Diff for /imach/src/imach.c between versions 1.26 and 1.133

version 1.26, 2002/02/27 15:42:00 version 1.133, 2009/07/06 10:21:25
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.133  2009/07/06 10:21:25  brouard
      just nforces
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.132  2009/07/06 08:22:05  brouard
   first survey ("cross") where individuals from different ages are    Many tings
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.131  2009/06/20 16:22:47  brouard
   second wave of interviews ("longitudinal") which measure each change    Some dimensions resccaled
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.130  2009/05/26 06:44:34  brouard
   model. More health states you consider, more time is necessary to reach the    (Module): Max Covariate is now set to 20 instead of 8. A
   Maximum Likelihood of the parameters involved in the model.  The    lot of cleaning with variables initialized to 0. Trying to make
   simplest model is the multinomial logistic model where pij is the    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.129  2007/08/31 13:49:27  lievre
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.128  2006/06/30 13:02:05  brouard
   where the markup *Covariates have to be included here again* invites    (Module): Clarifications on computing e.j
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
   The advantage of this computer programme, compared to a simple    imach-114 because nhstepm was no more computed in the age
   multinomial logistic model, is clear when the delay between waves is not    loop. Now we define nhstepma in the age loop.
   identical for each individual. Also, if a individual missed an    (Module): In order to speed up (in case of numerous covariates) we
   intermediate interview, the information is lost, but taken into    compute health expectancies (without variances) in a first step
   account using an interpolation or extrapolation.      and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
   hPijx is the probability to be observed in state i at age x+h    computation.
   conditional to the observed state i at age x. The delay 'h' can be    In the future we should be able to stop the program is only health
   split into an exact number (nh*stepm) of unobserved intermediate    expectancies and graph are needed without standard deviations.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.126  2006/04/28 17:23:28  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Yes the sum of survivors was wrong since
   and the contribution of each individual to the likelihood is simply    imach-114 because nhstepm was no more computed in the age
   hPijx.    loop. Now we define nhstepma in the age loop.
     Version 0.98h
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.125  2006/04/04 15:20:31  lievre
      Errors in calculation of health expectancies. Age was not initialized.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Forecasting file added.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.124  2006/03/22 17:13:53  lievre
   from the European Union.    Parameters are printed with %lf instead of %f (more numbers after the comma).
   It is copyrighted identically to a GNU software product, ie programme and    The log-likelihood is printed in the log file
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.123  2006/03/20 10:52:43  brouard
   **********************************************************************/    * imach.c (Module): <title> changed, corresponds to .htm file
      name. <head> headers where missing.
 #include <math.h>  
 #include <stdio.h>    * imach.c (Module): Weights can have a decimal point as for
 #include <stdlib.h>    English (a comma might work with a correct LC_NUMERIC environment,
 #include <unistd.h>    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define MAXLINE 256    1.
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Version 0.98g
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.122  2006/03/20 09:45:41  brouard
 #define windows    (Module): Weights can have a decimal point as for
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    English (a comma might work with a correct LC_NUMERIC environment,
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    1.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Version 0.98g
   
 #define NINTERVMAX 8    Revision 1.121  2006/03/16 17:45:01  lievre
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    * imach.c (Module): Comments concerning covariates added
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    * imach.c (Module): refinements in the computation of lli if
 #define MAXN 20000    status=-2 in order to have more reliable computation if stepm is
 #define YEARM 12. /* Number of months per year */    not 1 month. Version 0.98f
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 int erreur; /* Error number */    not 1 month. Version 0.98f
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.119  2006/03/15 17:42:26  brouard
 int npar=NPARMAX;    (Module): Bug if status = -2, the loglikelihood was
 int nlstate=2; /* Number of live states */    computed as likelihood omitting the logarithm. Version O.98e
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.118  2006/03/14 18:20:07  brouard
 int popbased=0;    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int maxwav; /* Maxim number of waves */    (Module): Function pstamp added
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Version 0.98d
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.117  2006/03/14 17:16:22  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): varevsij Comments added explaining the second
 double jmean; /* Mean space between 2 waves */    table of variances if popbased=1 .
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Function pstamp added
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    (Module): Version 0.98d
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.116  2006/03/06 10:29:27  brouard
   char filerese[FILENAMELENGTH];    (Module): Variance-covariance wrong links and
  FILE  *ficresvij;    varian-covariance of ej. is needed (Saito).
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.115  2006/02/27 12:17:45  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): One freematrix added in mlikeli! 0.98c
   
 #define NR_END 1    Revision 1.114  2006/02/26 12:57:58  brouard
 #define FREE_ARG char*    (Module): Some improvements in processing parameter
 #define FTOL 1.0e-10    filename with strsep.
   
 #define NRANSI    Revision 1.113  2006/02/24 14:20:24  brouard
 #define ITMAX 200    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 #define TOL 2.0e-4    allocation too.
   
 #define CGOLD 0.3819660    Revision 1.112  2006/01/30 09:55:26  brouard
 #define ZEPS 1.0e-10    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.111  2006/01/25 20:38:18  brouard
 #define GOLD 1.618034    (Module): Lots of cleaning and bugs added (Gompertz)
 #define GLIMIT 100.0    (Module): Comments can be added in data file. Missing date values
 #define TINY 1.0e-20    can be a simple dot '.'.
   
 static double maxarg1,maxarg2;    Revision 1.110  2006/01/25 00:51:50  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): Lots of cleaning and bugs added (Gompertz)
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.109  2006/01/24 19:37:15  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Comments (lines starting with a #) are allowed in data.
 #define rint(a) floor(a+0.5)  
     Revision 1.108  2006/01/19 18:05:42  lievre
 static double sqrarg;    Gnuplot problem appeared...
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    To be fixed
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.107  2006/01/19 16:20:37  brouard
 int imx;    Test existence of gnuplot in imach path
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.105  2006/01/05 20:23:19  lievre
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    *** empty log message ***
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 double *weight;    (Module): If the status is missing at the last wave but we know
 int **s; /* Status */    that the person is alive, then we can code his/her status as -2
 double *agedc, **covar, idx;    (instead of missing=-1 in earlier versions) and his/her
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    the healthy state at last known wave). Version is 0.98
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.103  2005/09/30 15:54:49  lievre
 /**************** split *************************/    (Module): sump fixed, loop imx fixed, and simplifications.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.102  2004/09/15 17:31:30  brouard
    char *s;                             /* pointer */    Add the possibility to read data file including tab characters.
    int  l1, l2;                         /* length counters */  
     Revision 1.101  2004/09/15 10:38:38  brouard
    l1 = strlen( path );                 /* length of path */    Fix on curr_time
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.100  2004/07/12 18:29:06  brouard
    s = strrchr( path, '\\' );           /* find last / */    Add version for Mac OS X. Just define UNIX in Makefile
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.99  2004/06/05 08:57:40  brouard
 #endif    *** empty log message ***
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.98  2004/05/16 15:05:56  brouard
       extern char       *getwd( );    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
       if ( getwd( dirc ) == NULL ) {    state at each age, but using a Gompertz model: log u =a + b*age .
 #else    This is the basic analysis of mortality and should be done before any
       extern char       *getcwd( );    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    from other sources like vital statistic data.
 #endif  
          return( GLOCK_ERROR_GETCWD );    The same imach parameter file can be used but the option for mle should be -3.
       }  
       strcpy( name, path );             /* we've got it */    Agnès, who wrote this part of the code, tried to keep most of the
    } else {                             /* strip direcotry from path */    former routines in order to include the new code within the former code.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    The output is very simple: only an estimate of the intercept and of
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    the slope with 95% confident intervals.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Current limitations:
       dirc[l1-l2] = 0;                  /* add zero */    A) Even if you enter covariates, i.e. with the
    }    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    l1 = strlen( dirc );                 /* length of directory */    B) There is no computation of Life Expectancy nor Life Table.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.97  2004/02/20 13:25:42  lievre
 #else    Version 0.96d. Population forecasting command line is (temporarily)
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    suppressed.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.96  2003/07/15 15:38:55  brouard
    s++;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    strcpy(ext,s);                       /* save extension */    rewritten within the same printf. Workaround: many printfs.
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.95  2003/07/08 07:54:34  brouard
    strncpy( finame, name, l1-l2);    * imach.c (Repository):
    finame[l1-l2]= 0;    (Repository): Using imachwizard code to output a more meaningful covariance
    return( 0 );                         /* we're done */    matrix (cov(a12,c31) instead of numbers.
 }  
     Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /******************************************/  
     Revision 1.93  2003/06/25 16:33:55  brouard
 void replace(char *s, char*t)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int i;    (Module): Version 0.96b
   int lg=20;  
   i=0;    Revision 1.92  2003/06/25 16:30:45  brouard
   lg=strlen(t);    (Module): On windows (cygwin) function asctime_r doesn't
   for(i=0; i<= lg; i++) {    exist so I changed back to asctime which exists.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    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
     helps to forecast when convergence will be reached. Elapsed time
 int nbocc(char *s, char occ)    is stamped in powell.  We created a new html file for the graphs
 {    concerning matrix of covariance. It has extension -cov.htm.
   int i,j=0;  
   int lg=20;    Revision 1.90  2003/06/24 12:34:15  brouard
   i=0;    (Module): Some bugs corrected for windows. Also, when
   lg=strlen(s);    mle=-1 a template is output in file "or"mypar.txt with the design
   for(i=0; i<= lg; i++) {    of the covariance matrix to be input.
   if  (s[i] == occ ) j++;  
   }    Revision 1.89  2003/06/24 12:30:52  brouard
   return j;    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.88  2003/06/23 17:54:56  brouard
   int i,lg,j,p=0;    * 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.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.87  2003/06/18 12:26:01  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Version 0.96
   }  
     Revision 1.86  2003/06/17 20:04:08  brouard
   lg=strlen(t);    (Module): Change position of html and gnuplot routines and added
   for(j=0; j<p; j++) {    routine fileappend.
     (u[j] = t[j]);  
   }    Revision 1.85  2003/06/17 13:12:43  brouard
      u[p]='\0';    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
    for(j=0; j<= lg; j++) {    prior to the death. In this case, dh was negative and likelihood
     if (j>=(p+1))(v[j-p-1] = t[j]);    was wrong (infinity). We still send an "Error" but patch by
   }    assuming that the date of death was just one stepm after the
 }    interview.
     (Repository): Because some people have very long ID (first column)
 /********************** nrerror ********************/    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 void nrerror(char error_text[])    truncation)
 {    (Repository): No more line truncation errors.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.84  2003/06/13 21:44:43  brouard
   exit(1);    * imach.c (Repository): Replace "freqsummary" at a correct
 }    place. It differs from routine "prevalence" which may be called
 /*********************** vector *******************/    many times. Probs is memory consuming and must be used with
 double *vector(int nl, int nh)    parcimony.
 {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.83  2003/06/10 13:39:11  lievre
   if (!v) nrerror("allocation failure in vector");    *** empty log message ***
   return v-nl+NR_END;  
 }    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  */
 {  /*
   free((FREE_ARG)(v+nl-NR_END));     Interpolated Markov Chain
 }  
     Short summary of the programme:
 /************************ivector *******************************/    
 int *ivector(long nl,long nh)    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   int *v;    first survey ("cross") where individuals from different ages are
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    interviewed on their health status or degree of disability (in the
   if (!v) nrerror("allocation failure in ivector");    case of a health survey which is our main interest) -2- at least a
   return v-nl+NR_END;    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 /******************free ivector **************************/    model. More health states you consider, more time is necessary to reach the
 void free_ivector(int *v, long nl, long nh)    Maximum Likelihood of the parameters involved in the model.  The
 {    simplest model is the multinomial logistic model where pij is the
   free((FREE_ARG)(v+nl-NR_END));    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
 /******************* imatrix *******************************/    'age' is age and 'sex' is a covariate. If you want to have a more
 int **imatrix(long nrl, long nrh, long ncl, long nch)    complex model than "constant and age", you should modify the program
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    where the markup *Covariates have to be included here again* invites
 {    you to do it.  More covariates you add, slower the
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    convergence.
   int **m;  
      The advantage of this computer programme, compared to a simple
   /* allocate pointers to rows */    multinomial logistic model, is clear when the delay between waves is not
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    identical for each individual. Also, if a individual missed an
   if (!m) nrerror("allocation failure 1 in matrix()");    intermediate interview, the information is lost, but taken into
   m += NR_END;    account using an interpolation or extrapolation.  
   m -= nrl;  
      hPijx is the probability to be observed in state i at age x+h
      conditional to the observed state i at age x. The delay 'h' can be
   /* allocate rows and set pointers to them */    split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    states. This elementary transition (by month, quarter,
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    semester or year) is modelled as a multinomial logistic.  The hPx
   m[nrl] += NR_END;    matrix is simply the matrix product of nh*stepm elementary matrices
   m[nrl] -= ncl;    and the contribution of each individual to the likelihood is simply
      hPijx.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Also this programme outputs the covariance matrix of the parameters but also
   /* return pointer to array of pointers to rows */    of the life expectancies. It also computes the period (stable) prevalence. 
   return m;    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /****************** free_imatrix *************************/    This software have been partly granted by Euro-REVES, a concerted action
 void free_imatrix(m,nrl,nrh,ncl,nch)    from the European Union.
       int **m;    It is copyrighted identically to a GNU software product, ie programme and
       long nch,ncl,nrh,nrl;    software can be distributed freely for non commercial use. Latest version
      /* free an int matrix allocated by imatrix() */    can be accessed at http://euroreves.ined.fr/imach .
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   free((FREE_ARG) (m+nrl-NR_END));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 }    
     **********************************************************************/
 /******************* matrix *******************************/  /*
 double **matrix(long nrl, long nrh, long ncl, long nch)    main
 {    read parameterfile
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    read datafile
   double **m;    concatwav
     freqsummary
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if (mle >= 1)
   if (!m) nrerror("allocation failure 1 in matrix()");      mlikeli
   m += NR_END;    print results files
   m -= nrl;    if mle==1 
        computes hessian
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    read end of parameter file: agemin, agemax, bage, fage, estepm
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");        begin-prev-date,...
   m[nrl] += NR_END;    open gnuplot file
   m[nrl] -= ncl;    open html file
     period (stable) prevalence
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;     for age prevalim()
   return m;    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /*************************free matrix ************************/    health expectancies
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Variance-covariance of DFLE
 {    prevalence()
   free((FREE_ARG)(m[nrl]+ncl-NR_END));     movingaverage()
   free((FREE_ARG)(m+nrl-NR_END));    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
 /******************* ma3x *******************************/    Variance of period (stable) prevalence
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)   end
 {  */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));   
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <math.h>
   m += NR_END;  #include <stdio.h>
   m -= nrl;  #include <stdlib.h>
   #include <string.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <unistd.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #include <limits.h>
   m[nrl] -= ncl;  #include <sys/types.h>
   #include <sys/stat.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <errno.h>
   extern int errno;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  /* #include <sys/time.h> */
   m[nrl][ncl] += NR_END;  #include <time.h>
   m[nrl][ncl] -= nll;  #include "timeval.h"
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  /* #include <libintl.h> */
    /* #define _(String) gettext (String) */
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define MAXLINE 256
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define GNUPLOTPROGRAM "gnuplot"
   }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   return m;  #define FILENAMELENGTH 132
 }  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /*************************free ma3x ************************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #define NINTERVMAX 8
 }  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 /***************** f1dim *************************/  #define NCOVMAX 20 /* Maximum number of covariates */
 extern int ncom;  #define MAXN 20000
 extern double *pcom,*xicom;  #define YEARM 12. /* Number of months per year */
 extern double (*nrfunc)(double []);  #define AGESUP 130
    #define AGEBASE 40
 double f1dim(double x)  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 {  #ifdef UNIX
   int j;  #define DIRSEPARATOR '/'
   double f;  #define CHARSEPARATOR "/"
   double *xt;  #define ODIRSEPARATOR '\\'
    #else
   xt=vector(1,ncom);  #define DIRSEPARATOR '\\'
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define CHARSEPARATOR "\\"
   f=(*nrfunc)(xt);  #define ODIRSEPARATOR '/'
   free_vector(xt,1,ncom);  #endif
   return f;  
 }  /* $Id$ */
   /* $State$ */
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite ";
 {  char fullversion[]="$Revision$ $Date$"; 
   int iter;  char strstart[80];
   double a,b,d,etemp;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   double fu,fv,fw,fx;  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double ftemp;  int nvar=0, nforce=0; /* Number of variables, number of forces */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
   double e=0.0;  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
   a=(ax < cx ? ax : cx);  int ndeath=1; /* Number of dead states */
   b=(ax > cx ? ax : cx);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   x=w=v=bx;  int popbased=0;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  int *wav; /* Number of waves for this individuual 0 is possible */
     xm=0.5*(a+b);  int maxwav=0; /* Maxim number of waves */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     printf(".");fflush(stdout);  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("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);  int mle=1, weightopt=0;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #endif  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       *xmin=x;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       return fx;  double jmean=1; /* Mean space between 2 waves */
     }  double **oldm, **newm, **savm; /* Working pointers to matrices */
     ftemp=fu;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     if (fabs(e) > tol1) {  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       r=(x-w)*(fx-fv);  FILE *ficlog, *ficrespow;
       q=(x-v)*(fx-fw);  int globpr=0; /* Global variable for printing or not */
       p=(x-v)*q-(x-w)*r;  double fretone; /* Only one call to likelihood */
       q=2.0*(q-r);  long ipmx=0; /* Number of contributions */
       if (q > 0.0) p = -p;  double sw; /* Sum of weights */
       q=fabs(q);  char filerespow[FILENAMELENGTH];
       etemp=e;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       e=d;  FILE *ficresilk;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficresprobmorprev;
       else {  FILE *fichtm, *fichtmcov; /* Html File */
         d=p/q;  FILE *ficreseij;
         u=x+d;  char filerese[FILENAMELENGTH];
         if (u-a < tol2 || b-u < tol2)  FILE *ficresstdeij;
           d=SIGN(tol1,xm-x);  char fileresstde[FILENAMELENGTH];
       }  FILE *ficrescveij;
     } else {  char filerescve[FILENAMELENGTH];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE  *ficresvij;
     }  char fileresv[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  FILE  *ficresvpl;
     fu=(*f)(u);  char fileresvpl[FILENAMELENGTH];
     if (fu <= fx) {  char title[MAXLINE];
       if (u >= x) a=x; else b=x;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       SHFT(v,w,x,u)  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         } else {  char command[FILENAMELENGTH];
           if (u < x) a=u; else b=u;  int  outcmd=0;
           if (fu <= fw || w == x) {  
             v=w;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
             w=u;  
             fv=fw;  char filelog[FILENAMELENGTH]; /* Log file */
             fw=fu;  char filerest[FILENAMELENGTH];
           } else if (fu <= fv || v == x || v == w) {  char fileregp[FILENAMELENGTH];
             v=u;  char popfile[FILENAMELENGTH];
             fv=fu;  
           }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         }  
   }  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   nrerror("Too many iterations in brent");  struct timezone tzp;
   *xmin=x;  extern int gettimeofday();
   return fx;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 }  long time_value;
   extern long time();
 /****************** mnbrak ***********************/  char strcurr[80], strfor[80];
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char *endptr;
             double (*func)(double))  long lval;
 {  double dval;
   double ulim,u,r,q, dum;  
   double fu;  #define NR_END 1
    #define FREE_ARG char*
   *fa=(*func)(*ax);  #define FTOL 1.0e-10
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  #define NRANSI 
     SHFT(dum,*ax,*bx,dum)  #define ITMAX 200 
       SHFT(dum,*fb,*fa,dum)  
       }  #define TOL 2.0e-4 
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  #define CGOLD 0.3819660 
   while (*fb > *fc) {  #define ZEPS 1.0e-10 
     r=(*bx-*ax)*(*fb-*fc);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define GOLD 1.618034 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define GLIMIT 100.0 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define TINY 1.0e-20 
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  static double maxarg1,maxarg2;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       fu=(*func)(u);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       if (fu < *fc) {    
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
           SHFT(*fb,*fc,fu,(*func)(u))  #define rint(a) floor(a+0.5)
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  static double sqrarg;
       u=ulim;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       fu=(*func)(u);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     } else {  int agegomp= AGEGOMP;
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  int imx; 
     }  int stepm=1;
     SHFT(*ax,*bx,*cx,u)  /* Stepm, step in month: minimum step interpolation*/
       SHFT(*fa,*fb,*fc,fu)  
       }  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 /*************** linmin ************************/  int m,nb;
   long *num;
 int ncom;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double *pcom,*xicom;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double (*nrfunc)(double []);  double **pmmij, ***probs;
    double *ageexmed,*agecens;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  double dateintmean=0;
 {  
   double brent(double ax, double bx, double cx,  double *weight;
                double (*f)(double), double tol, double *xmin);  int **s; /* Status */
   double f1dim(double x);  double *agedc, **covar, idx;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
               double *fc, double (*func)(double));  double *lsurv, *lpop, *tpop;
   int j;  
   double xx,xmin,bx,ax;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double fx,fb,fa;  double ftolhess; /* Tolerance for computing hessian */
    
