Diff for /imach/src/imach.c between versions 1.25 and 1.128

version 1.25, 2002/02/26 17:11:54 version 1.128, 2006/06/30 13:02:05
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.128  2006/06/30 13:02:05  brouard
      (Module): Clarifications on computing e.j
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.127  2006/04/28 18:11:50  brouard
   first survey ("cross") where individuals from different ages are    (Module): Yes the sum of survivors was wrong since
   interviewed on their health status or degree of disability (in the    imach-114 because nhstepm was no more computed in the age
   case of a health survey which is our main interest) -2- at least a    loop. Now we define nhstepma in the age loop.
   second wave of interviews ("longitudinal") which measure each change    (Module): In order to speed up (in case of numerous covariates) we
   (if any) in individual health status.  Health expectancies are    compute health expectancies (without variances) in a first step
   computed from the time spent in each health state according to a    and then all the health expectancies with variances or standard
   model. More health states you consider, more time is necessary to reach the    deviation (needs data from the Hessian matrices) which slows the
   Maximum Likelihood of the parameters involved in the model.  The    computation.
   simplest model is the multinomial logistic model where pij is the    In the future we should be able to stop the program is only health
   probabibility to be observed in state j at the second wave    expectancies and graph are needed without standard deviations.
   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    Revision 1.126  2006/04/28 17:23:28  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): Yes the sum of survivors was wrong since
   complex model than "constant and age", you should modify the program    imach-114 because nhstepm was no more computed in the age
   where the markup *Covariates have to be included here again* invites    loop. Now we define nhstepma in the age loop.
   you to do it.  More covariates you add, slower the    Version 0.98h
   convergence.  
     Revision 1.125  2006/04/04 15:20:31  lievre
   The advantage of this computer programme, compared to a simple    Errors in calculation of health expectancies. Age was not initialized.
   multinomial logistic model, is clear when the delay between waves is not    Forecasting file added.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.124  2006/03/22 17:13:53  lievre
   account using an interpolation or extrapolation.      Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
   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    Revision 1.123  2006/03/20 10:52:43  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    * imach.c (Module): <title> changed, corresponds to .htm file
   states. This elementary transition (by month or quarter trimester,    name. <head> headers where missing.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    * imach.c (Module): Weights can have a decimal point as for
   and the contribution of each individual to the likelihood is simply    English (a comma might work with a correct LC_NUMERIC environment,
   hPijx.    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
   Also this programme outputs the covariance matrix of the parameters but also    1.
   of the life expectancies. It also computes the prevalence limits.    Version 0.98g
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.122  2006/03/20 09:45:41  brouard
            Institut national d'études démographiques, Paris.    (Module): Weights can have a decimal point as for
   This software have been partly granted by Euro-REVES, a concerted action    English (a comma might work with a correct LC_NUMERIC environment,
   from the European Union.    otherwise the weight is truncated).
   It is copyrighted identically to a GNU software product, ie programme and    Modification of warning when the covariates values are not 0 or
   software can be distributed freely for non commercial use. Latest version    1.
   can be accessed at http://euroreves.ined.fr/imach .    Version 0.98g
   **********************************************************************/  
      Revision 1.121  2006/03/16 17:45:01  lievre
 #include <math.h>    * imach.c (Module): Comments concerning covariates added
 #include <stdio.h>  
 #include <stdlib.h>    * imach.c (Module): refinements in the computation of lli if
 #include <unistd.h>    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Revision 1.120  2006/03/16 15:10:38  lievre
 #define FILENAMELENGTH 80    (Module): refinements in the computation of lli if
 /*#define DEBUG*/    status=-2 in order to have more reliable computation if stepm is
 #define windows    not 1 month. Version 0.98f
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    computed as likelihood omitting the logarithm. Version O.98e
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.118  2006/03/14 18:20:07  brouard
 #define NINTERVMAX 8    (Module): varevsij Comments added explaining the second
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    table of variances if popbased=1 .
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Function pstamp added
 #define MAXN 20000    (Module): Version 0.98d
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.117  2006/03/14 17:16:22  brouard
 #define AGEBASE 40    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int erreur; /* Error number */    (Module): Function pstamp added
 int nvar;    (Module): Version 0.98d
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.116  2006/03/06 10:29:27  brouard
 int nlstate=2; /* Number of live states */    (Module): Variance-covariance wrong links and
 int ndeath=1; /* Number of dead states */    varian-covariance of ej. is needed (Saito).
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.114  2006/02/26 12:57:58  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Some improvements in processing parameter
 int mle, weightopt;    filename with strsep.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.113  2006/02/24 14:20:24  brouard
 double jmean; /* Mean space between 2 waves */    (Module): Memory leaks checks with valgrind and:
 double **oldm, **newm, **savm; /* Working pointers to matrices */    datafile was not closed, some imatrix were not freed and on matrix
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    allocation too.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.112  2006/01/30 09:55:26  brouard
 FILE *ficreseij;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.111  2006/01/25 20:38:18  brouard
   char fileresv[FILENAMELENGTH];    (Module): Lots of cleaning and bugs added (Gompertz)
  FILE  *ficresvpl;    (Module): Comments can be added in data file. Missing date values
   char fileresvpl[FILENAMELENGTH];    can be a simple dot '.'.
   
 #define NR_END 1    Revision 1.110  2006/01/25 00:51:50  brouard
 #define FREE_ARG char*    (Module): Lots of cleaning and bugs added (Gompertz)
 #define FTOL 1.0e-10  
     Revision 1.109  2006/01/24 19:37:15  brouard
 #define NRANSI    (Module): Comments (lines starting with a #) are allowed in data.
 #define ITMAX 200  
     Revision 1.108  2006/01/19 18:05:42  lievre
 #define TOL 2.0e-4    Gnuplot problem appeared...
     To be fixed
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.107  2006/01/19 16:20:37  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Test existence of gnuplot in imach path
   
 #define GOLD 1.618034    Revision 1.106  2006/01/19 13:24:36  brouard
 #define GLIMIT 100.0    Some cleaning and links added in html output
 #define TINY 1.0e-20  
     Revision 1.105  2006/01/05 20:23:19  lievre
 static double maxarg1,maxarg2;    *** empty log message ***
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.104  2005/09/30 16:11:43  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): If the status is missing at the last wave but we know
 #define rint(a) floor(a+0.5)    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 static double sqrarg;    contributions to the likelihood is 1 - Prob of dying from last
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    the healthy state at last known wave). Version is 0.98
   
 int imx;    Revision 1.103  2005/09/30 15:54:49  lievre
 int stepm;    (Module): sump fixed, loop imx fixed, and simplifications.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.102  2004/09/15 17:31:30  brouard
 int m,nb;    Add the possibility to read data file including tab characters.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.101  2004/09/15 10:38:38  brouard
 double **pmmij, ***probs, ***mobaverage;    Fix on curr_time
 double dateintmean=0;  
     Revision 1.100  2004/07/12 18:29:06  brouard
 double *weight;    Add version for Mac OS X. Just define UNIX in Makefile
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.99  2004/06/05 08:57:40  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    *** empty log message ***
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.98  2004/05/16 15:05:56  brouard
 double ftolhess; /* Tolerance for computing hessian */    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 /**************** split *************************/    state at each age, but using a Gompertz model: log u =a + b*age .
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    This is the basic analysis of mortality and should be done before any
 {    other analysis, in order to test if the mortality estimated from the
    char *s;                             /* pointer */    cross-longitudinal survey is different from the mortality estimated
    int  l1, l2;                         /* length counters */    from other sources like vital statistic data.
   
