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        }
            for(i=1; i<=nlstate;i++) 
     free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
            fprintf(ficresp, "\n");
            
     free_ivector(num,1,n);        for(i=iagemin; i <= iagemax+3; i++){
     free_vector(agedc,1,n);          if(i==iagemax+3){
     free_vector(weight,1,n);            fprintf(ficlog,"Total");
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          }else{
     fclose(ficparo);            if(first==1){
     fclose(ficres);              first=0;
     /*  }*/              printf("See log file for details...\n");
                }
    /*________fin mle=1_________*/            fprintf(ficlog,"Age %d", i);
              }
           for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     /* No more information from the sample is required now */              pp[jk] += freq[jk][m][i]; 
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){          for(jk=1; jk <=nlstate ; jk++){
     ungetc(c,ficpar);            for(m=-1, pos=0; m <=0 ; m++)
     fgets(line, MAXLINE, ficpar);              pos += freq[jk][m][i];
     puts(line);            if(pp[jk]>=1.e-10){
     fputs(line,ficparo);              if(first==1){
   }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   ungetc(c,ficpar);              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            }else{
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              if(first==1)
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /*--------- index.htm --------*/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   if((fichtm=fopen("index.htm","w"))==NULL)    {          }
     printf("Problem with index.htm \n");goto end;  
   }          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n              pp[jk] += freq[jk][m][i];
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          }       
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            pos += pp[jk];
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            posprop += prop[jk][i];
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          for(jk=1; jk <=nlstate ; jk++){
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            if(pos>=1.e-5){
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>              if(first==1)
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  fprintf(fichtm," <li>Graphs</li>\n<p>");            }else{
               if(first==1)
  m=cptcoveff;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
  j1=0;            if( i <= iagemax){
  for(k1=1; k1<=m;k1++){              if(pos>=1.e-5){
    for(i1=1; i1<=ncodemax[k1];i1++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
        j1++;                /*probs[i][jk][j1]= pp[jk]/pos;*/
        if (cptcovn > 0) {                /*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(fichtm,"<hr>************ Results for covariates");              }
          for (cpt=1; cpt<=cptcoveff;cpt++)              else
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
          fprintf(fichtm," ************\n<hr>");            }
        }          }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              for(jk=-1; jk <=nlstate+ndeath; jk++)
        for(cpt=1; cpt<nlstate;cpt++){            for(m=-1; m <=nlstate+ndeath; m++)
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              if(freq[jk][m][i] !=0 ) {
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              if(first==1)
        }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(cpt=1; cpt<=nlstate;cpt++) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              }
 interval) in state (%d): v%s%d%d.gif <br>          if(i <= iagemax)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              fprintf(ficresp,"\n");
      }          if(first==1)
      for(cpt=1; cpt<=nlstate;cpt++) {            printf("Others in log...\n");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          fprintf(ficlog,"\n");
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        }
      }        /*}*/
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    }
 health expectancies in states (1) and (2): e%s%d.gif<br>    dateintmean=dateintsum/k2cpt; 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);   
 fprintf(fichtm,"\n</body>");    fclose(ficresp);
    }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
  }    free_vector(pp,1,nlstate);
 fclose(fichtm);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   /*--------------- Prevalence limit --------------*/  }
    