   ncom=n;  /**************** split *************************/
   pcom=vector(1,n);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   xicom=vector(1,n);  {
   nrfunc=func;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   for (j=1;j<=n;j++) {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     pcom[j]=p[j];    */ 
     xicom[j]=xi[j];    char  *ss;                            /* pointer */
   }    int   l1, l2;                         /* length counters */
   ax=0.0;  
   xx=1.0;    l1 = strlen(path );                   /* length of path */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 #ifdef DEBUG    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      strcpy( name, path );               /* we got the fullname name because no directory */
 #endif      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   for (j=1;j<=n;j++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     xi[j] *= xmin;      /* get current working directory */
     p[j] += xi[j];      /*    extern  char* getcwd ( char *buf , int len);*/
   }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   free_vector(xicom,1,n);        return( GLOCK_ERROR_GETCWD );
   free_vector(pcom,1,n);      }
 }      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
 /*************** powell ************************/    } else {                              /* strip direcotry from path */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      ss++;                               /* after this, the filename */
             double (*func)(double []))      l2 = strlen( ss );                  /* length of filename */
 {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   void linmin(double p[], double xi[], int n, double *fret,      strcpy( name, ss );         /* save file name */
               double (*func)(double []));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   int i,ibig,j;      dirc[l1-l2] = 0;                    /* add zero */
   double del,t,*pt,*ptt,*xit;      printf(" DIRC2 = %s \n",dirc);
   double fp,fptt;    }
   double *xits;    /* We add a separator at the end of dirc if not exists */
   pt=vector(1,n);    l1 = strlen( dirc );                  /* length of directory */
   ptt=vector(1,n);    if( dirc[l1-1] != DIRSEPARATOR ){
   xit=vector(1,n);      dirc[l1] =  DIRSEPARATOR;
   xits=vector(1,n);      dirc[l1+1] = 0; 
   *fret=(*func)(p);      printf(" DIRC3 = %s \n",dirc);
   for (j=1;j<=n;j++) pt[j]=p[j];    }
   for (*iter=1;;++(*iter)) {    ss = strrchr( name, '.' );            /* find last / */
     fp=(*fret);    if (ss >0){
     ibig=0;      ss++;
     del=0.0;      strcpy(ext,ss);                     /* save extension */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      l1= strlen( name);
     for (i=1;i<=n;i++)      l2= strlen(ss)+1;
       printf(" %d %.12f",i, p[i]);      strncpy( finame, name, l1-l2);
     printf("\n");      finame[l1-l2]= 0;
     for (i=1;i<=n;i++) {    }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);    return( 0 );                          /* we're done */
 #ifdef DEBUG  }
       printf("fret=%lf \n",*fret);  
 #endif  
       printf("%d",i);fflush(stdout);  /******************************************/
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  void replace_back_to_slash(char *s, char*t)
         del=fabs(fptt-(*fret));  {
         ibig=i;    int i;
       }    int lg=0;
 #ifdef DEBUG    i=0;
       printf("%d %.12e",i,(*fret));    lg=strlen(t);
       for (j=1;j<=n;j++) {    for(i=0; i<= lg; i++) {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      (s[i] = t[i]);
         printf(" x(%d)=%.12e",j,xit[j]);      if (t[i]== '\\') s[i]='/';
       }    }
       for(j=1;j<=n;j++)  }
         printf(" p=%.12e",p[j]);  
       printf("\n");  char *trimbb(char *out, char *in)
 #endif  { /* Trim multiple blanks in line */
     }    char *s;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    s=out;
 #ifdef DEBUG    while (*in != '\0'){
       int k[2],l;      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
       k[0]=1;        in++;
       k[1]=-1;      }
       printf("Max: %.12e",(*func)(p));      *out++ = *in++;
       for (j=1;j<=n;j++)    }
         printf(" %.12e",p[j]);    *out='\0';
       printf("\n");    return s;
       for(l=0;l<=1;l++) {  }
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  int nbocc(char *s, char occ)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    int i,j=0;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    int lg=20;
       }    i=0;
 #endif    lg=strlen(s);
     for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
       free_vector(xit,1,n);    }
       free_vector(xits,1,n);    return j;
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  
       return;  void cutv(char *u,char *v, char*t, char occ)
     }  {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     for (j=1;j<=n;j++) {       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       ptt[j]=2.0*p[j]-pt[j];       gives u="abcedf" and v="ghi2j" */
       xit[j]=p[j]-pt[j];    int i,lg,j,p=0;
       pt[j]=p[j];    i=0;
     }    for(j=0; j<=strlen(t)-1; j++) {
     fptt=(*func)(ptt);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     if (fptt < fp) {    }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {    lg=strlen(t);
         linmin(p,xit,n,fret,func);    for(j=0; j<p; j++) {
         for (j=1;j<=n;j++) {      (u[j] = t[j]);
           xi[j][ibig]=xi[j][n];    }
           xi[j][n]=xit[j];       u[p]='\0';
         }  
 #ifdef DEBUG     for(j=0; j<= lg; j++) {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      if (j>=(p+1))(v[j-p-1] = t[j]);
         for(j=1;j<=n;j++)    }
           printf(" %.12e",xit[j]);  }
         printf("\n");  
 #endif  /********************** nrerror ********************/
       }  
     }  void nrerror(char error_text[])
   }  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /**** Prevalence limit ****************/    exit(EXIT_FAILURE);
   }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /*********************** vector *******************/
 {  double *vector(int nl, int nh)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  {
      matrix by transitions matrix until convergence is reached */    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   int i, ii,j,k;    if (!v) nrerror("allocation failure in vector");
   double min, max, maxmin, maxmax,sumnew=0.;    return v-nl+NR_END;
   double **matprod2();  }
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /************************ free vector ******************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  void free_vector(double*v, int nl, int nh)
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    free((FREE_ARG)(v+nl-NR_END));
     for (j=1;j<=nlstate+ndeath;j++){  }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /************************ivector *******************************/
   int *ivector(long nl,long nh)
    cov[1]=1.;  {
      int *v;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    if (!v) nrerror("allocation failure in ivector");
     newm=savm;    return v-nl+NR_END;
     /* Covariates have to be included here again */  }
      cov[2]=agefin;  
    /******************free ivector **************************/
       for (k=1; k<=cptcovn;k++) {  void free_ivector(int *v, long nl, long nh)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    free((FREE_ARG)(v+nl-NR_END));
       }  }
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /************************lvector *******************************/
       for (k=1; k<=cptcovprod;k++)  long *lvector(long nl,long nh)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     long *v;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   
     savm=oldm;  /******************free lvector **************************/
     oldm=newm;  void free_lvector(long *v, long nl, long nh)
     maxmax=0.;  {
     for(j=1;j<=nlstate;j++){    free((FREE_ARG)(v+nl-NR_END));
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /******************* imatrix *******************************/
         sumnew=0;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         prlim[i][j]= newm[i][j]/(1-sumnew);  { 
         max=FMAX(max,prlim[i][j]);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         min=FMIN(min,prlim[i][j]);    int **m; 
       }    
       maxmin=max-min;    /* allocate pointers to rows */ 
       maxmax=FMAX(maxmax,maxmin);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     if(maxmax < ftolpl){    m += NR_END; 
       return prlim;    m -= nrl; 
     }    
   }    
 }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 /*************** transition probabilities ***************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m[nrl] -= ncl; 
 {    
   double s1, s2;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   /*double t34;*/    
   int i,j,j1, nc, ii, jj;    /* return pointer to array of pointers to rows */ 
     return m; 
     for(i=1; i<= nlstate; i++){  } 
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /****************** free_imatrix *************************/
         /*s2 += param[i][j][nc]*cov[nc];*/  void free_imatrix(m,nrl,nrh,ncl,nch)
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        int **m;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        long nch,ncl,nrh,nrl; 
       }       /* free an int matrix allocated by imatrix() */ 
       ps[i][j]=s2;  { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     }    free((FREE_ARG) (m+nrl-NR_END)); 
     for(j=i+1; j<=nlstate+ndeath;j++){  } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /******************* matrix *******************************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  double **matrix(long nrl, long nrh, long ncl, long nch)
       }  {
       ps[i][j]=s2;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
   }  
     /*ps[3][2]=1;*/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
   for(i=1; i<= nlstate; i++){    m += NR_END;
      s1=0;    m -= nrl;
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for(j=i+1; j<=nlstate+ndeath; j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       s1+=exp(ps[i][j]);    m[nrl] += NR_END;
     ps[i][i]=1./(s1+1.);    m[nrl] -= ncl;
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=i+1; j<=nlstate+ndeath; j++)    return m;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */     */
   } /* end i */  }
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  /*************************free matrix ************************/
     for(jj=1; jj<= nlstate+ndeath; jj++){  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       ps[ii][jj]=0;  {
       ps[ii][ii]=1;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
   }  }
   