    l1 = strlen( path );                 /* length of path */    The same imach parameter file can be used but the option for mle should be -3.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Agnès, who wrote this part of the code, tried to keep most of the
    s = strrchr( path, '\\' );           /* find last / */    former routines in order to include the new code within the former code.
 #else  
    s = strrchr( path, '/' );            /* find last / */    The output is very simple: only an estimate of the intercept and of
 #endif    the slope with 95% confident intervals.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Current limitations:
       extern char       *getwd( );    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.
       if ( getwd( dirc ) == NULL ) {    B) There is no computation of Life Expectancy nor Life Table.
 #else  
       extern char       *getcwd( );    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    suppressed.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.96  2003/07/15 15:38:55  brouard
       }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       strcpy( name, path );             /* we've got it */    rewritten within the same printf. Workaround: many printfs.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.95  2003/07/08 07:54:34  brouard
       l2 = strlen( s );                 /* length of filename */    * imach.c (Repository):
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Repository): Using imachwizard code to output a more meaningful covariance
       strcpy( name, s );                /* save file name */    matrix (cov(a12,c31) instead of numbers.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.94  2003/06/27 13:00:02  brouard
    }    Just cleaning
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.93  2003/06/25 16:33:55  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): On windows (cygwin) function asctime_r doesn't
 #else    exist so I changed back to asctime which exists.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): Version 0.96b
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.92  2003/06/25 16:30:45  brouard
    s++;    (Module): On windows (cygwin) function asctime_r doesn't
    strcpy(ext,s);                       /* save extension */    exist so I changed back to asctime which exists.
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.91  2003/06/25 15:30:29  brouard
    strncpy( finame, name, l1-l2);    * imach.c (Repository): Duplicated warning errors corrected.
    finame[l1-l2]= 0;    (Repository): Elapsed time after each iteration is now output. It
    return( 0 );                         /* we're done */    helps to forecast when convergence will be reached. Elapsed time
 }    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
   
 /******************************************/    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 void replace(char *s, char*t)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int i;  
   int lg=20;    Revision 1.89  2003/06/24 12:30:52  brouard
   i=0;    (Module): Some bugs corrected for windows. Also, when
   lg=strlen(t);    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.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.88  2003/06/23 17:54:56  brouard
   }    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 int nbocc(char *s, char occ)    Version 0.96
 {  
   int i,j=0;    Revision 1.86  2003/06/17 20:04:08  brouard
   int lg=20;    (Module): Change position of html and gnuplot routines and added
   i=0;    routine fileappend.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.85  2003/06/17 13:12:43  brouard
   if  (s[i] == occ ) j++;    * imach.c (Repository): Check when date of death was earlier that
   }    current date of interview. It may happen when the death was just
   return j;    prior to the death. In this case, dh was negative and likelihood
 }    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 void cutv(char *u,char *v, char*t, char occ)    interview.
 {    (Repository): Because some people have very long ID (first column)
   int i,lg,j,p=0;    we changed int to long in num[] and we added a new lvector for
   i=0;    memory allocation. But we also truncated to 8 characters (left
   for(j=0; j<=strlen(t)-1; j++) {    truncation)
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Repository): No more line truncation errors.
   }  
     Revision 1.84  2003/06/13 21:44:43  brouard
   lg=strlen(t);    * imach.c (Repository): Replace "freqsummary" at a correct
   for(j=0; j<p; j++) {    place. It differs from routine "prevalence" which may be called
     (u[j] = t[j]);    many times. Probs is memory consuming and must be used with
   }    parcimony.
      u[p]='\0';    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
    for(j=0; j<= lg; j++) {    Revision 1.83  2003/06/10 13:39:11  lievre
     if (j>=(p+1))(v[j-p-1] = t[j]);    *** empty log message ***
   }  
 }    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 /********************** nrerror ********************/  
   */
 void nrerror(char error_text[])  /*
 {     Interpolated Markov Chain
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Short summary of the programme:
   exit(1);    
 }    This program computes Healthy Life Expectancies from
 /*********************** vector *******************/    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 double *vector(int nl, int nh)    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   double *v;    case of a health survey which is our main interest) -2- at least a
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    second wave of interviews ("longitudinal") which measure each change
   if (!v) nrerror("allocation failure in vector");    (if any) in individual health status.  Health expectancies are
   return v-nl+NR_END;    computed from the time spent in each health state according to a
 }    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 /************************ free vector ******************/    simplest model is the multinomial logistic model where pij is the
 void free_vector(double*v, int nl, int nh)    probability to be observed in state j at the second wave
 {    conditional to be observed in state i at the first wave. Therefore
   free((FREE_ARG)(v+nl-NR_END));    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 }    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 /************************ivector *******************************/    where the markup *Covariates have to be included here again* invites
 int *ivector(long nl,long nh)    you to do it.  More covariates you add, slower the
 {    convergence.
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    The advantage of this computer programme, compared to a simple
   if (!v) nrerror("allocation failure in ivector");    multinomial logistic model, is clear when the delay between waves is not
   return v-nl+NR_END;    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    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
   free((FREE_ARG)(v+nl-NR_END));    split into an exact number (nh*stepm) of unobserved intermediate
 }    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 /******************* imatrix *******************************/    matrix is simply the matrix product of nh*stepm elementary matrices
 int **imatrix(long nrl, long nrh, long ncl, long nch)    and the contribution of each individual to the likelihood is simply
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    hPijx.
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Also this programme outputs the covariance matrix of the parameters but also
   int **m;    of the life expectancies. It also computes the period (stable) prevalence. 
      