   strcpy(filerespl,"pl");  /************ Prevalence ********************/
   strcat(filerespl,fileres);  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((ficrespl=fopen(filerespl,"w"))==NULL) {  {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   }       in each health status at the date of interview (if between dateprev1 and dateprev2).
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       We still use firstpass and lastpass as another selection.
   fprintf(ficrespl,"#Prevalence limit\n");    */
   fprintf(ficrespl,"#Age ");   
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int i, m, jk, k1, i1, j1, bool, z1,j;
   fprintf(ficrespl,"\n");    double ***freq; /* Frequencies */
      double *pp, **prop;
   prlim=matrix(1,nlstate,1,nlstate);    double pos,posprop; 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double  y2; /* in fractional years */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int iagemin, iagemax;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int first; /** to stop verbosity which is redirected to log file */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    iagemin= (int) agemin;
   k=0;    iagemax= (int) agemax;
   agebase=agemin;    /*pp=vector(1,nlstate);*/
   agelim=agemax;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   ftolpl=1.e-10;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   i1=cptcoveff;    j1=0;
   if (cptcovn < 1){i1=1;}    
     /*j=cptcoveff;*/
   for(cptcov=1;cptcov<=i1;cptcov++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
         k=k+1;    first=1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
         fprintf(ficrespl,"\n#******");      /*for(i1=1; i1<=ncodemax[k1];i1++){
         for(j=1;j<=cptcoveff;j++)        j1++;*/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        
         fprintf(ficrespl,"******\n");        for (i=1; i<=nlstate; i++)  
                  for(m=iagemin; m <= iagemax+3; m++)
         for (age=agebase; age<=agelim; age++){            prop[i][m]=0.0;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       
           fprintf(ficrespl,"%.0f",age );        for (i=1; i<=imx; i++) { /* Each individual */
           for(i=1; i<=nlstate;i++)          bool=1;
           fprintf(ficrespl," %.5f", prlim[i][i]);          if  (cptcovn>0) {
           fprintf(ficrespl,"\n");            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                bool=0;
     }          } 
   fclose(ficrespl);          if (bool==1) { 
   /*------------- h Pij x at various ages ------------*/            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   printf("Computing pij: result on file '%s' \n", filerespij);                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]]);*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if (stepm<=24) stepsize=2;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
   agelim=AGESUP;              }
   hstepm=stepsize*YEARM; /* Every year of age */            } /* end selection of waves */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          }
          }
   k=0;        for(i=iagemin; i <= iagemax+3; i++){  
   for(cptcov=1;cptcov<=i1;cptcov++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            posprop += prop[jk][i]; 
       k=k+1;          } 
         fprintf(ficrespij,"\n#****** ");          
         for(j=1;j<=cptcoveff;j++)          for(jk=1; jk <=nlstate ; jk++){     
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if( i <=  iagemax){ 
         fprintf(ficrespij,"******\n");              if(posprop>=1.e-5){ 
                        probs[i][jk][j1]= prop[jk][i]/posprop;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */              } else{
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                if(first==1){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                  first=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  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]);
           oldm=oldms;savm=savms;                }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                }
           fprintf(ficrespij,"# Age");            } 
           for(i=1; i<=nlstate;i++)          }/* end jk */ 
             for(j=1; j<=nlstate+ndeath;j++)        }/* end i */ 
               fprintf(ficrespij," %1d-%1d",i,j);      /*} *//* end i1 */
           fprintf(ficrespij,"\n");    } /* end j1 */
           for (h=0; h<=nhstepm; h++){    
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
             for(i=1; i<=nlstate;i++)    /*free_vector(pp,1,nlstate);*/
               for(j=1; j<=nlstate+ndeath;j++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  }  /* End of prevalence */
             fprintf(ficrespij,"\n");  
           }  /************* Waves Concatenation ***************/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");  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)
         }  {
     }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   }       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   fclose(ficrespij);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   /*---------- Health expectancies and variances ------------*/       */
   
   strcpy(filerest,"t");    int i, mi, m;
   strcat(filerest,fileres);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   if((ficrest=fopen(filerest,"w"))==NULL) {       double sum=0., jmean=0.;*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    int first;
   }    int j, k=0,jk, ju, jl;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double sum=0.;
     first=0;
     jmin=1e+5;
   strcpy(filerese,"e");    jmax=-1;
   strcat(filerese,fileres);    jmean=0.;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    for(i=1; i<=imx; i++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      mi=0;
   }      m=firstpass;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
  strcpy(fileresv,"v");          mw[++mi][i]=m;
   strcat(fileresv,fileres);        if(m >=lastpass)
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          break;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        else
   }          m++;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      }/* end while */
       if (s[m][i] > nlstate){
   k=0;        mi++;     /* Death is another wave */
   for(cptcov=1;cptcov<=i1;cptcov++){        /* if(mi==0)  never been interviewed correctly before death */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           /* Only death is a correct wave */
       k=k+1;        mw[mi][i]=m;
       fprintf(ficrest,"\n#****** ");      }
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      wav[i]=mi;
       fprintf(ficrest,"******\n");      if(mi==0){
         nbwarn++;
       fprintf(ficreseij,"\n#****** ");        if(first==0){
       for(j=1;j<=cptcoveff;j++)          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          first=1;
       fprintf(ficreseij,"******\n");        }
         if(first==1){
       fprintf(ficresvij,"\n#****** ");          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      } /* end mi==0 */
       fprintf(ficresvij,"******\n");    } /* End individuals */
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for(i=1; i<=imx; i++){
       oldm=oldms;savm=savms;      for(mi=1; mi<wav[i];mi++){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);          if (stepm <=0)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          dh[mi][i]=1;
       oldm=oldms;savm=savms;        else{
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                  if (agedc[i] < 2*AGESUP) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              if(j==0) j=1;  /* Survives at least one month after exam */
       fprintf(ficrest,"\n");              else if(j<0){
                        nberr++;
       hf=1;                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       if (stepm >= YEARM) hf=stepm/YEARM;                j=1; /* Temporary Dangerous patch */
       epj=vector(1,nlstate+1);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for(age=bage; age <=fage ;age++){                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]);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
         fprintf(ficrest," %.0f",age);              }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              k=k+1;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              if (j >= jmax){
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                jmax=j;
           }                ijmax=i;
           epj[nlstate+1] +=epj[j];              }
         }              if (j <= jmin){
         for(i=1, vepp=0.;i <=nlstate;i++)                jmin=j;
           for(j=1;j <=nlstate;j++)                ijmin=i;
             vepp += vareij[i][j][(int)age];              }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));              sum=sum+j;
         for(j=1;j <=nlstate;j++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         }            }
         fprintf(ficrest,"\n");          }
       }          else{
     }            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]); */
          