   /******************* ma3x *******************************/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
      printf("%lf ",ps[ii][jj]);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
    }    double ***m;
     printf("\n ");  
     }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     printf("\n ");printf("%lf ",cov[2]);*/    if (!m) nrerror("allocation failure 1 in matrix()");
 /*    m += NR_END;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    m -= nrl;
   goto end;*/  
     return ps;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 /**************** Product of 2 matrices ******************/    m[nrl] -= ncl;
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   /* in, b, out are matrice of pointers which should have been initialized    m[nrl][ncl] += NR_END;
      before: only the contents of out is modified. The function returns    m[nrl][ncl] -= nll;
      a pointer to pointers identical to out */    for (j=ncl+1; j<=nch; j++) 
   long i, j, k;      m[nrl][j]=m[nrl][j-1]+nlay;
   for(i=nrl; i<= nrh; i++)    
     for(k=ncolol; k<=ncoloh; k++)    for (i=nrl+1; i<=nrh; i++) {
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         out[i][k] +=in[i][j]*b[j][k];      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
   return out;    }
 }    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 /************* Higher Matrix Product ***************/    */
   }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /*************************free ma3x ************************/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      (typically every 2 years instead of every month which is too big).    free((FREE_ARG)(m+nrl-NR_END));
      Model is determined by parameters x and covariates have to be  }
      included manually here.  
   /*************** function subdirf ***********/
      */  char *subdirf(char fileres[])
   {
   int i, j, d, h, k;    /* Caution optionfilefiname is hidden */
   double **out, cov[NCOVMAX];    strcpy(tmpout,optionfilefiname);
   double **newm;    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
   /* Hstepm could be zero and should return the unit matrix */    return tmpout;
   for (i=1;i<=nlstate+ndeath;i++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /*************** function subdirf2 ***********/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  char *subdirf2(char fileres[], char *preop)
     }  {
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    
   for(h=1; h <=nhstepm; h++){    /* Caution optionfilefiname is hidden */
     for(d=1; d <=hstepm; d++){    strcpy(tmpout,optionfilefiname);
       newm=savm;    strcat(tmpout,"/");
       /* Covariates have to be included here again */    strcat(tmpout,preop);
       cov[1]=1.;    strcat(tmpout,fileres);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return tmpout;
       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];  /*************** function subdirf3 ***********/
       for (k=1; k<=cptcovprod;k++)  char *subdirf3(char fileres[], char *preop, char *preop2)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     
     /* Caution optionfilefiname is hidden */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    strcpy(tmpout,optionfilefiname);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    strcat(tmpout,"/");
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    strcat(tmpout,preop);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    strcat(tmpout,preop2);
       savm=oldm;    strcat(tmpout,fileres);
       oldm=newm;    return tmpout;
     }  }
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  /***************** f1dim *************************/
         po[i][j][h]=newm[i][j];  extern int ncom; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  extern double *pcom,*xicom;
          */  extern double (*nrfunc)(double []); 
       }   
   } /* end h */  double f1dim(double x) 
   return po;  { 
 }    int j; 
     double f;
     double *xt; 
 /*************** log-likelihood *************/   
 double func( double *x)    xt=vector(1,ncom); 
 {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   int i, ii, j, k, mi, d, kk;    f=(*nrfunc)(xt); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    free_vector(xt,1,ncom); 
   double **out;    return f; 
   double sw; /* Sum of weights */  } 
   double lli; /* Individual log likelihood */  
   long ipmx;  /*****************brent *************************/
   /*extern weight */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   /* We are differentiating ll according to initial status */  { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    int iter; 
   /*for(i=1;i<imx;i++)    double a,b,d,etemp;
     printf(" %d\n",s[4][i]);    double fu,fv,fw,fx;
   */    double ftemp;
   cov[1]=1.;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;   
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    a=(ax < cx ? ax : cx); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    b=(ax > cx ? ax : cx); 
     for(mi=1; mi<= wav[i]-1; mi++){    x=w=v=bx; 
       for (ii=1;ii<=nlstate+ndeath;ii++)    fw=fv=fx=(*f)(x); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for (iter=1;iter<=ITMAX;iter++) { 
       for(d=0; d<dh[mi][i]; d++){      xm=0.5*(a+b); 
         newm=savm;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         for (kk=1; kk<=cptcovage;kk++) {      printf(".");fflush(stdout);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      fprintf(ficlog,".");fflush(ficlog);
         }  #ifdef DEBUG
              printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      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);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         savm=oldm;  #endif
         oldm=newm;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
                *xmin=x; 
                return fx; 
       } /* end mult */      } 
            ftemp=fu;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      if (fabs(e) > tol1) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        r=(x-w)*(fx-fv); 
       ipmx +=1;        q=(x-v)*(fx-fw); 
       sw += weight[i];        p=(x-v)*q-(x-w)*r; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        q=2.0*(q-r); 
     } /* end of wave */        if (q > 0.0) p = -p; 
   } /* end of individual */        q=fabs(q); 
         etemp=e; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        e=d; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   return -l;        else { 
 }          d=p/q; 
           u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
 /*********** Maximum Likelihood Estimation ***************/            d=SIGN(tol1,xm-x); 
         } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i,j, iter;      } 
   double **xi,*delti;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double fret;      fu=(*f)(u); 
   xi=matrix(1,npar,1,npar);      if (fu <= fx) { 
   for (i=1;i<=npar;i++)        if (u >= x) a=x; else b=x; 
     for (j=1;j<=npar;j++)        SHFT(v,w,x,u) 
       xi[i][j]=(i==j ? 1.0 : 0.0);          SHFT(fv,fw,fx,fu) 
   printf("Powell\n");          } else { 
   powell(p,xi,npar,ftol,&iter,&fret,func);            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));              v=w; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));              w=u; 
               fv=fw; 
 }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 /**** Computes Hessian and covariance matrix ***/              v=u; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))              fv=fu; 
 {            } 
   double  **a,**y,*x,pd;          } 
   double **hess;    } 
   int i, j,jk;    nrerror("Too many iterations in brent"); 
   int *indx;    *xmin=x; 
     return fx; 
   double hessii(double p[], double delta, int theta, double delti[]);  } 
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /****************** mnbrak ***********************/
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   hess=matrix(1,npar,1,npar);              double (*func)(double)) 
   { 
   printf("\nCalculation of the hessian matrix. Wait...\n");    double ulim,u,r,q, dum;
   for (i=1;i<=npar;i++){    double fu; 
     printf("%d",i);fflush(stdout);   
     hess[i][i]=hessii(p,ftolhess,i,delti);    *fa=(*func)(*ax); 
     /*printf(" %f ",p[i]);*/    *fb=(*func)(*bx); 
     /*printf(" %lf ",hess[i][i]);*/    if (*fb > *fa) { 
   }      SHFT(dum,*ax,*bx,dum) 
          SHFT(dum,*fb,*fa,dum) 
   for (i=1;i<=npar;i++) {        } 
     for (j=1;j<=npar;j++)  {    *cx=(*bx)+GOLD*(*bx-*ax); 
       if (j>i) {    *fc=(*func)(*cx); 
         printf(".%d%d",i,j);fflush(stdout);    while (*fb > *fc) { 
         hess[i][j]=hessij(p,delti,i,j);      r=(*bx-*ax)*(*fb-*fc); 
         hess[j][i]=hess[i][j];          q=(*bx-*cx)*(*fb-*fa); 
         /*printf(" %lf ",hess[i][j]);*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   }      if ((*bx-u)*(u-*cx) > 0.0) { 
   printf("\n");        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        fu=(*func)(u); 
          if (fu < *fc) { 
   a=matrix(1,npar,1,npar);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   y=matrix(1,npar,1,npar);            SHFT(*fb,*fc,fu,(*func)(u)) 
   x=vector(1,npar);            } 
   indx=ivector(1,npar);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for (i=1;i<=npar;i++)        u=ulim; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fu=(*func)(u); 
   ludcmp(a,npar,indx,&pd);      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   for (j=1;j<=npar;j++) {        fu=(*func)(u); 
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      SHFT(*ax,*bx,*cx,u) 
     lubksb(a,npar,indx,x);        SHFT(*fa,*fb,*fc,fu) 
     for (i=1;i<=npar;i++){        } 
       matcov[i][j]=x[i];  } 
     }  
   }  /*************** linmin ************************/
   
   printf("\n#Hessian matrix#\n");  int ncom; 
   for (i=1;i<=npar;i++) {  double *pcom,*xicom;
     for (j=1;j<=npar;j++) {  double (*nrfunc)(double []); 
       printf("%.3e ",hess[i][j]);   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("\n");  { 
   }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
   /* Recompute Inverse */    double f1dim(double x); 
   for (i=1;i<=npar;i++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];                double *fc, double (*func)(double)); 
   ludcmp(a,npar,indx,&pd);    int j; 
     double xx,xmin,bx,ax; 
   /*  printf("\n#Hessian matrix recomputed#\n");    double fx,fb,fa;
    
   for (j=1;j<=npar;j++) {    ncom=n; 
     for (i=1;i<=npar;i++) x[i]=0;    pcom=vector(1,n); 
     x[j]=1;    xicom=vector(1,n); 
     lubksb(a,npar,indx,x);    nrfunc=func; 
     for (i=1;i<=npar;i++){    for (j=1;j<=n;j++) { 
       y[i][j]=x[i];      pcom[j]=p[j]; 
       printf("%.3e ",y[i][j]);      xicom[j]=xi[j]; 
     }    } 
     printf("\n");    ax=0.0; 
   }    xx=1.0; 
   */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   free_matrix(a,1,npar,1,npar);  #ifdef DEBUG
   free_matrix(y,1,npar,1,npar);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_vector(x,1,npar);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_ivector(indx,1,npar);  #endif
   free_matrix(hess,1,npar,1,npar);    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
       p[j] += xi[j]; 
 }    } 
     free_vector(xicom,1,n); 
 /*************** hessian matrix ****************/    free_vector(pcom,1,n); 
 double hessii( double x[], double delta, int theta, double delti[])  } 
 {  
   int i;  char *asc_diff_time(long time_sec, char ascdiff[])
   int l=1, lmax=20;  {
   double k1,k2;    long sec_left, days, hours, minutes;
   double p2[NPARMAX+1];    days = (time_sec) / (60*60*24);
   double res;    sec_left = (time_sec) % (60*60*24);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    hours = (sec_left) / (60*60) ;
   double fx;    sec_left = (sec_left) %(60*60);
   int k=0,kmax=10;    minutes = (sec_left) /60;
   double l1;    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   fx=func(x);    return ascdiff;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  /*************** powell ************************/
     delts=delt;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     for(k=1 ; k <kmax; k=k+1){              double (*func)(double [])) 
       delt = delta*(l1*k);  { 
       p2[theta]=x[theta] +delt;    void linmin(double p[], double xi[], int n, double *fret, 
       k1=func(p2)-fx;                double (*func)(double [])); 
       p2[theta]=x[theta]-delt;    int i,ibig,j; 
       k2=func(p2)-fx;    double del,t,*pt,*ptt,*xit;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double fp,fptt;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double *xits;
          int niterf, itmp;
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    pt=vector(1,n); 
 #endif    ptt=vector(1,n); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    xit=vector(1,n); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    xits=vector(1,n); 
         k=kmax;    *fret=(*func)(p); 
       }    for (j=1;j<=n;j++) pt[j]=p[j]; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    for (*iter=1;;++(*iter)) { 
         k=kmax; l=lmax*10.;      fp=(*fret); 
       }      ibig=0; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      del=0.0; 
         delts=delt;      last_time=curr_time;
       }      (void) gettimeofday(&curr_time,&tzp);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   }      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);
   delti[theta]=delts;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   return res;     for (i=1;i<=n;i++) {
          printf(" %d %.12f",i, p[i]);
 }        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
 double hessij( double x[], double delti[], int thetai,int thetaj)      }
 {      printf("\n");
   int i;      fprintf(ficlog,"\n");
   int l=1, l1, lmax=20;      fprintf(ficrespow,"\n");fflush(ficrespow);
   double k1,k2,k3,k4,res,fx;      if(*iter <=3){
   double p2[NPARMAX+1];        tm = *localtime(&curr_time.tv_sec);
   int k;        strcpy(strcurr,asctime(&tm));
   /*       asctime_r(&tm,strcurr); */
   fx=func(x);        forecast_time=curr_time; 
   for (k=1; k<=2; k++) {        itmp = strlen(strcurr);
     for (i=1;i<=npar;i++) p2[i]=x[i];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     p2[thetai]=x[thetai]+delti[thetai]/k;          strcurr[itmp-1]='\0';
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     k1=func(p2)-fx;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
          for(niterf=10;niterf<=30;niterf+=10){
     p2[thetai]=x[thetai]+delti[thetai]/k;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          tmf = *localtime(&forecast_time.tv_sec);
     k2=func(p2)-fx;  /*      asctime_r(&tmf,strfor); */
            strcpy(strfor,asctime(&tmf));
     p2[thetai]=x[thetai]-delti[thetai]/k;          itmp = strlen(strfor);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          if(strfor[itmp-1]=='\n')
     k3=func(p2)-fx;          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);
     p2[thetai]=x[thetai]-delti[thetai]/k;          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);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k4=func(p2)-fx;      }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      for (i=1;i<=n;i++) { 
 #ifdef DEBUG        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        fptt=(*fret); 
 #endif  #ifdef DEBUG
   }        printf("fret=%lf \n",*fret);
   return res;        fprintf(ficlog,"fret=%lf \n",*fret);
 }  #endif
         printf("%d",i);fflush(stdout);
 /************** Inverse of matrix **************/        fprintf(ficlog,"%d",i);fflush(ficlog);
 void ludcmp(double **a, int n, int *indx, double *d)        linmin(p,xit,n,fret,func); 
 {        if (fabs(fptt-(*fret)) > del) { 
   int i,imax,j,k;          del=fabs(fptt-(*fret)); 
   double big,dum,sum,temp;          ibig=i; 
   double *vv;        } 
    #ifdef DEBUG
   vv=vector(1,n);        printf("%d %.12e",i,(*fret));
   *d=1.0;        fprintf(ficlog,"%d %.12e",i,(*fret));
   for (i=1;i<=n;i++) {        for (j=1;j<=n;j++) {
     big=0.0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=n;j++)          printf(" x(%d)=%.12e",j,xit[j]);
       if ((temp=fabs(a[i][j])) > big) big=temp;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        }
     vv[i]=1.0/big;        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
   for (j=1;j<=n;j++) {          fprintf(ficlog," p=%.12e",p[j]);
     for (i=1;i<j;i++) {        }
       sum=a[i][j];        printf("\n");
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        fprintf(ficlog,"\n");
       a[i][j]=sum;  #endif
     }      } 
     big=0.0;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for (i=j;i<=n;i++) {  #ifdef DEBUG
       sum=a[i][j];        int k[2],l;
       for (k=1;k<j;k++)        k[0]=1;
         sum -= a[i][k]*a[k][j];        k[1]=-1;
       a[i][j]=sum;        printf("Max: %.12e",(*func)(p));
       if ( (dum=vv[i]*fabs(sum)) >= big) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
         big=dum;        for (j=1;j<=n;j++) {
         imax=i;          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
     }        }
     if (j != imax) {        printf("\n");
       for (k=1;k<=n;k++) {        fprintf(ficlog,"\n");
         dum=a[imax][k];        for(l=0;l<=1;l++) {
         a[imax][k]=a[j][k];          for (j=1;j<=n;j++) {
         a[j][k]=dum;            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]);
       *d = -(*d);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       vv[imax]=vv[j];          }
     }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     indx[j]=imax;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {  #endif
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }        free_vector(xit,1,n); 
   }        free_vector(xits,1,n); 
   free_vector(vv,1,n);  /* Doesn't work */        free_vector(ptt,1,n); 
 ;        free_vector(pt,1,n); 
 }        return; 
       } 
 void lubksb(double **a, int n, int *indx, double b[])      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 {      for (j=1;j<=n;j++) { 
   int i,ii=0,ip,j;        ptt[j]=2.0*p[j]-pt[j]; 
   double sum;        xit[j]=p[j]-pt[j]; 
          pt[j]=p[j]; 
   for (i=1;i<=n;i++) {      } 
     ip=indx[i];      fptt=(*func)(ptt); 
     sum=b[ip];      if (fptt < fp) { 
     b[ip]=b[i];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     if (ii)        if (t < 0.0) { 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          linmin(p,xit,n,fret,func); 
     else if (sum) ii=i;          for (j=1;j<=n;j++) { 
     b[i]=sum;            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
   for (i=n;i>=1;i--) {          }
     sum=b[i];  #ifdef DEBUG
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     b[i]=sum/a[i][i];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   }          for(j=1;j<=n;j++){
 }            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
 /************ Frequencies ********************/          }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)          printf("\n");
 {  /* Some frequencies */          fprintf(ficlog,"\n");
    #endif
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        }
   double ***freq; /* Frequencies */      } 
   double *pp;    } 
   double pos, k2, dateintsum=0,k2cpt=0;  } 
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  /**** Prevalence limit (stable or period prevalence)  ****************/
   