   /* allocate pointers to rows */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));             Institut national d'études démographiques, Paris.
   if (!m) nrerror("allocation failure 1 in matrix()");    This software have been partly granted by Euro-REVES, a concerted action
   m += NR_END;    from the European Union.
   m -= nrl;    It is copyrighted identically to a GNU software product, ie programme and
      software can be distributed freely for non commercial use. Latest version
      can be accessed at http://euroreves.ined.fr/imach .
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    **********************************************************************/
    /*
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    main
      read parameterfile
   /* return pointer to array of pointers to rows */    read datafile
   return m;    concatwav
 }    freqsummary
     if (mle >= 1)
 /****************** free_imatrix *************************/      mlikeli
 void free_imatrix(m,nrl,nrh,ncl,nch)    print results files
       int **m;    if mle==1 
       long nch,ncl,nrh,nrl;       computes hessian
      /* free an int matrix allocated by imatrix() */    read end of parameter file: agemin, agemax, bage, fage, estepm
 {        begin-prev-date,...
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    open gnuplot file
   free((FREE_ARG) (m+nrl-NR_END));    open html file
 }    period (stable) prevalence
      for age prevalim()
 /******************* matrix *******************************/    h Pij x
 double **matrix(long nrl, long nrh, long ncl, long nch)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    health expectancies
   double **m;    Variance-covariance of DFLE
     prevalence()
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));     movingaverage()
   if (!m) nrerror("allocation failure 1 in matrix()");    varevsij() 
   m += NR_END;    if popbased==1 varevsij(,popbased)
   m -= nrl;    total life expectancies
     Variance of period (stable) prevalence
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));   end
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;   
   return m;  #include <math.h>
 }  #include <stdio.h>
   #include <stdlib.h>
 /*************************free matrix ************************/  #include <string.h>
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <unistd.h>
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <limits.h>
   free((FREE_ARG)(m+nrl-NR_END));  #include <sys/types.h>
 }  #include <sys/stat.h>
   #include <errno.h>
 /******************* ma3x *******************************/  extern int errno;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  /* #include <sys/time.h> */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #include <time.h>
   double ***m;  #include "timeval.h"
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /* #include <libintl.h> */
   if (!m) nrerror("allocation failure 1 in matrix()");  /* #define _(String) gettext (String) */
   m += NR_END;  
   m -= nrl;  #define MAXLINE 256
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define GNUPLOTPROGRAM "gnuplot"
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m[nrl] += NR_END;  #define FILENAMELENGTH 132
   m[nrl] -= ncl;  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  #define NINTERVMAX 8
   for (j=ncl+1; j<=nch; j++)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
     m[nrl][j]=m[nrl][j-1]+nlay;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    #define NCOVMAX 8 /* Maximum number of covariates */
   for (i=nrl+1; i<=nrh; i++) {  #define MAXN 20000
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define YEARM 12. /* Number of months per year */
     for (j=ncl+1; j<=nch; j++)  #define AGESUP 130
       m[i][j]=m[i][j-1]+nlay;  #define AGEBASE 40
   }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   return m;  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /*************************free ma3x ************************/  #define ODIRSEPARATOR '\\'
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #else
 {  #define DIRSEPARATOR '\\'
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define CHARSEPARATOR "\\"
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define ODIRSEPARATOR '/'
   free((FREE_ARG)(m+nrl-NR_END));  #endif
 }  
   /* $Id$ */
 /***************** f1dim *************************/  /* $State$ */
 extern int ncom;  
 extern double *pcom,*xicom;  char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
 extern double (*nrfunc)(double []);  char fullversion[]="$Revision$ $Date$"; 
    char strstart[80];
 double f1dim(double x)  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int j;  int nvar;
   double f;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   double *xt;  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
   xt=vector(1,ncom);  int ndeath=1; /* Number of dead states */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   f=(*nrfunc)(xt);  int popbased=0;
   free_vector(xt,1,ncom);  
   return f;  int *wav; /* Number of waves for this individuual 0 is possible */
 }  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 /*****************brent *************************/  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   int iter;  int mle, weightopt;
   double a,b,d,etemp;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double fu,fv,fw,fx;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double ftemp;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double p,q,r,tol1,tol2,u,v,w,x,xm;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double e=0.0;  double jmean; /* Mean space between 2 waves */
    double **oldm, **newm, **savm; /* Working pointers to matrices */
   a=(ax < cx ? ax : cx);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   b=(ax > cx ? ax : cx);  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   x=w=v=bx;  FILE *ficlog, *ficrespow;
   fw=fv=fx=(*f)(x);  int globpr; /* Global variable for printing or not */
   for (iter=1;iter<=ITMAX;iter++) {  double fretone; /* Only one call to likelihood */
     xm=0.5*(a+b);  long ipmx; /* Number of contributions */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double sw; /* Sum of weights */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  char filerespow[FILENAMELENGTH];
     printf(".");fflush(stdout);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 #ifdef DEBUG  FILE *ficresilk;
     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);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  FILE *ficresprobmorprev;
 #endif  FILE *fichtm, *fichtmcov; /* Html File */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  FILE *ficreseij;
       *xmin=x;  char filerese[FILENAMELENGTH];
       return fx;  FILE *ficresstdeij;
     }  char fileresstde[FILENAMELENGTH];
     ftemp=fu;  FILE *ficrescveij;
     if (fabs(e) > tol1) {  char filerescve[FILENAMELENGTH];
       r=(x-w)*(fx-fv);  FILE  *ficresvij;
       q=(x-v)*(fx-fw);  char fileresv[FILENAMELENGTH];
       p=(x-v)*q-(x-w)*r;  FILE  *ficresvpl;
       q=2.0*(q-r);  char fileresvpl[FILENAMELENGTH];
       if (q > 0.0) p = -p;  char title[MAXLINE];
       q=fabs(q);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       etemp=e;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       e=d;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char command[FILENAMELENGTH];
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int  outcmd=0;
       else {  
         d=p/q;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  char filelog[FILENAMELENGTH]; /* Log file */
           d=SIGN(tol1,xm-x);  char filerest[FILENAMELENGTH];
       }  char fileregp[FILENAMELENGTH];
     } else {  char popfile[FILENAMELENGTH];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     if (fu <= fx) {  struct timezone tzp;
       if (u >= x) a=x; else b=x;  extern int gettimeofday();
       SHFT(v,w,x,u)  struct tm tmg, tm, tmf, *gmtime(), *localtime();
         SHFT(fv,fw,fx,fu)  long time_value;
         } else {  extern long time();
           if (u < x) a=u; else b=u;  char strcurr[80], strfor[80];
           if (fu <= fw || w == x) {  
             v=w;  char *endptr;
             w=u;  long lval;
             fv=fw;  double dval;
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  #define NR_END 1
             v=u;  #define FREE_ARG char*
             fv=fu;  #define FTOL 1.0e-10
           }  
         }  #define NRANSI 
   }  #define ITMAX 200 
   nrerror("Too many iterations in brent");  
   *xmin=x;  #define TOL 2.0e-4 
   return fx;  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /****************** mnbrak ***********************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define GOLD 1.618034 
             double (*func)(double))  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   double ulim,u,r,q, dum;  
   double fu;  static double maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   *fa=(*func)(*ax);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   *fb=(*func)(*bx);    
   if (*fb > *fa) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     SHFT(dum,*ax,*bx,dum)  #define rint(a) floor(a+0.5)
       SHFT(dum,*fb,*fa,dum)  
       }  static double sqrarg;
   *cx=(*bx)+GOLD*(*bx-*ax);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   *fc=(*func)(*cx);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   while (*fb > *fc) {  int agegomp= AGEGOMP;