  fclose(ficreseij);            k=k+1;
  fclose(ficresvij);            if (j >= jmax) {
   fclose(ficrest);              jmax=j;
   fclose(ficpar);              ijmax=i;
   free_vector(epj,1,nlstate+1);            }
   /*  scanf("%d ",i); */            else if (j <= jmin){
               jmin=j;
   /*------- Variance limit prevalence------*/                ijmin=i;
             }
 strcpy(fileresvpl,"vpl");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   strcat(fileresvpl,fileres);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            if(j<0){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);              nberr++;
     exit(0);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            }
             sum=sum+j;
  k=0;          }
  for(cptcov=1;cptcov<=i1;cptcov++){          jk= j/stepm;
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          jl= j -jk*stepm;
      k=k+1;          ju= j -(jk+1)*stepm;
      fprintf(ficresvpl,"\n#****** ");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
      for(j=1;j<=cptcoveff;j++)            if(jl==0){
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              dh[mi][i]=jk;
      fprintf(ficresvpl,"******\n");              bh[mi][i]=0;
                  }else{ /* We want a negative bias in order to only have interpolation ie
      varpl=matrix(1,nlstate,(int) bage, (int) fage);                    * to avoid the price of an extra matrix product in likelihood */
      oldm=oldms;savm=savms;              dh[mi][i]=jk+1;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);              bh[mi][i]=ju;
    }            }
  }          }else{
             if(jl <= -ju){
   fclose(ficresvpl);              dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
   /*---------- End : free ----------------*/                                   * is higher than the multiple of stepm and negative otherwise.
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                                   */
              }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            else{
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
              }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            if(dh[mi][i]==0){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);              dh[mi][i]=1; /* At least one step */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);              bh[mi][i]=ju; /* At least one step */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);              /*  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);*/
              }
   free_matrix(matcov,1,npar,1,npar);          } /* end if mle */
   free_vector(delti,1,npar);        }
        } /* end wave */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     jmean=sum/k;
   printf("End of Imach\n");    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);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    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("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);*/  /*********** Tricode ****************************/
   /*------ End -----------*/  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
  end:    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
 #ifdef windows    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
  chdir(pathcd);    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
 #endif     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
  system("wgnuplot graph.plt");    /* nbcode[Tvar[j]][1]= 
     */
 #ifdef windows  
   while (z[0] != 'q') {    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     chdir(pathcd);    int modmaxcovj=0; /* Modality max of covariates j */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    int cptcode=0; /* Modality max of covariates j */
     scanf("%s",z);    int modmincovj=0; /* Modality min of covariates j */
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {  
       chdir(path);    cptcoveff=0; 
       system("index.htm");   
     }    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     else if (z[0] == 'q') exit(0);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   }  
 #endif    /* 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 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   */
         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
           modmaxcovj=ij; 
         else if (ij < modmincovj) 
           modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
         }else
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         /* 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.*/
       }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
       /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
      /*for (i=0; i<=cptcode; i++) {*/
       for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
         if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         }
         /* 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 */
       } /* Ndum[-1] number of undefined modalities */
   
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
       /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
          There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
          variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
          nbcode[Tvar[j]][3]=2;
       */
       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 (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           /*recode from 0 */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                        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 (ij > ncodemax[j]) break; 
         }  /* end of loop on */
       } /* end of loop on modality */ 
     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     
     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.*/ 
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; 
    } 
   
    ij=1;
    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]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
        ij++;
      }else
          Tvaraff[ij]=0;
    }
    ij--;
    cptcoveff=ij; /*Number of total covariates*/
   
   }
   
   
   /*********** Health Expectancies ****************/
   
   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
   {
     /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3mat;
     double eip;
   
     pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\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 */ 
   
     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 */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
     
   }
   
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small 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.1.7  
changed lines
  Added in v.1.148


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