   pp=vector(1,nlstate);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
   strcpy(fileresp,"p");    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   strcat(fileresp,fileres);       matrix by transitions matrix until convergence is reached */
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);    int i, ii,j,k;
     exit(0);    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double **out, cov[NCOVMAX+1], **pmij();
   j1=0;    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   for(k1=1; k1<=j;k1++){        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    for(i1=1; i1<=ncodemax[k1];i1++){      }
        j1++;  
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);     cov[1]=1.;
          scanf("%d", i);*/   
         for (i=-1; i<=nlstate+ndeath; i++)     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
            for(m=agemin; m <= agemax+3; m++)      newm=savm;
              freq[i][jk][m]=0;      /* Covariates have to be included here again */
        cov[2]=agefin;
         dateintsum=0;    
         k2cpt=0;        for (k=1; k<=cptcovn;k++) {
        for (i=1; i<=imx; i++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          bool=1;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
          if  (cptcovn>0) {        }
            for (z1=1; z1<=cptcoveff; z1++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for (k=1; k<=cptcovprod;k++)
                bool=0;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          }  
          if (bool==1) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
            for(m=firstpass; m<=lastpass; m++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
              k2=anint[m][i]+(mint[m][i]/12.);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
                if(agev[m][i]==0) agev[m][i]=agemax+1;  
                if(agev[m][i]==1) agev[m][i]=agemax+2;      savm=oldm;
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      oldm=newm;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      maxmax=0.;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      for(j=1;j<=nlstate;j++){
                  dateintsum=dateintsum+k2;        min=1.;
                  k2cpt++;        max=0.;
                }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
              }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            }          prlim[i][j]= newm[i][j]/(1-sumnew);
          }          max=FMAX(max,prlim[i][j]);
        }          min=FMIN(min,prlim[i][j]);
                }
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
         if  (cptcovn>0) {      }
          fprintf(ficresp, "\n#********** Variable ");      if(maxmax < ftolpl){
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        return prlim;
        fprintf(ficresp, "**********\n#");      }
         }    }
        for(i=1; i<=nlstate;i++)  }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");  /*************** transition probabilities ***************/ 
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     if(i==(int)agemax+3)  {
       printf("Total");    double s1, s2;
     else    /*double t34;*/
       printf("Age %d", i);    int i,j,j1, nc, ii, jj;
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for(i=1; i<= nlstate; i++){
         pp[jk] += freq[jk][m][i];        for(j=1; j<i;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(jk=1; jk <=nlstate ; jk++){            /*s2 += param[i][j][nc]*cov[nc];*/
       for(m=-1, pos=0; m <=0 ; m++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         pos += freq[jk][m][i];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       if(pp[jk]>=1.e-10)          }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          ps[i][j]=s2;
       else  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
      for(jk=1; jk <=nlstate ; jk++){            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         pp[jk] += freq[jk][m][i];          }
      }          ps[i][j]=s2;
         }
     for(jk=1,pos=0; jk <=nlstate ; jk++)      }
       pos += pp[jk];      /*ps[3][2]=1;*/
     for(jk=1; jk <=nlstate ; jk++){      
       if(pos>=1.e-5)      for(i=1; i<= nlstate; i++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        s1=0;
       else        for(j=1; j<i; j++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          s1+=exp(ps[i][j]);
       if( i <= (int) agemax){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         if(pos>=1.e-5){        }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for(j=i+1; j<=nlstate+ndeath; j++){
           probs[i][jk][j1]= pp[jk]/pos;          s1+=exp(ps[i][j]);
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }        }
       else        ps[i][i]=1./(s1+1.);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        for(j=1; j<i; j++)
       }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        for(j=i+1; j<=nlstate+ndeath; j++)
     for(jk=-1; jk <=nlstate+ndeath; jk++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(m=-1; m <=nlstate+ndeath; m++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      } /* end i */
     if(i <= (int) agemax)      
       fprintf(ficresp,"\n");      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     printf("\n");        for(jj=1; jj<= nlstate+ndeath; jj++){
     }          ps[ii][jj]=0;
     }          ps[ii][ii]=1;
  }        }
   dateintmean=dateintsum/k2cpt;      }
        
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   free_vector(pp,1,nlstate);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
   /* End of Freq */  /*       } */
 }  /*       printf("\n "); */
   /*        } */
 /************ Prevalence ********************/  /*        printf("\n ");printf("%lf ",cov[2]); */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)         /*
 {  /* Some frequencies */        for(i=1; i<= npar; i++) printf("%f ",x[i]);
          goto end;*/
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      return ps;
   double ***freq; /* Frequencies */  }
   double *pp;  
   double pos, k2;  /**************** Product of 2 matrices ******************/
   
   pp=vector(1,nlstate);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
      /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   j1=0;    /* in, b, out are matrice of pointers which should have been initialized 
         before: only the contents of out is modified. The function returns
   j=cptcoveff;       a pointer to pointers identical to out */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    long i, j, k;
      for(i=nrl; i<= nrh; i++)
  for(k1=1; k1<=j;k1++){      for(k=ncolol; k<=ncoloh; k++)
     for(i1=1; i1<=ncodemax[k1];i1++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       j1++;          out[i][k] +=in[i][j]*b[j][k];
    
       for (i=-1; i<=nlstate+ndeath; i++)      return out;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    }
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  
        /************* Higher Matrix Product ***************/
       for (i=1; i<=imx; i++) {  
         bool=1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         if  (cptcovn>0) {  {
           for (z1=1; z1<=cptcoveff; z1++)    /* Computes the transition matrix starting at age 'age' over 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       'nhstepm*hstepm*stepm' months (i.e. until
               bool=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         }       nhstepm*hstepm matrices. 
         if (bool==1) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           for(m=firstpass; m<=lastpass; m++){       (typically every 2 years instead of every month which is too big 
             k2=anint[m][i]+(mint[m][i]/12.);       for the memory).
             if ((k2>=dateprev1) && (k2<=dateprev2)) {       Model is determined by parameters x and covariates have to be 
               if(agev[m][i]==0) agev[m][i]=agemax+1;       included manually here. 
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];       */
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];    
             }    int i, j, d, h, k;
           }    double **out, cov[NCOVMAX+1];
         }    double **newm;
       }  
          /* Hstepm could be zero and should return the unit matrix */
         for(i=(int)agemin; i <= (int)agemax+3; i++){    for (i=1;i<=nlstate+ndeath;i++)
           for(jk=1; jk <=nlstate ; jk++){      for (j=1;j<=nlstate+ndeath;j++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
               pp[jk] += freq[jk][m][i];        po[i][j][0]=(i==j ? 1.0 : 0.0);
           }      }
           for(jk=1; jk <=nlstate ; jk++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             for(m=-1, pos=0; m <=0 ; m++)    for(h=1; h <=nhstepm; h++){
             pos += freq[jk][m][i];      for(d=1; d <=hstepm; d++){
         }        newm=savm;
                /* Covariates have to be included here again */
          for(jk=1; jk <=nlstate ; jk++){        cov[1]=1.;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
              pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) 
          }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                  for (k=1; k<=cptcovage;k++)
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
          for(jk=1; jk <=nlstate ; jk++){                    cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            if( i <= (int) agemax){  
              if(pos>=1.e-5){  
                probs[i][jk][j1]= pp[jk]/pos;        /*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));
                  savm=oldm;
         }        oldm=newm;
     }      }
   }      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   free_vector(pp,1,nlstate);        }
        /*printf("h=%d ",h);*/
 }  /* End of Freq */    } /* end h */
   /*     printf("\n H=%d \n",h); */
 /************* Waves Concatenation ***************/    return po;
   }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  /*************** log-likelihood *************/
      Death is a valid wave (if date is known).  double func( double *x)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    int i, ii, j, k, mi, d, kk;
      and mw[mi+1][i]. dh depends on stepm.    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      */    double **out;
     double sw; /* Sum of weights */
   int i, mi, m;    double lli; /* Individual log likelihood */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    int s1, s2;
      double sum=0., jmean=0.;*/    double bbh, survp;
     long ipmx;
   int j, k=0,jk, ju, jl;    /*extern weight */
   double sum=0.;    /* We are differentiating ll according to initial status */
   jmin=1e+5;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   jmax=-1;    /*for(i=1;i<imx;i++) 
   jmean=0.;      printf(" %d\n",s[4][i]);
   for(i=1; i<=imx; i++){    */
     mi=0;    cov[1]=1.;
     m=firstpass;  
     while(s[m][i] <= nlstate){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    if(mle==1){
       if(m >=lastpass)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         break;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else        for(mi=1; mi<= wav[i]-1; mi++){
         m++;          for (ii=1;ii<=nlstate+ndeath;ii++)
     }/* end while */            for (j=1;j<=nlstate+ndeath;j++){
     if (s[m][i] > nlstate){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       mi++;     /* Death is another wave */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */            }
          /* Only death is a correct wave */          for(d=0; d<dh[mi][i]; d++){
       mw[mi][i]=m;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     wav[i]=mi;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if(mi==0)            }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for(i=1; i<=imx; i++){            oldm=newm;
     for(mi=1; mi<wav[i];mi++){          } /* end mult */
       if (stepm <=0)        
         dh[mi][i]=1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       else{          /* But now since version 0.9 we anticipate for bias at large stepm.
         if (s[mw[mi+1][i]][i] > nlstate) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           if (agedc[i] < 2*AGESUP) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);           * the nearest (and in case of equal distance, to the lowest) interval but now
           if(j==0) j=1;  /* Survives at least one month after exam */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           k=k+1;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           if (j >= jmax) jmax=j;           * probability in order to take into account the bias as a fraction of the way
           if (j <= jmin) jmin=j;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           sum=sum+j;           * -stepm/2 to stepm/2 .
           /* if (j<10) printf("j=%d num=%d ",j,i); */           * For stepm=1 the results are the same as for previous versions of Imach.
           }           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
         else{          s1=s[mw[mi][i]][i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          s2=s[mw[mi+1][i]][i];
           k=k+1;          bbh=(double)bh[mi][i]/(double)stepm; 
           if (j >= jmax) jmax=j;          /* bias bh is positive if real duration
           else if (j <= jmin)jmin=j;           * is higher than the multiple of stepm and negative otherwise.
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */           */
           sum=sum+j;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         }          if( s2 > nlstate){ 
         jk= j/stepm;            /* i.e. if s2 is a death state and if the date of death is known 
         jl= j -jk*stepm;               then the contribution to the likelihood is the probability to 
         ju= j -(jk+1)*stepm;               die between last step unit time and current  step unit time, 
         if(jl <= -ju)               which is also equal to probability to die before dh 
           dh[mi][i]=jk;               minus probability to die before dh-stepm . 
         else               In version up to 0.92 likelihood was computed
           dh[mi][i]=jk+1;          as if date of death was unknown. Death was treated as any other
         if(dh[mi][i]==0)          health state: the date of the interview describes the actual state
           dh[mi][i]=1; /* At least one step */          and not the date of a change in health state. The former idea was
       }          to consider that at each interview the state was recorded
     }          (healthy, disable or death) and IMaCh was corrected; but when we
   }          introduced the exact date of death then we should have modified
   jmean=sum/k;          the contribution of an exact death to the likelihood. This new
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          contribution is smaller and very dependent of the step unit
  }          stepm. It is no more the probability to die between last interview
 /*********** Tricode ****************************/          and month of death but the probability to survive from last
 void tricode(int *Tvar, int **nbcode, int imx)          interview up to one month before death multiplied by the
 {          probability to die within a month. Thanks to Chris
   int Ndum[20],ij=1, k, j, i;          Jackson for correcting this bug.  Former versions increased
   int cptcode=0;          mortality artificially. The bad side is that we add another loop
   cptcoveff=0;          which slows down the processing. The difference can be up to 10%
            lower mortality.
   for (k=0; k<19; k++) Ndum[k]=0;            */
   for (k=1; k<=7; k++) ncodemax[k]=0;            lli=log(out[s1][s2] - savm[s1][s2]);
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {          } else if  (s2==-2) {
       ij=(int)(covar[Tvar[j]][i]);            for (j=1,survp=0. ; j<=nlstate; j++) 
       Ndum[ij]++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            /*survp += out[s1][j]; */
       if (ij > cptcode) cptcode=ij;            lli= log(survp);
     }          }
           
     for (i=0; i<=cptcode; i++) {          else if  (s2==-4) { 
       if(Ndum[i]!=0) ncodemax[j]++;            for (j=3,survp=0. ; j<=nlstate; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     ij=1;            lli= log(survp); 
           } 
   