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  int imx; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int stepm=1;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /* Stepm, step in month: minimum step interpolation*/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  int estepm;
       fu=(*func)(u);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  int m,nb;
       if (fu < *fc) {  long *num;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
           SHFT(*fb,*fc,fu,(*func)(u))  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
           }  double **pmmij, ***probs;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double *ageexmed,*agecens;
       u=ulim;  double dateintmean=0;
       fu=(*func)(u);  
     } else {  double *weight;
       u=(*cx)+GOLD*(*cx-*bx);  int **s; /* Status */
       fu=(*func)(u);  double *agedc, **covar, idx;
     }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     SHFT(*ax,*bx,*cx,u)  double *lsurv, *lpop, *tpop;
       SHFT(*fa,*fb,*fc,fu)  
       }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
 /*************** linmin ************************/  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 int ncom;  {
 double *pcom,*xicom;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 double (*nrfunc)(double []);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
      */ 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    char  *ss;                            /* pointer */
 {    int   l1, l2;                         /* length counters */
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);    l1 = strlen(path );                   /* length of path */
   double f1dim(double x);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
               double *fc, double (*func)(double));    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   int j;      strcpy( name, path );               /* we got the fullname name because no directory */
   double xx,xmin,bx,ax;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double fx,fb,fa;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
        /* get current working directory */
   ncom=n;      /*    extern  char* getcwd ( char *buf , int len);*/
   pcom=vector(1,n);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   xicom=vector(1,n);        return( GLOCK_ERROR_GETCWD );
   nrfunc=func;      }
   for (j=1;j<=n;j++) {      /* got dirc from getcwd*/
     pcom[j]=p[j];      printf(" DIRC = %s \n",dirc);
     xicom[j]=xi[j];    } else {                              /* strip direcotry from path */
   }      ss++;                               /* after this, the filename */
   ax=0.0;      l2 = strlen( ss );                  /* length of filename */
   xx=1.0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      strcpy( name, ss );         /* save file name */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 #ifdef DEBUG      dirc[l1-l2] = 0;                    /* add zero */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      printf(" DIRC2 = %s \n",dirc);
 #endif    }
   for (j=1;j<=n;j++) {    /* We add a separator at the end of dirc if not exists */
     xi[j] *= xmin;    l1 = strlen( dirc );                  /* length of directory */
     p[j] += xi[j];    if( dirc[l1-1] != DIRSEPARATOR ){
   }      dirc[l1] =  DIRSEPARATOR;
   free_vector(xicom,1,n);      dirc[l1+1] = 0; 
   free_vector(pcom,1,n);      printf(" DIRC3 = %s \n",dirc);
 }    }
     ss = strrchr( name, '.' );            /* find last / */
 /*************** powell ************************/    if (ss >0){
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      ss++;
             double (*func)(double []))      strcpy(ext,ss);                     /* save extension */
 {      l1= strlen( name);
   void linmin(double p[], double xi[], int n, double *fret,      l2= strlen(ss)+1;
               double (*func)(double []));      strncpy( finame, name, l1-l2);
   int i,ibig,j;      finame[l1-l2]= 0;
   double del,t,*pt,*ptt,*xit;    }
   double fp,fptt;  
   double *xits;    return( 0 );                          /* we're done */
   pt=vector(1,n);  }
   ptt=vector(1,n);  
   xit=vector(1,n);  
   xits=vector(1,n);  /******************************************/
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  void replace_back_to_slash(char *s, char*t)
   for (*iter=1;;++(*iter)) {  {
     fp=(*fret);    int i;
     ibig=0;    int lg=0;
     del=0.0;    i=0;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    lg=strlen(t);
     for (i=1;i<=n;i++)    for(i=0; i<= lg; i++) {
       printf(" %d %.12f",i, p[i]);      (s[i] = t[i]);
     printf("\n");      if (t[i]== '\\') s[i]='/';
     for (i=1;i<=n;i++) {    }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  }
       fptt=(*fret);  
 #ifdef DEBUG  int nbocc(char *s, char occ)
       printf("fret=%lf \n",*fret);  {
 #endif    int i,j=0;
       printf("%d",i);fflush(stdout);    int lg=20;
       linmin(p,xit,n,fret,func);    i=0;
       if (fabs(fptt-(*fret)) > del) {    lg=strlen(s);
         del=fabs(fptt-(*fret));    for(i=0; i<= lg; i++) {
         ibig=i;    if  (s[i] == occ ) j++;
       }    }
 #ifdef DEBUG    return j;
       printf("%d %.12e",i,(*fret));  }
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  void cutv(char *u,char *v, char*t, char occ)
         printf(" x(%d)=%.12e",j,xit[j]);  {
       }    /* 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')
         printf(" p=%.12e",p[j]);       gives u="abcedf" and v="ghi2j" */
       printf("\n");    int i,lg,j,p=0;
 #endif    i=0;
     }    for(j=0; j<=strlen(t)-1; j++) {
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 #ifdef DEBUG    }
       int k[2],l;  
       k[0]=1;    lg=strlen(t);
       k[1]=-1;    for(j=0; j<p; j++) {
       printf("Max: %.12e",(*func)(p));      (u[j] = t[j]);
       for (j=1;j<=n;j++)    }
         printf(" %.12e",p[j]);       u[p]='\0';
       printf("\n");  
       for(l=0;l<=1;l++) {     for(j=0; j<= lg; j++) {
         for (j=1;j<=n;j++) {      if (j>=(p+1))(v[j-p-1] = t[j]);
           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]);  }
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /********************** nrerror ********************/
       }  
 #endif  void nrerror(char error_text[])
   {
     fprintf(stderr,"ERREUR ...\n");
       free_vector(xit,1,n);    fprintf(stderr,"%s\n",error_text);
       free_vector(xits,1,n);    exit(EXIT_FAILURE);
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  /*********************** vector *******************/
       return;  double *vector(int nl, int nh)
     }  {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    double *v;
     for (j=1;j<=n;j++) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       ptt[j]=2.0*p[j]-pt[j];    if (!v) nrerror("allocation failure in vector");
       xit[j]=p[j]-pt[j];    return v-nl+NR_END;
       pt[j]=p[j];  }
     }  
     fptt=(*func)(ptt);  /************************ free vector ******************/
     if (fptt < fp) {  void free_vector(double*v, int nl, int nh)
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  {
       if (t < 0.0) {    free((FREE_ARG)(v+nl-NR_END));
         linmin(p,xit,n,fret,func);  }
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  /************************ivector *******************************/
           xi[j][n]=xit[j];  int *ivector(long nl,long nh)
         }  {
 #ifdef DEBUG    int *v;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         for(j=1;j<=n;j++)    if (!v) nrerror("allocation failure in ivector");
           printf(" %.12e",xit[j]);    return v-nl+NR_END;
         printf("\n");  }
 #endif  
       }  /******************free ivector **************************/
     }  void free_ivector(int *v, long nl, long nh)
   }  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /**** Prevalence limit ****************/  
   /************************lvector *******************************/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  long *lvector(long nl,long nh)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    long *v;
      matrix by transitions matrix until convergence is reached */    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
   int i, ii,j,k;    return v-nl+NR_END;
   double min, max, maxmin, maxmax,sumnew=0.;  }
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /******************free lvector **************************/
   double **newm;  void free_lvector(long *v, long nl, long nh)
   double agefin, delaymax=50 ; /* Max number of years to converge */  {
     free((FREE_ARG)(v+nl-NR_END));
   for (ii=1;ii<=nlstate+ndeath;ii++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /******************* imatrix *******************************/
     }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    cov[1]=1.;  { 
      long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int **m; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    
     newm=savm;    /* allocate pointers to rows */ 
     /* Covariates have to be included here again */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
      cov[2]=agefin;    if (!m) nrerror("allocation failure 1 in matrix()"); 
      m += NR_END; 
       for (k=1; k<=cptcovn;k++) {    m -= nrl; 
         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]);*/    
       }    /* allocate rows and set pointers to them */ 
       for (k=1; k<=cptcovage;k++)    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for (k=1; k<=cptcovprod;k++)    m[nrl] += NR_END; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl] -= ncl; 
     