     for (i=1; i<=ncodemax[j]; i++) {          else if  (s2==-5) { 
       for (k=0; k<=19; k++) {            for (j=1,survp=0. ; j<=2; j++)  
         if (Ndum[k] != 0) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           nbcode[Tvar[j]][ij]=k;            lli= log(survp); 
           ij++;          } 
         }          
         if (ij > ncodemax[j]) break;          else{
       }              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   }            } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
  for (k=0; k<19; k++) Ndum[k]=0;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
  for (i=1; i<=ncovmodel-2; i++) {          ipmx +=1;
       ij=Tvar[i];          sw += weight[i];
       Ndum[ij]++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
       } /* end of individual */
  ij=1;    }  else if(mle==2){
  for (i=1; i<=10; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    if((Ndum[i]!=0) && (i<=ncov)){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Tvaraff[ij]=i;        for(mi=1; mi<= wav[i]-1; mi++){
      ij++;          for (ii=1;ii<=nlstate+ndeath;ii++)
    }            for (j=1;j<=nlstate+ndeath;j++){
  }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
     cptcoveff=ij-1;            }
 }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
 /*********** Health Expectancies ****************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   /* Health expectancies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, j, nhstepm, hstepm, h;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double age, agelim,hf;            savm=oldm;
   double ***p3mat;            oldm=newm;
            } /* end mult */
   fprintf(ficreseij,"# Health expectancies\n");        
   fprintf(ficreseij,"# Age");          s1=s[mw[mi][i]][i];
   for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
     for(j=1; j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
       fprintf(ficreseij," %1d-%1d",i,j);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   fprintf(ficreseij,"\n");          ipmx +=1;
           sw += weight[i];
   hstepm=1*YEARM; /*  Every j years of age (in month) */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } /* end of wave */
       } /* end of individual */
   agelim=AGESUP;    }  else if(mle==3){  /* exponential inter-extrapolation */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* nhstepm age range expressed in number of stepm */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for(mi=1; mi<= wav[i]-1; mi++){
     /* Typically if 20 years = 20*12/6=40 stepm */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (stepm >= YEARM) hstepm=1;            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(d=0; d<dh[mi][i]; d++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           eij[i][j][(int)age] +=p3mat[i][j][h];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
                oldm=newm;
     hf=1;          } /* end mult */
     if (stepm >= YEARM) hf=stepm/YEARM;        
     fprintf(ficreseij,"%.0f",age );          s1=s[mw[mi][i]][i];
     for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       for(j=1; j<=nlstate;j++){          bbh=(double)bh[mi][i]/(double)stepm; 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          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;
     fprintf(ficreseij,"\n");          sw += weight[i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
 }      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
 /************ Variance ******************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   /* Variance of health expectancies */          for (ii=1;ii<=nlstate+ndeath;ii++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (j=1;j<=nlstate+ndeath;j++){
   double **newm;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **dnewm,**doldm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h;            }
   int k, cptcode;          for(d=0; d<dh[mi][i]; d++){
   double *xp;            newm=savm;
   double **gp, **gm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***gradg, ***trgradg;            for (kk=1; kk<=cptcovage;kk++) {
   double ***p3mat;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double age,agelim;            }
   int theta;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    fprintf(ficresvij,"# Covariances of life expectancies\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficresvij,"# Age");            savm=oldm;
   for(i=1; i<=nlstate;i++)            oldm=newm;
     for(j=1; j<=nlstate;j++)          } /* end mult */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        
   fprintf(ficresvij,"\n");          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   xp=vector(1,npar);          if( s2 > nlstate){ 
   dnewm=matrix(1,nlstate,1,npar);            lli=log(out[s1][s2] - savm[s1][s2]);
   doldm=matrix(1,nlstate,1,nlstate);          }else{
              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   hstepm=1*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          ipmx +=1;
   agelim = AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     if (stepm >= YEARM) hstepm=1;        } /* end of wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } /* end of individual */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gp=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gm=matrix(0,nhstepm,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){ /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (popbased==1) {            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<= nlstate; j++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(h=0; h<=nhstepm; h++){            savm=oldm;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            oldm=newm;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          } /* end mult */
         }        
       }          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ipmx +=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            sw += weight[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
            /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       if (popbased==1) {        } /* end of wave */
         for(i=1; i<=nlstate;i++)      } /* end of individual */
           prlim[i][i]=probs[(int)age][i][ij];    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<= nlstate; j++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(h=0; h<=nhstepm; h++){    return -l;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  /*************** log-likelihood *************/
       }  double funcone( double *x)
   {
       for(j=1; j<= nlstate; j++)    /* Same as likeli but slower because of a lot of printf and if */
         for(h=0; h<=nhstepm; h++){    int i, ii, j, k, mi, d, kk;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         }    double **out;
     } /* End theta */    double lli; /* Individual log likelihood */
     double llt;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int s1, s2;
     double bbh, survp;
     for(h=0; h<=nhstepm; h++)    /*extern weight */
       for(j=1; j<=nlstate;j++)    /* We are differentiating ll according to initial status */
         for(theta=1; theta <=npar; theta++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           trgradg[h][j][theta]=gradg[h][theta][j];    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     for(i=1;i<=nlstate;i++)    */
       for(j=1;j<=nlstate;j++)    cov[1]=1.;
         vareij[i][j][(int)age] =0.;  
     for(h=0;h<=nhstepm;h++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=1;i<=nlstate;i++)      for(mi=1; mi<= wav[i]-1; mi++){
           for(j=1;j<=nlstate;j++)        for (ii=1;ii<=nlstate+ndeath;ii++)
             vareij[i][j][(int)age] += doldm[i][j];          for (j=1;j<=nlstate+ndeath;j++){
       }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     h=1;          }
     if (stepm >= YEARM) h=stepm/YEARM;        for(d=0; d<dh[mi][i]; d++){
     fprintf(ficresvij,"%.0f ",age );          newm=savm;
     for(i=1; i<=nlstate;i++)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(j=1; j<=nlstate;j++){          for (kk=1; kk<=cptcovage;kk++) {
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }          }
     fprintf(ficresvij,"\n");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_matrix(gp,0,nhstepm,1,nlstate);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_matrix(gm,0,nhstepm,1,nlstate);          savm=oldm;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          oldm=newm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        } /* end mult */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
   } /* End age */        s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
   free_vector(xp,1,npar);        bbh=(double)bh[mi][i]/(double)stepm; 
   free_matrix(doldm,1,nlstate,1,npar);        /* bias is positive if real duration
   free_matrix(dnewm,1,nlstate,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
          */
 }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
 /************ Variance of prevlim ******************/        } else if  (s2==-2) {
 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)          for (j=1,survp=0. ; j<=nlstate; j++) 
 {            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* Variance of prevalence limit */          lli= log(survp);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }else if (mle==1){
   double **newm;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **dnewm,**doldm;        } else if(mle==2){
   int i, j, nhstepm, hstepm;          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 */
   int k, cptcode;        } else if(mle==3){  /* exponential inter-extrapolation */
   double *xp;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double *gp, *gm;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **gradg, **trgradg;          lli=log(out[s1][s2]); /* Original formula */
   double age,agelim;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   int theta;          lli=log(out[s1][s2]); /* Original formula */
            } /* End of if */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        ipmx +=1;
   fprintf(ficresvpl,"# Age");        sw += weight[i];
   for(i=1; i<=nlstate;i++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresvpl," %1d-%1d",i,i);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   fprintf(ficresvpl,"\n");        if(globpr){
           fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   xp=vector(1,npar);   %11.6f %11.6f %11.6f ", \
   dnewm=matrix(1,nlstate,1,npar);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   doldm=matrix(1,nlstate,1,nlstate);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   hstepm=1*YEARM; /* Every year of age */            llt +=ll[k]*gipmx/gsw;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   agelim = AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          fprintf(ficresilk," %10.6f\n", -llt);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;      } /* end of wave */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    } /* end of individual */
     gradg=matrix(1,npar,1,nlstate);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     gp=vector(1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     gm=vector(1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
     for(theta=1; theta <=npar; theta++){      gipmx=ipmx;
       for(i=1; i<=npar; i++){ /* Computes gradient */      gsw=sw;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    return -l;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];  
      /*************** function likelione ***********/
       for(i=1; i<=npar; i++) /* Computes gradient */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* This routine should help understanding what is done with 
       for(i=1;i<=nlstate;i++)       the selection of individuals/waves and
         gm[i] = prlim[i][i];       to check the exact contribution to the likelihood.
        Plotting could be done.
       for(i=1;i<=nlstate;i++)     */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int k;
     } /* End theta */  
     if(*globpri !=0){ /* Just counts and sums, no printings */
     trgradg =matrix(1,nlstate,1,npar);      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
     for(j=1; j<=nlstate;j++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(theta=1; theta <=npar; theta++)        printf("Problem with resultfile: %s\n", fileresilk);
         trgradg[j][theta]=gradg[theta][j];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
     for(i=1;i<=nlstate;i++)      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");
       varpl[i][(int)age] =0.;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for(k=1; k<=nlstate; k++) 
     for(i=1;i<=nlstate;i++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    *fretone=(*funcone)(p);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    if(*globpri !=0){
     fprintf(ficresvpl,"\n");      fclose(ficresilk);
     free_vector(gp,1,nlstate);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     free_vector(gm,1,nlstate);      fflush(fichtm); 
     free_matrix(gradg,1,npar,1,nlstate);    } 
     free_matrix(trgradg,1,nlstate,1,npar);    return;
   } /* End age */  }
   
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  /*********** Maximum Likelihood Estimation ***************/
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 }  {
     int i,j, iter;
 /************ Variance of one-step probabilities  ******************/    double **xi;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double fret;
 {    double fretone; /* Only one call to likelihood */
   int i, j;    /*  char filerespow[FILENAMELENGTH];*/
   int k=0, cptcode;    xi=matrix(1,npar,1,npar);
   double **dnewm,**doldm;    for (i=1;i<=npar;i++)
   double *xp;      for (j=1;j<=npar;j++)
   double *gp, *gm;        xi[i][j]=(i==j ? 1.0 : 0.0);
   double **gradg, **trgradg;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double age,agelim, cov[NCOVMAX];    strcpy(filerespow,"pow"); 
   int theta;    strcat(filerespow,fileres);
   char fileresprob[FILENAMELENGTH];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   strcpy(fileresprob,"prob");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   strcat(fileresprob,fileres);    }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     printf("Problem with resultfile: %s\n", fileresprob);    for (i=1;i<=nlstate;i++)
   }      for(j=1;j<=nlstate+ndeath;j++)
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   
   xp=vector(1,npar);    powell(p,xi,npar,ftol,&iter,&fret,func);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   cov[1]=1;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for (age=bage; age<=fage; age ++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     cov[2]=age;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  /**** Computes Hessian and covariance matrix ***/
      void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++)    double  **a,**y,*x,pd;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **hess;
          int i, j,jk;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    int *indx;
      
       k=0;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(i=1; i<= (nlstate+ndeath); i++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         for(j=1; j<=(nlstate+ndeath);j++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
            k=k+1;    void ludcmp(double **a, int npar, int *indx, double *d) ;
           gp[k]=pmmij[i][j];    double gompertz(double p[]);
         }    hess=matrix(1,npar,1,npar);
       }  
     printf("\nCalculation of the hessian matrix. Wait...\n");
       for(i=1; i<=npar; i++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++){
          printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);     
       k=0;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(i=1; i<=(nlstate+ndeath); i++){      
         for(j=1; j<=(nlstate+ndeath);j++){      /*  printf(" %f ",p[i]);
           k=k+1;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
           gm[k]=pmmij[i][j];    }
         }    
       }    for (i=1;i<=npar;i++) {
            for (j=1;j<=npar;j++)  {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        if (j>i) { 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          
       for(theta=1; theta <=npar; theta++)          hess[j][i]=hess[i][j];    
       trgradg[j][theta]=gradg[theta][j];          /*printf(" %lf ",hess[i][j]);*/
          }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    }
     printf("\n");
      pmij(pmmij,cov,ncovmodel,x,nlstate);    fprintf(ficlog,"\n");
   
      k=0;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        for(j=1; j<=(nlstate+ndeath);j++){    
          k=k+1;    a=matrix(1,npar,1,npar);
          gm[k]=pmmij[i][j];    y=matrix(1,npar,1,npar);
         }    x=vector(1,npar);
      }    indx=ivector(1,npar);
          for (i=1;i<=npar;i++)
      /*printf("\n%d ",(int)age);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    ludcmp(a,npar,indx,&pd);
          
     for (j=1;j<=npar;j++) {
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      for (i=1;i<=npar;i++) x[i]=0;
      }*/      x[j]=1;
       lubksb(a,npar,indx,x);
   fprintf(ficresprob,"\n%d ",(int)age);      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      }
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=1;i<=npar;i++) { 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=npar;j++) { 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        printf("%.3e ",hess[i][j]);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        fprintf(ficlog,"%.3e ",hess[i][j]);
 }      }
  free_vector(xp,1,npar);      printf("\n");
 fclose(ficresprob);      fprintf(ficlog,"\n");
     }
 }  
     /* Recompute Inverse */
 /******************* Printing html file ***********/    for (i=1;i<=npar;i++)
 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 optionfile[],char optionfilehtm[] ){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   int jj1, k1, i1, cpt;    ludcmp(a,npar,indx,&pd);
   FILE *fichtm;  
   /*char optionfilehtm[FILENAMELENGTH];*/    /*  printf("\n#Hessian matrix recomputed#\n");
   
   strcpy(optionfilehtm,optionfile);    for (j=1;j<=npar;j++) {
   strcat(optionfilehtm,".htm");      for (i=1;i<=npar;i++) x[i]=0;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      x[j]=1;
     printf("Problem with %s \n",optionfilehtm), exit(0);      lubksb(a,npar,indx,x);
   }      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">        printf("%.3e ",y[i][j]);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        fprintf(ficlog,"%.3e ",y[i][j]);
       }
 Total number of observations=%d <br>      printf("\n");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      fprintf(ficlog,"\n");
 <hr  size=\"2\" color=\"#EC5E5E\">    }
 <li>Outputs files<br><br>\n    */
         - 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>    free_matrix(a,1,npar,1,npar);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    free_matrix(y,1,npar,1,npar);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    free_vector(x,1,npar);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    free_ivector(indx,1,npar);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    free_matrix(hess,1,npar,1,npar);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  }
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>  
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  /*************** hessian matrix ****************/
    double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 fprintf(fichtm," <li>Graphs</li><p>");  {
     int i;
  m=cptcoveff;    int l=1, lmax=20;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
  jj1=0;    double res;
  for(k1=1; k1<=m;k1++){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    for(i1=1; i1<=ncodemax[k1];i1++){    double fx;
        jj1++;    int k=0,kmax=10;
        if (cptcovn > 0) {    double l1;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)    fx=func(x);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    for (i=1;i<=npar;i++) p2[i]=x[i];
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    for(l=0 ; l <=lmax; l++){
        }      l1=pow(10,l);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      delts=delt;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for(k=1 ; k <kmax; k=k+1){
        for(cpt=1; cpt<nlstate;cpt++){        delt = delta*(l1*k);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        p2[theta]=x[theta] +delt;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        k1=func(p2)-fx;
        }        p2[theta]=x[theta]-delt;
     for(cpt=1; cpt<=nlstate;cpt++) {        k2=func(p2)-fx;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        /*res= (k1-2.0*fx+k2)/delt/delt; */
 interval) in state (%d): v%s%d%d.gif <br>        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          
      }  #ifdef DEBUGHESS
      for(cpt=1; cpt<=nlstate;cpt++) {        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        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);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  #endif
      }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 health expectancies in states (1) and (2): e%s%d.gif<br>          k=kmax;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
 fprintf(fichtm,"\n</body>");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
    }          k=kmax; l=lmax*10.;
    }        }
 fclose(fichtm);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 }          delts=delt;
         }
 /******************* Gnuplot file **************/      }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){    }
     delti[theta]=delts;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    return res; 
     