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    
     /* return pointer to array of pointers to rows */ 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    return m; 
   } 
     savm=oldm;  
     oldm=newm;  /****************** free_imatrix *************************/
     maxmax=0.;  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(j=1;j<=nlstate;j++){        int **m;
       min=1.;        long nch,ncl,nrh,nrl; 
       max=0.;       /* free an int matrix allocated by imatrix() */ 
       for(i=1; i<=nlstate; i++) {  { 
         sumnew=0;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    free((FREE_ARG) (m+nrl-NR_END)); 
         prlim[i][j]= newm[i][j]/(1-sumnew);  } 
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
       maxmin=max-min;  {
       maxmax=FMAX(maxmax,maxmin);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     if(maxmax < ftolpl){  
       return prlim;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
 }    m -= nrl;
   
 /*************** transition probabilities ***************/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   double s1, s2;  
   /*double t34;*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int i,j,j1, nc, ii, jj;    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     for(i=1; i<= nlstate; i++){     */
     for(j=1; j<i;j++){  }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /*************************free matrix ************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       ps[i][j]=s2;    free((FREE_ARG)(m+nrl-NR_END));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  }
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  /******************* ma3x *******************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  {
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       }    double ***m;
       ps[i][j]=s2;  
     }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
     /*ps[3][2]=1;*/    m += NR_END;
     m -= nrl;
   for(i=1; i<= nlstate; i++){  
      s1=0;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for(j=1; j<i; j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       s1+=exp(ps[i][j]);    m[nrl] += NR_END;
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl] -= ncl;
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for(j=i+1; j<=nlstate+ndeath; j++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl][ncl] += NR_END;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m[nrl][ncl] -= nll;
   } /* end i */    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (i=nrl+1; i<=nrh; i++) {
       ps[ii][jj]=0;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       ps[ii][ii]=1;      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
   }    }
     return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     for(jj=1; jj<= nlstate+ndeath; jj++){    */
      printf("%lf ",ps[ii][jj]);  }
    }  
     printf("\n ");  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   goto end;*/    free((FREE_ARG)(m+nrl-NR_END));
     return ps;  }
 }  
   /*************** function subdirf ***********/
 /**************** Product of 2 matrices ******************/  char *subdirf(char fileres[])
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcat(tmpout,"/"); /* Add to the right */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,fileres);
   /* in, b, out are matrice of pointers which should have been initialized    return tmpout;
      before: only the contents of out is modified. The function returns  }
      a pointer to pointers identical to out */  
   long i, j, k;  /*************** function subdirf2 ***********/
   for(i=nrl; i<= nrh; i++)  char *subdirf2(char fileres[], char *preop)
     for(k=ncolol; k<=ncoloh; k++)  {
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    
         out[i][k] +=in[i][j]*b[j][k];    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   return out;    strcat(tmpout,"/");
 }    strcat(tmpout,preop);
     strcat(tmpout,fileres);
     return tmpout;
 /************* 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 )  /*************** function subdirf3 ***********/
 {  char *subdirf3(char fileres[], char *preop, char *preop2)
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  {
      duration (i.e. until    
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /* Caution optionfilefiname is hidden */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    strcpy(tmpout,optionfilefiname);
      (typically every 2 years instead of every month which is too big).    strcat(tmpout,"/");
      Model is determined by parameters x and covariates have to be    strcat(tmpout,preop);
      included manually here.    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
      */    return tmpout;
   }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  /***************** f1dim *************************/
   double **newm;  extern int ncom; 
   extern double *pcom,*xicom;
   /* Hstepm could be zero and should return the unit matrix */  extern double (*nrfunc)(double []); 
   for (i=1;i<=nlstate+ndeath;i++)   
     for (j=1;j<=nlstate+ndeath;j++){  double f1dim(double x) 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    int j; 
     }    double f;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double *xt; 
   for(h=1; h <=nhstepm; h++){   
     for(d=1; d <=hstepm; d++){    xt=vector(1,ncom); 
       newm=savm;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       /* Covariates have to be included here again */    f=(*nrfunc)(xt); 
       cov[1]=1.;    free_vector(xt,1,ncom); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return f; 
       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];  /*****************brent *************************/
       for (k=1; k<=cptcovprod;k++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  { 
     int iter; 
     double a,b,d,etemp;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double fu,fv,fw,fx;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double ftemp;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double p,q,r,tol1,tol2,u,v,w,x,xm; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double e=0.0; 
       savm=oldm;   
       oldm=newm;    a=(ax < cx ? ax : cx); 
     }    b=(ax > cx ? ax : cx); 
     for(i=1; i<=nlstate+ndeath; i++)    x=w=v=bx; 
       for(j=1;j<=nlstate+ndeath;j++) {    fw=fv=fx=(*f)(x); 
         po[i][j][h]=newm[i][j];    for (iter=1;iter<=ITMAX;iter++) { 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      xm=0.5*(a+b); 
          */      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   } /* end h */      printf(".");fflush(stdout);
   return po;      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);
       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);
 /*************** log-likelihood *************/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 double func( double *x)  #endif
 {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   int i, ii, j, k, mi, d, kk;        *xmin=x; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        return fx; 
   double **out;      } 
   double sw; /* Sum of weights */      ftemp=fu;
   double lli; /* Individual log likelihood */      if (fabs(e) > tol1) { 
   long ipmx;        r=(x-w)*(fx-fv); 
   /*extern weight */        q=(x-v)*(fx-fw); 
   /* We are differentiating ll according to initial status */        p=(x-v)*q-(x-w)*r; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        q=2.0*(q-r); 
   /*for(i=1;i<imx;i++)        if (q > 0.0) p = -p; 
     printf(" %d\n",s[4][i]);        q=fabs(q); 
   */        etemp=e; 
   cov[1]=1.;        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for(k=1; k<=nlstate; k++) ll[k]=0.;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        else { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          d=p/q; 
     for(mi=1; mi<= wav[i]-1; mi++){          u=x+d; 
       for (ii=1;ii<=nlstate+ndeath;ii++)          if (u-a < tol2 || b-u < tol2) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);            d=SIGN(tol1,xm-x); 
       for(d=0; d<dh[mi][i]; d++){        } 
         newm=savm;      } else { 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         for (kk=1; kk<=cptcovage;kk++) {      } 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         }      fu=(*f)(u); 
              if (fu <= fx) { 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        if (u >= x) a=x; else b=x; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        SHFT(v,w,x,u) 
         savm=oldm;          SHFT(fv,fw,fx,fu) 
         oldm=newm;          } else { 
                    if (u < x) a=u; else b=u; 
                    if (fu <= fw || w == x) { 
       } /* end mult */              v=w; 
                    w=u; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);              fv=fw; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/              fw=fu; 
       ipmx +=1;            } else if (fu <= fv || v == x || v == w) { 
       sw += weight[i];              v=u; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;              fv=fu; 
     } /* end of wave */            } 
   } /* end of individual */          } 
     } 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    nrerror("Too many iterations in brent"); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    *xmin=x; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    return fx; 
   return -l;  } 
 }  
   /****************** mnbrak ***********************/
   
 /*********** Maximum Likelihood Estimation ***************/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  { 
 {    double ulim,u,r,q, dum;
   int i,j, iter;    double fu; 
   double **xi,*delti;   
   double fret;    *fa=(*func)(*ax); 
   xi=matrix(1,npar,1,npar);    *fb=(*func)(*bx); 
   for (i=1;i<=npar;i++)    if (*fb > *fa) { 
     for (j=1;j<=npar;j++)      SHFT(dum,*ax,*bx,dum) 
       xi[i][j]=(i==j ? 1.0 : 0.0);        SHFT(dum,*fb,*fa,dum) 
   printf("Powell\n");        } 
   powell(p,xi,npar,ftol,&iter,&fret,func);    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    while (*fb > *fc) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 /**** Computes Hessian and covariance matrix ***/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double  **a,**y,*x,pd;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double **hess;        fu=(*func)(u); 
   int i, j,jk;        if (fu < *fc) { 
   int *indx;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
   double hessii(double p[], double delta, int theta, double delti[]);            } 
   double hessij(double p[], double delti[], int i, int j);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        u=ulim; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fu=(*func)(u); 
       } else { 
   hess=matrix(1,npar,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
   printf("\nCalculation of the hessian matrix. Wait...\n");      } 
   for (i=1;i<=npar;i++){      SHFT(*ax,*bx,*cx,u) 
     printf("%d",i);fflush(stdout);        SHFT(*fa,*fb,*fc,fu) 
     hess[i][i]=hessii(p,ftolhess,i,delti);        } 
     /*printf(" %f ",p[i]);*/  } 
     /*printf(" %lf ",hess[i][i]);*/  
   }  /*************** linmin ************************/
    
   for (i=1;i<=npar;i++) {  int ncom; 
     for (j=1;j<=npar;j++)  {  double *pcom,*xicom;
       if (j>i) {  double (*nrfunc)(double []); 
         printf(".%d%d",i,j);fflush(stdout);   
         hess[i][j]=hessij(p,delti,i,j);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         hess[j][i]=hess[i][j];      { 
         /*printf(" %lf ",hess[i][j]);*/    double brent(double ax, double bx, double cx, 
       }                 double (*f)(double), double tol, double *xmin); 
     }    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   printf("\n");                double *fc, double (*func)(double)); 
     int j; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double xx,xmin,bx,ax; 
      double fx,fb,fa;
   a=matrix(1,npar,1,npar);   
   y=matrix(1,npar,1,npar);    ncom=n; 
   x=vector(1,npar);    pcom=vector(1,n); 
   indx=ivector(1,npar);    xicom=vector(1,n); 
   for (i=1;i<=npar;i++)    nrfunc=func; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    for (j=1;j<=n;j++) { 
   ludcmp(a,npar,indx,&pd);      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   for (j=1;j<=npar;j++) {    } 
     for (i=1;i<=npar;i++) x[i]=0;    ax=0.0; 
     x[j]=1;    xx=1.0; 
     lubksb(a,npar,indx,x);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for (i=1;i<=npar;i++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       matcov[i][j]=x[i];  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   printf("\n#Hessian matrix#\n");    for (j=1;j<=n;j++) { 
   for (i=1;i<=npar;i++) {      xi[j] *= xmin; 
     for (j=1;j<=npar;j++) {      p[j] += xi[j]; 
       printf("%.3e ",hess[i][j]);    } 
     }    free_vector(xicom,1,n); 
     printf("\n");    free_vector(pcom,1,n); 
   }  } 
   
   /* Recompute Inverse */  char *asc_diff_time(long time_sec, char ascdiff[])
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    long sec_left, days, hours, minutes;
   ludcmp(a,npar,indx,&pd);    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
   /*  printf("\n#Hessian matrix recomputed#\n");    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
   for (j=1;j<=npar;j++) {    minutes = (sec_left) /60;
     for (i=1;i<=npar;i++) x[i]=0;    sec_left = (sec_left) % (60);
     x[j]=1;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     lubksb(a,npar,indx,x);    return ascdiff;
     for (i=1;i<=npar;i++){  }
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  /*************** powell ************************/
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     printf("\n");              double (*func)(double [])) 
   }  { 
   */    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   free_matrix(a,1,npar,1,npar);    int i,ibig,j; 
   free_matrix(y,1,npar,1,npar);    double del,t,*pt,*ptt,*xit;
   free_vector(x,1,npar);    double fp,fptt;
   free_ivector(indx,1,npar);    double *xits;
   free_matrix(hess,1,npar,1,npar);    int niterf, itmp;
   