   strcpy(optionfilegnuplot,optionfilefiname);  }
   strcat(optionfilegnuplot,".plt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     printf("Problem with file %s",optionfilegnuplot);  {
   }    int i;
     int l=1, l1, lmax=20;
 #ifdef windows    double k1,k2,k3,k4,res,fx;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double p2[MAXPARM+1];
 #endif    int k;
 m=pow(2,cptcoveff);  
      fx=func(x);
  /* 1eme*/    for (k=1; k<=2; k++) {
   for (cpt=1; cpt<= nlstate ; cpt ++) {      for (i=1;i<=npar;i++) p2[i]=x[i];
    for (k1=1; k1<= m ; k1 ++) {      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 #ifdef windows      k1=func(p2)-fx;
     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);    
 #endif      p2[thetai]=x[thetai]+delti[thetai]/k;
 #ifdef unix      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      k2=func(p2)-fx;
 #endif    
       p2[thetai]=x[thetai]-delti[thetai]/k;
 for (i=1; i<= nlstate ; i ++) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      k3=func(p2)-fx;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      p2[thetai]=x[thetai]-delti[thetai]/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);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for (i=1; i<= nlstate ; i ++) {      k4=func(p2)-fx;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #ifdef DEBUG
 }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      for (i=1; i<= nlstate ; i ++) {  #endif
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    return res;
 }    }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix  /************** Inverse of matrix **************/
 fprintf(ficgp,"\nset ter gif small size 400,300");  void ludcmp(double **a, int n, int *indx, double *d) 
 #endif  { 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int i,imax,j,k; 
    }    double big,dum,sum,temp; 
   }    double *vv; 
   /*2 eme*/   
     vv=vector(1,n); 
   for (k1=1; k1<= m ; k1 ++) {    *d=1.0; 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    for (i=1;i<=n;i++) { 
          big=0.0; 
     for (i=1; i<= nlstate+1 ; i ++) {      for (j=1;j<=n;j++) 
       k=2*i;        if ((temp=fabs(a[i][j])) > big) big=temp; 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for (j=1; j<= nlstate+1 ; j ++) {      vv[i]=1.0/big; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (j=1;j<=n;j++) { 
 }        for (i=1;i<j;i++) { 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        sum=a[i][j]; 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        a[i][j]=sum; 
       for (j=1; j<= nlstate+1 ; j ++) {      } 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      big=0.0; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");      for (i=j;i<=n;i++) { 
 }          sum=a[i][j]; 
       fprintf(ficgp,"\" t\"\" w l 0,");        for (k=1;k<j;k++) 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          sum -= a[i][k]*a[k][j]; 
       for (j=1; j<= nlstate+1 ; j ++) {        a[i][j]=sum; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          big=dum; 
 }            imax=i; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        } 
       else fprintf(ficgp,"\" t\"\" w l 0,");      } 
     }      if (j != imax) { 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        for (k=1;k<=n;k++) { 
   }          dum=a[imax][k]; 
            a[imax][k]=a[j][k]; 
   /*3eme*/          a[j][k]=dum; 
         } 
   for (k1=1; k1<= m ; k1 ++) {        *d = -(*d); 
     for (cpt=1; cpt<= nlstate ; cpt ++) {        vv[imax]=vv[j]; 
       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);      indx[j]=imax; 
       for (i=1; i< nlstate ; i ++) {      if (a[j][j] == 0.0) a[j][j]=TINY; 
         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);      if (j != n) { 
       }        dum=1.0/(a[j][j]); 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     }    } 
      free_vector(vv,1,n);  /* Doesn't work */
   /* CV preval stat */  ;
     for (k1=1; k1<= m ; k1 ++) {  } 
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;  void lubksb(double **a, int n, int *indx, double b[]) 
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  { 
     int i,ii=0,ip,j; 
       for (i=1; i< nlstate ; i ++)    double sum; 
         fprintf(ficgp,"+$%d",k+i+1);   
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    for (i=1;i<=n;i++) { 
            ip=indx[i]; 
       l=3+(nlstate+ndeath)*cpt;      sum=b[ip]; 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      b[ip]=b[i]; 
       for (i=1; i< nlstate ; i ++) {      if (ii) 
         l=3+(nlstate+ndeath)*cpt;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         fprintf(ficgp,"+$%d",l+i+1);      else if (sum) ii=i; 
       }      b[i]=sum; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      } 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for (i=n;i>=1;i--) { 
     }      sum=b[i]; 
   }        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        b[i]=sum/a[i][i]; 
   /* proba elementaires */    } 
    for(i=1,jk=1; i <=nlstate; i++){  } 
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {  void pstamp(FILE *fichier)
         for(j=1; j <=ncovmodel; j++){  {
            fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  }
           jk++;  
           fprintf(ficgp,"\n");  /************ Frequencies ********************/
         }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
       }  {  /* Some frequencies */
     }    
     }    int i, m, jk, k1,i1, j1, bool, z1,j;
     int first;
     for(jk=1; jk <=m; jk++) {    double ***freq; /* Frequencies */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    double *pp, **prop;
    i=1;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
    for(k2=1; k2<=nlstate; k2++) {    char fileresp[FILENAMELENGTH];
      k3=i;    
      for(k=1; k<=(nlstate+ndeath); k++) {    pp=vector(1,nlstate);
        if (k != k2){    prop=matrix(1,nlstate,iagemin,iagemax+3);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    strcpy(fileresp,"p");
 ij=1;    strcat(fileresp,fileres);
         for(j=3; j <=ncovmodel; j++) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             ij++;      exit(0);
           }    }
           else    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    j1=0;
         }    
           fprintf(ficgp,")/(1");    j=cptcoveff;
            if (cptcovn<1) {j=1;ncodemax[1]=1;}
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    first=1;
 ij=1;  
           for(j=3; j <=ncovmodel; j++){    for(k1=1; k1<=j;k1++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(i1=1; i1<=ncodemax[k1];i1++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        j1++;
             ij++;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           }          scanf("%d", i);*/
           else        for (i=-5; i<=nlstate+ndeath; i++)  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           }            for(m=iagemin; m <= iagemax+3; m++)
           fprintf(ficgp,")");              freq[i][jk][m]=0;
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      for (i=1; i<=nlstate; i++)  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for(m=iagemin; m <= iagemax+3; m++)
         i=i+ncovmodel;          prop[i][m]=0;
        }        
      }        dateintsum=0;
    }        k2cpt=0;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        for (i=1; i<=imx; i++) {
    }          bool=1;
              if  (cptcovn>0) {
   fclose(ficgp);            for (z1=1; z1<=cptcoveff; z1++) 
 }  /* end gnuplot */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
           }
 /*************** Moving average **************/          if (bool==1){
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   int i, cpt, cptcod;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     for (agedeb=agemin; agedeb<=fage; agedeb++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for (i=1; i<=nlstate;i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
           mobaverage[(int)agedeb][i][cptcod]=0.;                if (m<lastpass) {
                      freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       for (i=1; i<=nlstate;i++){                }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                
           for (cpt=0;cpt<=4;cpt++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                  dateintsum=dateintsum+k2;
           }                  k2cpt++;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                }
         }                /*}*/
       }            }
     }          }
            }
 }         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 /***********************************************/        pstamp(ficresp);
 /**************** Main Program *****************/        if  (cptcovn>0) {
 /***********************************************/          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 int main(int argc, char *argv[])          fprintf(ficresp, "**********\n#");
 {        }
         for(i=1; i<=nlstate;i++) 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double agedeb, agefin,hf;        fprintf(ficresp, "\n");
   double agemin=1.e20, agemax=-1.e20;        
         for(i=iagemin; i <= iagemax+3; i++){
   double fret;          if(i==iagemax+3){
   double **xi,tmp,delta;            fprintf(ficlog,"Total");
           }else{
   double dum; /* Dummy variable */            if(first==1){
   double ***p3mat;              first=0;
   int *indx;              printf("See log file for details...\n");
   char line[MAXLINE], linepar[MAXLINE];            }
   char title[MAXLINE];            fprintf(ficlog,"Age %d", i);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];              pp[jk] += freq[jk][m][i]; 
           }
   char filerest[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char fileregp[FILENAMELENGTH];            for(m=-1, pos=0; m <=0 ; m++)
   char popfile[FILENAMELENGTH];              pos += freq[jk][m][i];
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            if(pp[jk]>=1.e-10){
   int firstobs=1, lastobs=10;              if(first==1){
   int sdeb, sfin; /* Status at beginning and end */                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int c,  h , cpt,l;              }
   int ju,jl, mi;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            }else{
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              if(first==1)
   int mobilav=0,popforecast=0;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int hstepm, nhstepm;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int *popage;/*boolprev=0 if date and zero if wave*/            }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;          }
   
   double bage, fage, age, agelim, agebase;          for(jk=1; jk <=nlstate ; jk++){
   double ftolpl=FTOL;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double **prlim;              pp[jk] += freq[jk][m][i];
   double *severity;          }       
   double ***param; /* Matrix of parameters */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double  *p;            pos += pp[jk];
   double **matcov; /* Matrix of covariance */            posprop += prop[jk][i];
   double ***delti3; /* Scale */          }
   double *delti; /* Scale */          for(jk=1; jk <=nlstate ; jk++){
   double ***eij, ***vareij;            if(pos>=1.e-5){
   double **varpl; /* Variances of prevalence limits by age */              if(first==1)
   double *epj, vepp;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double kk1, kk2;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double *popeffectif,*popcount;            }else{
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;              if(first==1)
   double yp,yp1,yp2;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";            }
   char *alph[]={"a","a","b","c","d","e"}, str[4];            if( i <= iagemax){
               if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   char z[1]="c", occ;                /*probs[i][jk][j1]= pp[jk]/pos;*/
 #include <sys/time.h>                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 #include <time.h>              }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              else
                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   /* long total_usecs;            }
   struct timeval start_time, end_time;          }
            
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   printf("\n%s",version);              if(first==1)
   if(argc <=1){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     printf("\nEnter the parameter file name: ");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     scanf("%s",pathtot);              }
   }          if(i <= iagemax)
   else{            fprintf(ficresp,"\n");
     strcpy(pathtot,argv[1]);          if(first==1)
   }            printf("Others in log...\n");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          fprintf(ficlog,"\n");
   /*cygwin_split_path(pathtot,path,optionfile);        }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      }
   /* cutv(path,optionfile,pathtot,'\\');*/    }
     dateintmean=dateintsum/k2cpt; 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);   
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    fclose(ficresp);
   chdir(path);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   replace(pathc,path);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 /*-------- arguments in the command line --------*/    /* End of Freq */
   }
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);  /************ Prevalence ********************/
   strcat(fileres,".txt");    /* Other files have txt extension */  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)
   {  
   /*---------arguments file --------*/    /* 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).
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       We still use firstpass and lastpass as another selection.
     printf("Problem with optionfile %s\n",optionfile);    */
     goto end;   
   }    int i, m, jk, k1, i1, j1, bool, z1,j;
     double ***freq; /* Frequencies */
   strcpy(filereso,"o");    double *pp, **prop;
   strcat(filereso,fileres);    double pos,posprop; 
   if((ficparo=fopen(filereso,"w"))==NULL) {    double  y2; /* in fractional years */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    int iagemin, iagemax;
   }  
     iagemin= (int) agemin;
   /* Reads comments: lines beginning with '#' */    iagemax= (int) agemax;
   while((c=getc(ficpar))=='#' && c!= EOF){    /*pp=vector(1,nlstate);*/
     ungetc(c,ficpar);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     fgets(line, MAXLINE, ficpar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     puts(line);    j1=0;
     fputs(line,ficparo);    
   }    j=cptcoveff;
   ungetc(c,ficpar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   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);    for(k1=1; k1<=j;k1++){
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);      for(i1=1; i1<=ncodemax[k1];i1++){
   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);        j1++;
 while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        for (i=1; i<=nlstate; i++)  
     fgets(line, MAXLINE, ficpar);          for(m=iagemin; m <= iagemax+3; m++)
     puts(line);            prop[i][m]=0.0;
     fputs(line,ficparo);       
   }        for (i=1; i<=imx; i++) { /* Each individual */
   ungetc(c,ficpar);          bool=1;
            if  (cptcovn>0) {
                for (z1=1; z1<=cptcoveff; z1++) 
   covar=matrix(0,NCOVMAX,1,n);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   cptcovn=0;                bool=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          } 
           if (bool==1) { 
   ncovmodel=2+cptcovn;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   /* Read guess parameters */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /* Reads comments: lines beginning with '#' */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   while((c=getc(ficpar))=='#' && c!= EOF){                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); 
     ungetc(c,ficpar);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     fgets(line, MAXLINE, ficpar);                  /*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]]);*/
     puts(line);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fputs(line,ficparo);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   }                } 
   ungetc(c,ficpar);              }
              } /* end selection of waves */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          }
     for(i=1; i <=nlstate; i++)        }
     for(j=1; j <=nlstate+ndeath-1; j++){        for(i=iagemin; i <= iagemax+3; i++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);          
       fprintf(ficparo,"%1d%1d",i1,j1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       printf("%1d%1d",i,j);            posprop += prop[jk][i]; 
       for(k=1; k<=ncovmodel;k++){          } 
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);          for(jk=1; jk <=nlstate ; jk++){     
         fprintf(ficparo," %lf",param[i][j][k]);            if( i <=  iagemax){ 
       }              if(posprop>=1.e-5){ 
       fscanf(ficpar,"\n");                probs[i][jk][j1]= prop[jk][i]/posprop;
       printf("\n");              } else
       fprintf(ficparo,"\n");                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
     }            } 
            }/* end jk */ 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        }/* end i */ 
       } /* end i1 */
   p=param[1][1];    } /* end k1 */
      
   /* Reads comments: lines beginning with '#' */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   while((c=getc(ficpar))=='#' && c!= EOF){    /*free_vector(pp,1,nlstate);*/
     ungetc(c,ficpar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     fgets(line, MAXLINE, ficpar);  }  /* End of prevalence */
     puts(line);  
     fputs(line,ficparo);  /************* Waves Concatenation ***************/
   }  
   ungetc(c,ficpar);  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)
   {
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       Death is a valid wave (if date is known).
   for(i=1; i <=nlstate; i++){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     for(j=1; j <=nlstate+ndeath-1; j++){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       fscanf(ficpar,"%1d%1d",&i1,&j1);       and mw[mi+1][i]. dh depends on stepm.
       printf("%1d%1d",i,j);       */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){    int i, mi, m;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         printf(" %le",delti3[i][j][k]);       double sum=0., jmean=0.;*/
         fprintf(ficparo," %le",delti3[i][j][k]);    int first;
       }    int j, k=0,jk, ju, jl;
       fscanf(ficpar,"\n");    double sum=0.;
       printf("\n");    first=0;
       fprintf(ficparo,"\n");    jmin=1e+5;
     }    jmax=-1;
   }    jmean=0.;
   delti=delti3[1][1];    for(i=1; i<=imx; i++){
        mi=0;
   /* Reads comments: lines beginning with '#' */      m=firstpass;
   while((c=getc(ficpar))=='#' && c!= EOF){      while(s[m][i] <= nlstate){
     ungetc(c,ficpar);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     fgets(line, MAXLINE, ficpar);          mw[++mi][i]=m;
     puts(line);        if(m >=lastpass)
     fputs(line,ficparo);          break;
   }        else
   ungetc(c,ficpar);          m++;
        }/* end while */
   matcov=matrix(1,npar,1,npar);      if (s[m][i] > nlstate){
   for(i=1; i <=npar; i++){        mi++;     /* Death is another wave */
     fscanf(ficpar,"%s",&str);        /* if(mi==0)  never been interviewed correctly before death */
     printf("%s",str);           /* Only death is a correct wave */
     fprintf(ficparo,"%s",str);        mw[mi][i]=m;
     for(j=1; j <=i; j++){      }
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);      wav[i]=mi;
       fprintf(ficparo," %.5le",matcov[i][j]);      if(mi==0){
     }        nbwarn++;
     fscanf(ficpar,"\n");        if(first==0){
     printf("\n");          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fprintf(ficparo,"\n");          first=1;
   }        }
   for(i=1; i <=npar; i++)        if(first==1){
     for(j=i+1;j<=npar;j++)          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       matcov[i][j]=matcov[j][i];        }
          } /* end mi==0 */
   printf("\n");    } /* End individuals */
   
     for(i=1; i<=imx; i++){
     /*-------- data file ----------*/      for(mi=1; mi<wav[i];mi++){
     if((ficres =fopen(fileres,"w"))==NULL) {        if (stepm <=0)
       printf("Problem with resultfile: %s\n", fileres);goto end;          dh[mi][i]=1;
     }        else{
     fprintf(ficres,"#%s\n",version);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                if (agedc[i] < 2*AGESUP) {
     if((fic=fopen(datafile,"r"))==NULL)    {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       printf("Problem with datafile: %s\n", datafile);goto end;              if(j==0) j=1;  /* Survives at least one month after exam */
     }              else if(j<0){
                 nberr++;
     n= lastobs;                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]);
     severity = vector(1,maxwav);                j=1; /* Temporary Dangerous patch */
     outcome=imatrix(1,maxwav+1,1,n);                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);
     num=ivector(1,n);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     moisnais=vector(1,n);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     annais=vector(1,n);              }
     moisdc=vector(1,n);              k=k+1;
     andc=vector(1,n);              if (j >= jmax){
     agedc=vector(1,n);                jmax=j;
     cod=ivector(1,n);                ijmax=i;
     weight=vector(1,n);              }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              if (j <= jmin){
     mint=matrix(1,maxwav,1,n);                jmin=j;
     anint=matrix(1,maxwav,1,n);                ijmin=i;
     s=imatrix(1,maxwav+1,1,n);              }
     adl=imatrix(1,maxwav+1,1,n);                  sum=sum+j;
     tab=ivector(1,NCOVMAX);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     ncodemax=ivector(1,8);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
     i=1;          }
     while (fgets(line, MAXLINE, fic) != NULL)    {          else{
       if ((i >= firstobs) && (i <=lastobs)) {            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]); */
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            k=k+1;
           strcpy(line,stra);            if (j >= jmax) {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              jmax=j;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              ijmax=i;
         }            }
                    else if (j <= jmin){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              jmin=j;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              ijmin=i;
             }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              nberr++;
         for (j=ncov;j>=1;j--){              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              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]);
         }            }
         num[i]=atol(stra);            sum=sum+j;
                  }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          jk= j/stepm;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
         i=i+1;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       }            if(jl==0){
     }              dh[mi][i]=jk;
     /* printf("ii=%d", ij);              bh[mi][i]=0;
        scanf("%d",i);*/            }else{ /* We want a negative bias in order to only have interpolation ie
   imx=i-1; /* Number of individuals */                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   /* for (i=1; i<=imx; i++){              bh[mi][i]=ju;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            }
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          }else{
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            if(jl <= -ju){
     }              dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
     for (i=1; i<=imx; i++)                                   * is higher than the multiple of stepm and negative otherwise.
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/                                   */
             }
   /* Calculation of the number of parameter from char model*/            else{
   Tvar=ivector(1,15);              dh[mi][i]=jk+1;
   Tprod=ivector(1,15);              bh[mi][i]=ju;
   Tvaraff=ivector(1,15);            }
   Tvard=imatrix(1,15,1,2);            if(dh[mi][i]==0){
   Tage=ivector(1,15);                    dh[mi][i]=1; /* At least one step */
                  bh[mi][i]=ju; /* At least one step */
   if (strlen(model) >1){              /*  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);*/
     j=0, j1=0, k1=1, k2=1;            }
     j=nbocc(model,'+');          } /* end if mle */
     j1=nbocc(model,'*');        }
     cptcovn=j+1;      } /* end wave */
     cptcovprod=j1;    }
        jmean=sum/k;
        printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     strcpy(modelsav,model);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){   }
       printf("Error. Non available option model=%s ",model);  
       goto end;  /*********** Tricode ****************************/
     }  void tricode(int *Tvar, int **nbcode, int imx)
      {
     for(i=(j+1); i>=1;i--){    
       cutv(stra,strb,modelsav,'+');    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       /*scanf("%d",i);*/    int cptcode=0;
       if (strchr(strb,'*')) {    cptcoveff=0; 
         cutv(strd,strc,strb,'*');   
         if (strcmp(strc,"age")==0) {    for (k=0; k<maxncov; k++) Ndum[k]=0;
           cptcovprod--;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
           cptcovage++;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
             Tage[cptcovage]=i;                                 modality*/ 
             /*printf("stre=%s ", stre);*/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
         }        Ndum[ij]++; /*counts the occurence of this modality */
         else if (strcmp(strd,"age")==0) {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           cptcovprod--;        if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
           cutv(strb,stre,strc,'V');                                         Tvar[j]. If V=sex and male is 0 and 
           Tvar[i]=atoi(stre);                                         female is 1, then  cptcode=1.*/
           cptcovage++;      }
           Tage[cptcovage]=i;  
         }      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
         else {        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
           cutv(strb,stre,strc,'V');                                         th covariate. In fact
           Tvar[i]=ncov+k1;                                         ncodemax[j]=2
           cutv(strb,strc,strd,'V');                                         (dichotom. variables only) but
           Tprod[k1]=i;                                         it can be more */
           Tvard[k1][1]=atoi(strc);      } /* Ndum[-1] number of undefined modalities */
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];      ij=1; 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
           for (k=1; k<=lastobs;k++)        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
           k1++;            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
           k2=k2+2;                                       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++;
       else {          }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          if (ij > ncodemax[j]) break; 
        /*  scanf("%d",i);*/        }  
       cutv(strd,strc,strb,'V');      } 
       Tvar[i]=atoi(strc);    }  
       }  
       strcpy(modelsav,stra);     for (k=0; k< maxncov; k++) Ndum[k]=0;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/   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]++;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   }
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/   ij=1;
     fclose(fic);   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
     /*  if(mle==1){*/       Tvaraff[ij]=i; /*For printing */
     if (weightopt != 1) { /* Maximisation without weights*/       ij++;
       for(i=1;i<=n;i++) weight[i]=1.0;     }
     }   }
     /*-calculation of age at interview from date of interview and age at death -*/   ij--;
     agev=matrix(1,maxwav,1,imx);   cptcoveff=ij; /*Number of simple covariates*/
   }
    for (i=1; i<=imx; i++)  
      for(m=2; (m<= maxwav); m++)  /*********** Health Expectancies ****************/
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
          s[m][i]=-1;  
        }  {
        /* Health expectancies, no variances */
     for (i=1; i<=imx; i++)  {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    int nhstepma, nstepma; /* Decreasing with age */
       for(m=1; (m<= maxwav); m++){    double age, agelim, hf;
         if(s[m][i] >0){    double ***p3mat;
           if (s[m][i] == nlstate+1) {    double eip;
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)    pstamp(ficreseij);
               agev[m][i]=agedc[i];    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
             else {    fprintf(ficreseij,"# Age");
               if (andc[i]!=9999){    for(i=1; i<=nlstate;i++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      for(j=1; j<=nlstate;j++){
               agev[m][i]=-1;        fprintf(ficreseij," e%1d%1d ",i,j);
               }      }
             }      fprintf(ficreseij," e%1d. ",i);
           }    }
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(ficreseij,"\n");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    
               agev[m][i]=1;    if(estepm < stepm){
             else if(agev[m][i] <agemin){      printf ("Problem %d lower than %d\n",estepm, stepm);
               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  hstepm=estepm;   
             }    /* We compute the life expectancy from trapezoids spaced every estepm months
             else if(agev[m][i] >agemax){     * This is mainly to measure the difference between two models: for example
               agemax=agev[m][i];     * if stepm=24 months pijx are given only every 2 years and by summing them
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
             }     * progression in between and thus overestimating or underestimating according
             /*agev[m][i]=anint[m][i]-annais[i];*/     * to the curvature of the survival function. If, for the same date, we 
             /*   agev[m][i] = age[i]+2*m;*/     * 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 
           else { /* =9 */     * hypothesis. A more precise result, taking into account a more precise
             agev[m][i]=1;     * curvature will be obtained if estepm is as small as stepm. */
             s[m][i]=-1;  
           }    /* 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. 
         else /*= 0 Unknown */       nhstepm is the number of hstepm from age to agelim 
           agev[m][i]=1;       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
     for (i=1; i<=imx; i++)  {       survival function given by stepm (the optimization length). Unfortunately it
       for(m=1; (m<= maxwav); m++){       means that if the survival funtion is printed only each two years of age and if
         if (s[m][i] > (nlstate+ndeath)) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           printf("Error: Wrong value in nlstate or ndeath\n");         results. So we changed our mind and took the option of the best precision.
           goto end;    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }  
     }    agelim=AGESUP;
     /* If stepm=6 months */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     free_vector(severity,1,maxwav);      
     free_imatrix(outcome,1,maxwav+1,1,n);  /* nhstepm age range expressed in number of stepm */
     free_vector(moisnais,1,n);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     free_vector(annais,1,n);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* free_matrix(mint,1,maxwav,1,n);    /* if (stepm >= YEARM) hstepm=1;*/
        free_matrix(anint,1,maxwav,1,n);*/    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     free_vector(moisdc,1,n);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(andc,1,n);  
     for (age=bage; age<=fage; age ++){ 
          nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     wav=ivector(1,imx);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      /* if (stepm >= YEARM) hstepm=1;*/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      
     /* Concatenates waves */      /* If stepm=6 months */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       Tcode=ivector(1,100);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      
       ncodemax[1]=1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      
            printf("%d|",(int)age);fflush(stdout);
    codtab=imatrix(1,100,1,10);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
    h=0;      
    m=pow(2,cptcoveff);      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
    for(k=1;k<=cptcoveff; k++){        for(j=1; j<=nlstate;j++)
      for(i=1; i <=(m/pow(2,k));i++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        for(j=1; j <= ncodemax[k]; j++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            
            h++;            /* 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]);*/
            if (h>m) h=1;codtab[h][k]=j;  
          }          }
        }  
      }      fprintf(ficreseij,"%3.0f",age );
    }      for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
    /*for(i=1; i <=m ;i++){          eip +=eij[i][j][(int)age];
      for(k=1; k <=cptcovn; k++){          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        }
      }        fprintf(ficreseij,"%9.4f", eip );
      printf("\n");      }
    }      fprintf(ficreseij,"\n");
    scanf("%d",i);*/      
        }
    /* Calculates basic frequencies. Computes observed prevalence at single age    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        and prints on file fileres'p'. */    printf("\n");
     fprintf(ficlog,"\n");
        
      }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  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[] )
     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 */    /* Covariances of health expectancies eij and of total life expectancies according
           to initial status i, ei. .
     /* 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] */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     if(mle==1){    double ***p3matp, ***p3matm, ***varhe;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    double **dnewm,**doldm;
     }    double *xp, *xm;
        double **gp, **gm;
     /*--------- results files --------------*/    double ***gradg, ***trgradg;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    int theta;
    
     double eip, vip;
    jk=1;  
    fprintf(ficres,"# Parameters\n");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    printf("# Parameters\n");    xp=vector(1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    xm=vector(1,npar);
      for(k=1; k <=(nlstate+ndeath); k++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
        if (k != i)    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
          {    
            printf("%d%d ",i,k);    pstamp(ficresstdeij);
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
            for(j=1; j <=ncovmodel; j++){    fprintf(ficresstdeij,"# Age");
              printf("%f ",p[jk]);    for(i=1; i<=nlstate;i++){
              fprintf(ficres,"%f ",p[jk]);      for(j=1; j<=nlstate;j++)
              jk++;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
            }      fprintf(ficresstdeij," e%1d. ",i);
            printf("\n");    }
            fprintf(ficres,"\n");    fprintf(ficresstdeij,"\n");
          }  
      }    pstamp(ficrescveij);
    }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
  if(mle==1){    fprintf(ficrescveij,"# Age");
     /* Computing hessian and covariance matrix */    for(i=1; i<=nlstate;i++)
     ftolhess=ftol; /* Usually correct */      for(j=1; j<=nlstate;j++){
     hesscov(matcov, p, npar, delti, ftolhess, func);        cptj= (j-1)*nlstate+i;
  }        for(i2=1; i2<=nlstate;i2++)
     fprintf(ficres,"# Scales\n");          for(j2=1; j2<=nlstate;j2++){
     printf("# Scales\n");            cptj2= (j2-1)*nlstate+i2;
      for(i=1,jk=1; i <=nlstate; i++){            if(cptj2 <= cptj)
       for(j=1; j <=nlstate+ndeath; j++){              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         if (j!=i) {          }
           fprintf(ficres,"%1d%1d",i,j);      }
           printf("%1d%1d",i,j);    fprintf(ficrescveij,"\n");
           for(k=1; k<=ncovmodel;k++){    
             printf(" %.5e",delti[jk]);    if(estepm < stepm){
             fprintf(ficres," %.5e",delti[jk]);      printf ("Problem %d lower than %d\n",estepm, stepm);
             jk++;    }
           }    else  hstepm=estepm;   
           printf("\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
           fprintf(ficres,"\n");     * 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 
     k=1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     fprintf(ficres,"# Covariance\n");     * to compare the new estimate of Life expectancy with the same linear 
     printf("# Covariance\n");     * hypothesis. A more precise result, taking into account a more precise
     for(i=1;i<=npar;i++){     * curvature will be obtained if estepm is as small as stepm. */
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       printf("%s%d%d",alph[k],i1,tab[i]);*/       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficres,"%3d",i);       nstepm is the number of stepm from age to agelin. 
       printf("%3d",i);       Look at hpijx to understand the reason of that which relies in memory size
       for(j=1; j<=i;j++){       and note for a fixed period like estepm months */
         fprintf(ficres," %.5e",matcov[i][j]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         printf(" %.5e",matcov[i][j]);       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
       fprintf(ficres,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("\n");       results. So we changed our mind and took the option of the best precision.
       k++;    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      
     while((c=getc(ficpar))=='#' && c!= EOF){    /* If stepm=6 months */
       ungetc(c,ficpar);    /* nhstepm age range expressed in number of stepm */
       fgets(line, MAXLINE, ficpar);    agelim=AGESUP;
       puts(line);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
       fputs(line,ficparo);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     }    /* if (stepm >= YEARM) hstepm=1;*/
     ungetc(c,ficpar);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if (fage <= 2) {    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       bage = agemin;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       fage = agemax;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     }    gm=matrix(0,nhstepm,1,nlstate*nlstate);
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    for (age=bage; age<=fage; age ++){ 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
     while((c=getc(ficpar))=='#' && c!= EOF){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      /* If stepm=6 months */
     puts(line);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     fputs(line,ficparo);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   }      
   ungetc(c,ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      /* Computing  Variances of health expectancies */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         decrease memory allocation */
            for(theta=1; theta <=npar; theta++){
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=npar; i++){ 
     ungetc(c,ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fgets(line, MAXLINE, ficpar);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     puts(line);        }
     fputs(line,ficparo);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   ungetc(c,ficpar);    
          for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            for(h=0; h<=nhstepm-1; h++){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              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.;
   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){        for(ij=1; ij<= nlstate*nlstate; ij++)
     ungetc(c,ficpar);          for(h=0; h<=nhstepm-1; h++){
     fgets(line, MAXLINE, ficpar);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     puts(line);          }
     fputs(line,ficparo);      }/* End theta */
   }      
   ungetc(c,ficpar);      
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);      for(h=0; h<=nhstepm-1; h++)
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        for(j=1; j<=nlstate*nlstate;j++)
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      
   