     pt=vector(1,n); 
 }    ptt=vector(1,n); 
     xit=vector(1,n); 
 /*************** hessian matrix ****************/    xits=vector(1,n); 
 double hessii( double x[], double delta, int theta, double delti[])    *fret=(*func)(p); 
 {    for (j=1;j<=n;j++) pt[j]=p[j]; 
   int i;    for (*iter=1;;++(*iter)) { 
   int l=1, lmax=20;      fp=(*fret); 
   double k1,k2;      ibig=0; 
   double p2[NPARMAX+1];      del=0.0; 
   double res;      last_time=curr_time;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      (void) gettimeofday(&curr_time,&tzp);
   double fx;      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);
   int k=0,kmax=10;      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);
   double l1;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
      for (i=1;i<=n;i++) {
   fx=func(x);        printf(" %d %.12f",i, p[i]);
   for (i=1;i<=npar;i++) p2[i]=x[i];        fprintf(ficlog," %d %.12lf",i, p[i]);
   for(l=0 ; l <=lmax; l++){        fprintf(ficrespow," %.12lf", p[i]);
     l1=pow(10,l);      }
     delts=delt;      printf("\n");
     for(k=1 ; k <kmax; k=k+1){      fprintf(ficlog,"\n");
       delt = delta*(l1*k);      fprintf(ficrespow,"\n");fflush(ficrespow);
       p2[theta]=x[theta] +delt;      if(*iter <=3){
       k1=func(p2)-fx;        tm = *localtime(&curr_time.tv_sec);
       p2[theta]=x[theta]-delt;        strcpy(strcurr,asctime(&tm));
       k2=func(p2)-fx;  /*       asctime_r(&tm,strcurr); */
       /*res= (k1-2.0*fx+k2)/delt/delt; */        forecast_time=curr_time; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        itmp = strlen(strcurr);
              if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 #ifdef DEBUG          strcurr[itmp-1]='\0';
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 #endif        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        for(niterf=10;niterf<=30;niterf+=10){
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         k=kmax;          tmf = *localtime(&forecast_time.tv_sec);
       }  /*      asctime_r(&tmf,strfor); */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          strcpy(strfor,asctime(&tmf));
         k=kmax; l=lmax*10.;          itmp = strlen(strfor);
       }          if(strfor[itmp-1]=='\n')
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          strfor[itmp-1]='\0';
         delts=delt;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     }        }
   }      }
   delti[theta]=delts;      for (i=1;i<=n;i++) { 
   return res;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
          fptt=(*fret); 
 }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 double hessij( double x[], double delti[], int thetai,int thetaj)        fprintf(ficlog,"fret=%lf \n",*fret);
 {  #endif
   int i;        printf("%d",i);fflush(stdout);
   int l=1, l1, lmax=20;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double k1,k2,k3,k4,res,fx;        linmin(p,xit,n,fret,func); 
   double p2[NPARMAX+1];        if (fabs(fptt-(*fret)) > del) { 
   int k;          del=fabs(fptt-(*fret)); 
           ibig=i; 
   fx=func(x);        } 
   for (k=1; k<=2; k++) {  #ifdef DEBUG
     for (i=1;i<=npar;i++) p2[i]=x[i];        printf("%d %.12e",i,(*fret));
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog,"%d %.12e",i,(*fret));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for (j=1;j<=n;j++) {
     k1=func(p2)-fx;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            printf(" x(%d)=%.12e",j,xit[j]);
     p2[thetai]=x[thetai]+delti[thetai]/k;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k2=func(p2)-fx;        for(j=1;j<=n;j++) {
            printf(" p=%.12e",p[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;          fprintf(ficlog," p=%.12e",p[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        }
     k3=func(p2)-fx;        printf("\n");
          fprintf(ficlog,"\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;  #endif
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } 
     k4=func(p2)-fx;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #ifdef DEBUG
 #ifdef DEBUG        int k[2],l;
     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);        k[0]=1;
 #endif        k[1]=-1;
   }        printf("Max: %.12e",(*func)(p));
   return res;        fprintf(ficlog,"Max: %.12e",(*func)(p));
 }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
 /************** Inverse of matrix **************/          fprintf(ficlog," %.12e",p[j]);
 void ludcmp(double **a, int n, int *indx, double *d)        }
 {        printf("\n");
   int i,imax,j,k;        fprintf(ficlog,"\n");
   double big,dum,sum,temp;        for(l=0;l<=1;l++) {
   double *vv;          for (j=1;j<=n;j++) {
              ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   vv=vector(1,n);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   *d=1.0;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1;i<=n;i++) {          }
     big=0.0;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (j=1;j<=n;j++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  #endif
     vv[i]=1.0/big;  
   }  
   for (j=1;j<=n;j++) {        free_vector(xit,1,n); 
     for (i=1;i<j;i++) {        free_vector(xits,1,n); 
       sum=a[i][j];        free_vector(ptt,1,n); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        free_vector(pt,1,n); 
       a[i][j]=sum;        return; 
     }      } 
     big=0.0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (i=j;i<=n;i++) {      for (j=1;j<=n;j++) { 
       sum=a[i][j];        ptt[j]=2.0*p[j]-pt[j]; 
       for (k=1;k<j;k++)        xit[j]=p[j]-pt[j]; 
         sum -= a[i][k]*a[k][j];        pt[j]=p[j]; 
       a[i][j]=sum;      } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      fptt=(*func)(ptt); 
         big=dum;      if (fptt < fp) { 
         imax=i;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       }        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
     if (j != imax) {          for (j=1;j<=n;j++) { 
       for (k=1;k<=n;k++) {            xi[j][ibig]=xi[j][n]; 
         dum=a[imax][k];            xi[j][n]=xit[j]; 
         a[imax][k]=a[j][k];          }
         a[j][k]=dum;  #ifdef DEBUG
       }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       *d = -(*d);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       vv[imax]=vv[j];          for(j=1;j<=n;j++){
     }            printf(" %.12e",xit[j]);
     indx[j]=imax;            fprintf(ficlog," %.12e",xit[j]);
     if (a[j][j] == 0.0) a[j][j]=TINY;          }
     if (j != n) {          printf("\n");
       dum=1.0/(a[j][j]);          fprintf(ficlog,"\n");
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  #endif
     }        }
   }      } 
   free_vector(vv,1,n);  /* Doesn't work */    } 
 ;  } 
 }  
   /**** Prevalence limit (stable or period prevalence)  ****************/
 void lubksb(double **a, int n, int *indx, double b[])  
 {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int i,ii=0,ip,j;  {
   double sum;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         matrix by transitions matrix until convergence is reached */
   for (i=1;i<=n;i++) {  
     ip=indx[i];    int i, ii,j,k;
     sum=b[ip];    double min, max, maxmin, maxmax,sumnew=0.;
     b[ip]=b[i];    double **matprod2();
     if (ii)    double **out, cov[NCOVMAX], **pmij();
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    double **newm;
     else if (sum) ii=i;    double agefin, delaymax=50 ; /* Max number of years to converge */
     b[i]=sum;  
   }    for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=n;i>=1;i--) {      for (j=1;j<=nlstate+ndeath;j++){
     sum=b[i];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      }
     b[i]=sum/a[i][i];  
   }     cov[1]=1.;
 }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /************ Frequencies ********************/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 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)      newm=savm;
 {  /* Some frequencies */      /* Covariates have to be included here again */
         cov[2]=agefin;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    
   double ***freq; /* Frequencies */        for (k=1; k<=cptcovn;k++) {
   double *pp;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double pos, k2, dateintsum=0,k2cpt=0;          /*      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]]);*/
   FILE *ficresp;        }
   char fileresp[FILENAMELENGTH];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   pp=vector(1,nlstate);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   strcat(fileresp,fileres);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   if((ficresp=fopen(fileresp,"w"))==NULL) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     printf("Problem with prevalence resultfile: %s\n", fileresp);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     exit(0);  
   }      savm=oldm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      oldm=newm;
   j1=0;      maxmax=0.;
       for(j=1;j<=nlstate;j++){
   j=cptcoveff;        min=1.;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        max=0.;
         for(i=1; i<=nlstate; i++) {
   for(k1=1; k1<=j;k1++){          sumnew=0;
    for(i1=1; i1<=ncodemax[k1];i1++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
        j1++;          prlim[i][j]= newm[i][j]/(1-sumnew);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          max=FMAX(max,prlim[i][j]);
          scanf("%d", i);*/          min=FMIN(min,prlim[i][j]);
         for (i=-1; i<=nlstate+ndeath; i++)          }
          for (jk=-1; jk<=nlstate+ndeath; jk++)          maxmin=max-min;
            for(m=agemin; m <= agemax+3; m++)        maxmax=FMAX(maxmax,maxmin);
              freq[i][jk][m]=0;      }
       if(maxmax < ftolpl){
         dateintsum=0;        return prlim;
         k2cpt=0;      }
        for (i=1; i<=imx; i++) {    }
          bool=1;  }
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)  /*************** transition probabilities ***************/ 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
          }  {
          if (bool==1) {    double s1, s2;
            for(m=firstpass; m<=lastpass; m++){    /*double t34;*/
              k2=anint[m][i]+(mint[m][i]/12.);    int i,j,j1, nc, ii, jj;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  
                if(agev[m][i]==0) agev[m][i]=agemax+1;      for(i=1; i<= nlstate; i++){
                if(agev[m][i]==1) agev[m][i]=agemax+2;        for(j=1; j<i;j++){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            /*s2 += param[i][j][nc]*cov[nc];*/
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                  dateintsum=dateintsum+k2;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
                  k2cpt++;          }
                }          ps[i][j]=s2;
   /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
              }        }
            }        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];
         if  (cptcovn>0) {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
          fprintf(ficresp, "\n#********** Variable ");          }
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ps[i][j]=s2;
        fprintf(ficresp, "**********\n#");        }
         }      }
        for(i=1; i<=nlstate;i++)      /*ps[3][2]=1;*/
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      
        fprintf(ficresp, "\n");      for(i=1; i<= nlstate; i++){
                s1=0;
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for(j=1; j<i; j++)
     if(i==(int)agemax+3)          s1+=exp(ps[i][j]);
       printf("Total");        for(j=i+1; j<=nlstate+ndeath; j++)
     else          s1+=exp(ps[i][j]);
       printf("Age %d", i);        ps[i][i]=1./(s1+1.);
     for(jk=1; jk <=nlstate ; jk++){        for(j=1; j<i; j++)
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
         pp[jk] += freq[jk][m][i];        for(j=i+1; j<=nlstate+ndeath; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     for(jk=1; jk <=nlstate ; jk++){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for(m=-1, pos=0; m <=0 ; m++)      } /* end i */
         pos += freq[jk][m][i];      
       if(pp[jk]>=1.e-10)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for(jj=1; jj<= nlstate+ndeath; jj++){
       else          ps[ii][jj]=0;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          ps[ii][ii]=1;
     }        }
       }
      for(jk=1; jk <=nlstate ; jk++){      
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
         pp[jk] += freq[jk][m][i];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
      }  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
     for(jk=1,pos=0; jk <=nlstate ; jk++)  /*       } */
       pos += pp[jk];  /*       printf("\n "); */
     for(jk=1; jk <=nlstate ; jk++){  /*        } */
       if(pos>=1.e-5)  /*        printf("\n ");printf("%lf ",cov[2]); */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);         /*
       else        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        goto end;*/
       if( i <= (int) agemax){      return ps;
         if(pos>=1.e-5){  }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
           probs[i][jk][j1]= pp[jk]/pos;  /**************** Product of 2 matrices ******************/
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
         }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       else  {
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     }    /* in, b, out are matrice of pointers which should have been initialized 
     for(jk=-1; jk <=nlstate+ndeath; jk++)       before: only the contents of out is modified. The function returns
       for(m=-1; m <=nlstate+ndeath; m++)       a pointer to pointers identical to out */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    long i, j, k;
     if(i <= (int) agemax)    for(i=nrl; i<= nrh; i++)
       fprintf(ficresp,"\n");      for(k=ncolol; k<=ncoloh; k++)
     printf("\n");        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
     }  
  }    return out;
   dateintmean=dateintsum/k2cpt;  }
    