 /*------------ gnuplot -------------*/       for(ij=1;ij<=nlstate*nlstate;ij++)
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);        for(ji=1;ji<=nlstate*nlstate;ji++)
            varhe[ij][ji][(int)age] =0.;
 /*------------ free_vector  -------------*/  
  chdir(path);       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  free_ivector(wav,1,imx);       for(h=0;h<=nhstepm-1;h++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(k=0;k<=nhstepm-1;k++){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  free_ivector(num,1,n);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
  free_vector(agedc,1,n);          for(ij=1;ij<=nlstate*nlstate;ij++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            for(ji=1;ji<=nlstate*nlstate;ji++)
  fclose(ficparo);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
  fclose(ficres);        }
        }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Computing expectancies */
     ungetc(c,ficpar);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     fgets(line, MAXLINE, ficpar);      for(i=1; i<=nlstate;i++)
     puts(line);        for(j=1; j<=nlstate;j++)
     fputs(line,ficparo);          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;
   ungetc(c,ficpar);            
              /* 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]);*/
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/      fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);        eip=0.;
         vip=0.;
          for(j=1; j<=nlstate;j++){
   /*--------------- Prevalence limit --------------*/          eip += eij[i][j][(int)age];
            for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   strcpy(filerespl,"pl");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   strcat(filerespl,fileres);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   }      }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      fprintf(ficresstdeij,"\n");
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");      fprintf(ficrescveij,"%3.0f",age );
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(i=1; i<=nlstate;i++)
   fprintf(ficrespl,"\n");        for(j=1; j<=nlstate;j++){
            cptj= (j-1)*nlstate+i;
   prlim=matrix(1,nlstate,1,nlstate);          for(i2=1; i2<=nlstate;i2++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(j2=1; j2<=nlstate;j2++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              cptj2= (j2-1)*nlstate+i2;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if(cptj2 <= cptj)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            }
   k=0;        }
   agebase=agemin;      fprintf(ficrescveij,"\n");
   agelim=agemax;     
   ftolpl=1.e-10;    }
   i1=cptcoveff;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   if (cptcovn < 1){i1=1;}    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         k=k+1;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    printf("\n");
         fprintf(ficrespl,"\n#******");    fprintf(ficlog,"\n");
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(xm,1,npar);
         fprintf(ficrespl,"******\n");    free_vector(xp,1,npar);
            free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         for (age=agebase; age<=agelim; age++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           fprintf(ficrespl,"%.0f",age );  }
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  /************ Variance ******************/
           fprintf(ficrespl,"\n");  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);*/
   fclose(ficrespl);    /* double **newm;*/
     double **dnewm,**doldm;
   /*------------- h Pij x at various ages ------------*/    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    int k, cptcode;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double *xp;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
   printf("Computing pij: result on file '%s' \n", filerespij);    double **gradgp, **trgradgp; /* for var p point j */
      double *gpp, *gmp; /* for var p point j */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   /*if (stepm<=24) stepsize=2;*/    double ***p3mat;
     double age,agelim, hf;
   agelim=AGESUP;    double ***mobaverage;
   hstepm=stepsize*YEARM; /* Every year of age */    int theta;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    char digit[4];
      char digitp[25];
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    char fileresprobmorprev[FILENAMELENGTH];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    if(popbased==1){
         fprintf(ficrespij,"\n#****** ");      if(mobilav!=0)
         for(j=1;j<=cptcoveff;j++)        strcpy(digitp,"-populbased-mobilav-");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      else strcpy(digitp,"-populbased-nomobil-");
         fprintf(ficrespij,"******\n");    }
            else 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      strcpy(digitp,"-stablbased-");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    if (mobilav!=0) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           oldm=oldms;savm=savms;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficrespij,"# Age");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           for(i=1; i<=nlstate;i++)      }
             for(j=1; j<=nlstate+ndeath;j++)    }
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");    strcpy(fileresprobmorprev,"prmorprev"); 
           for (h=0; h<=nhstepm; h++){    sprintf(digit,"%-d",ij);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
             for(i=1; i<=nlstate;i++)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
               for(j=1; j<=nlstate+ndeath;j++)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    strcat(fileresprobmorprev,fileres);
             fprintf(ficrespij,"\n");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           fprintf(ficrespij,"\n");    }
         }    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);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    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);
   fclose(ficrespij);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
   if(stepm == 1) {      for(i=1; i<=nlstate;i++)
   /*---------- Forecasting ------------------*/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    }  
     fprintf(ficresprobmorprev,"\n");
      fprintf(ficgp,"\n# Routine varevsij");
      /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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);
    /*   } */
   strcpy(fileresf,"f");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcat(fileresf,fileres);    pstamp(ficresvij);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    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);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    else
        fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   free_matrix(mint,1,maxwav,1,n);    fprintf(ficresvij,"# Age");
   free_matrix(anint,1,maxwav,1,n);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    xp=vector(1,npar);
     movingaverage(agedeb, fage, agemin, mobaverage);    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (stepm<=12) stepsize=1;  
      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   agelim=AGESUP;    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
   hstepm=1;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   hstepm=hstepm/stepm;    
   yp1=modf(dateintmean,&yp);    if(estepm < stepm){
   anprojmean=yp;      printf ("Problem %d lower than %d\n",estepm, stepm);
   yp2=modf((yp1*12),&yp);    }
   mprojmean=yp;    else  hstepm=estepm;   
   yp1=modf((yp2*30.5),&yp);    /* For example we decided to compute the life expectancy with the smallest unit */
   jprojmean=yp;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if(jprojmean==0) jprojmean=1;       nhstepm is the number of hstepm from age to agelim 
   if(mprojmean==0) jprojmean=1;       nstepm is the number of stepm from age to agelin. 
         Look at function hpijx to understand why (it is linked to memory size questions) */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    /* 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
   if (popforecast==1) {       means that if the survival funtion is printed every two years of age and if
     if((ficpop=fopen(popfile,"r"))==NULL)    {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("Problem with population file : %s\n",popfile);goto end;       results. So we changed our mind and took the option of the best precision.
     }    */
     popage=ivector(0,AGESUP);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     popeffectif=vector(0,AGESUP);    agelim = AGESUP;
     popcount=vector(0,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 */ 
     i=1;        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         i=i+1;      gp=matrix(0,nhstepm,1,nlstate);
       }      gm=matrix(0,nhstepm,1,nlstate);
     imx=i;  
      
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      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);
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       k=k+1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {        if (popbased==1) {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          if(mobilav ==0){
       }            for(i=1; i<=nlstate;i++)
       fprintf(ficresf,"******\n");              prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficresf,"# StartingAge FinalAge");          }else{ /* mobilav */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            for(i=1; i<=nlstate;i++)
       if (popforecast==1)  fprintf(ficresf," [Population]");              prlim[i][i]=mobaverage[(int)age][i][ij];
                }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        }
         fprintf(ficresf,"\n");    
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          for(j=1; j<= nlstate; j++){
                  for(h=0; h<=nhstepm; h++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           nhstepm = nhstepm/hstepm;          }
                  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* This for computing probability of death (h=1 means
           oldm=oldms;savm=savms;           computed over hstepm matrices product = hstepm*stepm months) 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);             as a weighted average of prlim.
                */
           for (h=0; h<=nhstepm; h++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             if (h==(int) (calagedate+YEARM*cpt)) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
             }        }    
             for(j=1; j<=nlstate+ndeath;j++) {        /* end probability of death */
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                      for(i=1; i<=npar; i++) /* Computes gradient x - delta */
                 if (mobilav==1)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                 else {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   
                 }        if (popbased==1) {
                 if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];          if(mobilav ==0){
               }            for(i=1; i<=nlstate;i++)
               if (h==(int)(calagedate+12*cpt)){              prlim[i][i]=probs[(int)age][i][ij];
                 fprintf(ficresf," %.3f", kk1);          }else{ /* mobilav */ 
                          for(i=1; i<=nlstate;i++)
                 if (popforecast==1) fprintf(ficresf," [%.f]", kk2);              prlim[i][i]=mobaverage[(int)age][i][ij];
               }          }
             }        }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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];
   }          }
                }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   if (popforecast==1) {           as a weighted average of prlim.
     free_ivector(popage,0,AGESUP);        */
     free_vector(popeffectif,0,AGESUP);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     free_vector(popcount,0,AGESUP);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   free_imatrix(s,1,maxwav+1,1,n);        /* end probability of death */
   free_vector(weight,1,n);  
   fclose(ficresf);        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];
   /* End forecasting */          }
   else{  
     erreur=108;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   }        }
    
        } /* End theta */
   /*---------- Health expectancies and variances ------------*/  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   strcpy(filerest,"t");  
   strcat(filerest,fileres);      for(h=0; h<=nhstepm; h++) /* veij */
   if((ficrest=fopen(filerest,"w"))==NULL) {        for(j=1; j<=nlstate;j++)
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
   strcpy(filerese,"e");          trgradgp[j][theta]=gradgp[theta][j];
   strcat(filerese,fileres);    
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   }      for(i=1;i<=nlstate;i++)
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);      for(h=0;h<=nhstepm;h++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        for(k=0;k<=nhstepm;k++){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   k=0;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;    
       fprintf(ficrest,"\n#****** ");      /* pptj */
       for(j=1;j<=cptcoveff;j++)      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficrest,"******\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
       fprintf(ficreseij,"\n#****** ");          varppt[j][i]=doldmp[j][i];
       for(j=1;j<=cptcoveff;j++)      /* end ppptj */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      /*  x centered again */
       fprintf(ficreseij,"******\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       fprintf(ficresvij,"\n#****** ");   
       for(j=1;j<=cptcoveff;j++)      if (popbased==1) {
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        if(mobilav ==0){
       fprintf(ficresvij,"******\n");          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }else{ /* mobilav */ 
       oldm=oldms;savm=savms;          for(i=1; i<=nlstate;i++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);              prlim[i][i]=mobaverage[(int)age][i][ij];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }
       oldm=oldms;savm=savms;      }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);               
          /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficrest,"\n");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       hf=1;      }    
       if (stepm >= YEARM) hf=stepm/YEARM;      /* end probability of death */
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         if (popbased==1) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++){
             prlim[i][i]=probs[(int)age][i][k];          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }        }
              } 
         fprintf(ficrest," %.0f",age);      fprintf(ficresprobmorprev,"\n");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      fprintf(ficresvij,"%.0f ",age );
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++){
           epj[nlstate+1] +=epj[j];          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }        }
         for(i=1, vepp=0.;i <=nlstate;i++)      fprintf(ficresvij,"\n");
           for(j=1;j <=nlstate;j++)      free_matrix(gp,0,nhstepm,1,nlstate);
             vepp += vareij[i][j][(int)age];      free_matrix(gm,0,nhstepm,1,nlstate);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         for(j=1;j <=nlstate;j++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    } /* End age */
         fprintf(ficrest,"\n");    free_vector(gpp,nlstate+1,nlstate+ndeath);
       }    free_vector(gmp,nlstate+1,nlstate+ndeath);
     }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
            fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
            /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
  fclose(ficreseij);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  fclose(ficresvij);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fclose(ficrest);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   fclose(ficpar);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   free_vector(epj,1,nlstate+1);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   /*  scanf("%d ",i); */    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);
   /*------- Variance limit prevalence------*/      /*  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);
   */
 strcpy(fileresvpl,"vpl");  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   strcat(fileresvpl,fileres);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    free_vector(xp,1,npar);
     exit(0);    free_matrix(doldm,1,nlstate,1,nlstate);
   }    free_matrix(dnewm,1,nlstate,1,npar);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
  k=0;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  for(cptcov=1;cptcov<=i1;cptcov++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fclose(ficresprobmorprev);
      k=k+1;    fflush(ficgp);
      fprintf(ficresvpl,"\n#****** ");    fflush(fichtm); 
      for(j=1;j<=cptcoveff;j++)  }  /* end varevsij */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");  /************ 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[])
      varpl=matrix(1,nlstate,(int) bage, (int) fage);  {
      oldm=oldms;savm=savms;    /* Variance of prevalence limit */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /*  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;
   fclose(ficresvpl);    int k, cptcode;
     double *xp;
   /*---------- End : free ----------------*/    double *gp, *gm;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double **gradg, **trgradg;
      double age,agelim;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int theta;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    
      pstamp(ficresvpl);
      fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresvpl,"# Age");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    for(i=1; i<=nlstate;i++)
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficresvpl," %1d-%1d",i,i);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresvpl,"\n");
    
   free_matrix(matcov,1,npar,1,npar);    xp=vector(1,npar);
   free_vector(delti,1,npar);    dnewm=matrix(1,nlstate,1,npar);
   free_matrix(agev,1,maxwav,1,imx);    doldm=matrix(1,nlstate,1,nlstate);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    
     hstepm=1*YEARM; /* Every year of age */
   if(erreur >0)    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     printf("End of Imach with error %d\n",erreur);    agelim = AGESUP;
   else   printf("End of Imach\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        if (stepm >= YEARM) hstepm=1;
   /* 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);*/      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/      gradg=matrix(1,npar,1,nlstate);
   /*------ End -----------*/      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
  end:      for(theta=1; theta <=npar; theta++){
 #ifdef windows        for(i=1; i<=npar; i++){ /* Computes gradient */
   /* chdir(pathcd);*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #endif        }
  /*system("wgnuplot graph.plt");*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  /*system("../gp37mgw/wgnuplot graph.plt");*/        for(i=1;i<=nlstate;i++)
  /*system("cd ../gp37mgw");*/          gp[i] = prlim[i][i];
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      
  strcpy(plotcmd,GNUPLOTPROGRAM);        for(i=1; i<=npar; i++) /* Computes gradient */
  strcat(plotcmd," ");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
  strcat(plotcmd,optionfilegnuplot);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  system(plotcmd);        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
 #ifdef windows  
   while (z[0] != 'q') {        for(i=1;i<=nlstate;i++)
     chdir(path);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      } /* End theta */
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");      trgradg =matrix(1,nlstate,1,npar);
     else if (z[0] == 'e') {  
       chdir(path);      for(j=1; j<=nlstate;j++)
       system(optionfilehtm);        for(theta=1; theta <=npar; theta++)
     }          trgradg[j][theta]=gradg[theta][j];
     else if (z[0] == 'q') exit(0);  
   }      for(i=1;i<=nlstate;i++)
 #endif        varpl[i][(int)age] =0.;
 }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     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];
     char dummy[]="                         ";
     /*  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 linetmp[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, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*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 *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     /* where is ncovprod ?*/
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             goto end;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           goto end;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);fflush(ficlog);
           goto end;
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         goto end;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             goto end;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           goto end;
         }
         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 */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        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]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
         goto end;
       }
       
       /* 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 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         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 V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sums the number of covariates including age as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+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);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*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); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       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]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       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);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  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");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       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);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
    endfree:
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.26  
changed lines
  Added in v.1.133


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