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /************* Higher Matrix Product ***************/
   free_vector(pp,1,nlstate);  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   /* End of Freq */  {
 }    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
 /************ Prevalence ********************/       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 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)       nhstepm*hstepm matrices. 
 {  /* Some frequencies */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         (typically every 2 years instead of every month which is too big 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;       for the memory).
   double ***freq; /* Frequencies */       Model is determined by parameters x and covariates have to be 
   double *pp;       included manually here. 
   double pos, k2;  
        */
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, j, d, h, k;
      double **out, cov[NCOVMAX];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double **newm;
   j1=0;  
      /* Hstepm could be zero and should return the unit matrix */
   j=cptcoveff;    for (i=1;i<=nlstate+ndeath;i++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for (j=1;j<=nlstate+ndeath;j++){
          oldm[i][j]=(i==j ? 1.0 : 0.0);
  for(k1=1; k1<=j;k1++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
     for(i1=1; i1<=ncodemax[k1];i1++){      }
       j1++;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(h=1; h <=nhstepm; h++){
       for (i=-1; i<=nlstate+ndeath; i++)        for(d=1; d <=hstepm; d++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)          newm=savm;
           for(m=agemin; m <= agemax+3; m++)        /* Covariates have to be included here again */
             freq[i][jk][m]=0;        cov[1]=1.;
              cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         bool=1;        for (k=1; k<=cptcovage;k++)
         if  (cptcovn>0) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (z1=1; z1<=cptcoveff; z1++)        for (k=1; k<=cptcovprod;k++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
               bool=0;  
         }  
         if (bool==1) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
           for(m=firstpass; m<=lastpass; m++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
             k2=anint[m][i]+(mint[m][i]/12.);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
               if(agev[m][i]==0) agev[m][i]=agemax+1;        savm=oldm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        oldm=newm;
               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];        for(i=1; i<=nlstate+ndeath; i++)
             }        for(j=1;j<=nlstate+ndeath;j++) {
           }          po[i][j][h]=newm[i][j];
         }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
            /*printf("h=%d ",h);*/
         for(i=(int)agemin; i <= (int)agemax+3; i++){    } /* end h */
           for(jk=1; jk <=nlstate ; jk++){  /*     printf("\n H=%d \n",h); */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    return po;
               pp[jk] += freq[jk][m][i];  }
           }  
           for(jk=1; jk <=nlstate ; jk++){  
             for(m=-1, pos=0; m <=0 ; m++)  /*************** log-likelihood *************/
             pos += freq[jk][m][i];  double func( double *x)
         }  {
            int i, ii, j, k, mi, d, kk;
          for(jk=1; jk <=nlstate ; jk++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double **out;
              pp[jk] += freq[jk][m][i];    double sw; /* Sum of weights */
          }    double lli; /* Individual log likelihood */
              int s1, s2;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    double bbh, survp;
     long ipmx;
          for(jk=1; jk <=nlstate ; jk++){              /*extern weight */
            if( i <= (int) agemax){    /* We are differentiating ll according to initial status */
              if(pos>=1.e-5){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
                probs[i][jk][j1]= pp[jk]/pos;    /*for(i=1;i<imx;i++) 
              }      printf(" %d\n",s[4][i]);
            }    */
          }    cov[1]=1.;
            
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
   }    if(mle==1){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(mi=1; mi<= wav[i]-1; mi++){
   free_vector(pp,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
 }  /* End of Freq */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************* Waves Concatenation ***************/            }
           for(d=0; d<dh[mi][i]; d++){
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for (kk=1; kk<=cptcovage;kk++) {
      Death is a valid wave (if date is known).              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      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]            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      and mw[mi+1][i]. dh depends on stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      */            savm=oldm;
             oldm=newm;
   int i, mi, m;          } /* end mult */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        
      double sum=0., jmean=0.;*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
   int j, k=0,jk, ju, jl;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double sum=0.;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   jmin=1e+5;           * the nearest (and in case of equal distance, to the lowest) interval but now
   jmax=-1;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   jmean=0.;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   for(i=1; i<=imx; i++){           * probability in order to take into account the bias as a fraction of the way
     mi=0;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     m=firstpass;           * -stepm/2 to stepm/2 .
     while(s[m][i] <= nlstate){           * For stepm=1 the results are the same as for previous versions of Imach.
       if(s[m][i]>=1)           * For stepm > 1 the results are less biased than in previous versions. 
         mw[++mi][i]=m;           */
       if(m >=lastpass)          s1=s[mw[mi][i]][i];
         break;          s2=s[mw[mi+1][i]][i];
       else          bbh=(double)bh[mi][i]/(double)stepm; 
         m++;          /* bias bh is positive if real duration
     }/* end while */           * is higher than the multiple of stepm and negative otherwise.
     if (s[m][i] > nlstate){           */
       mi++;     /* Death is another wave */          /* 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(mi==0)  never been interviewed correctly before death */          if( s2 > nlstate){ 
          /* Only death is a correct wave */            /* i.e. if s2 is a death state and if the date of death is known 
       mw[mi][i]=m;               then the contribution to the likelihood is the probability to 
     }               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
     wav[i]=mi;               minus probability to die before dh-stepm . 
     if(mi==0)               In version up to 0.92 likelihood was computed
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          as if date of death was unknown. Death was treated as any other
   }          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
   for(i=1; i<=imx; i++){          to consider that at each interview the state was recorded
     for(mi=1; mi<wav[i];mi++){          (healthy, disable or death) and IMaCh was corrected; but when we
       if (stepm <=0)          introduced the exact date of death then we should have modified
         dh[mi][i]=1;          the contribution of an exact death to the likelihood. This new
       else{          contribution is smaller and very dependent of the step unit
         if (s[mw[mi+1][i]][i] > nlstate) {          stepm. It is no more the probability to die between last interview
           if (agedc[i] < 2*AGESUP) {          and month of death but the probability to survive from last
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          interview up to one month before death multiplied by the
           if(j==0) j=1;  /* Survives at least one month after exam */          probability to die within a month. Thanks to Chris
           k=k+1;          Jackson for correcting this bug.  Former versions increased
           if (j >= jmax) jmax=j;          mortality artificially. The bad side is that we add another loop
           if (j <= jmin) jmin=j;          which slows down the processing. The difference can be up to 10%
           sum=sum+j;          lower mortality.
           /* if (j<10) printf("j=%d num=%d ",j,i); */            */
           }            lli=log(out[s1][s2] - savm[s1][s2]);
         }  
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          } else if  (s2==-2) {
           k=k+1;            for (j=1,survp=0. ; j<=nlstate; j++) 
           if (j >= jmax) jmax=j;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           else if (j <= jmin)jmin=j;            /*survp += out[s1][j]; */
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            lli= log(survp);
           sum=sum+j;          }
         }          
         jk= j/stepm;          else if  (s2==-4) { 
         jl= j -jk*stepm;            for (j=3,survp=0. ; j<=nlstate; j++)  
         ju= j -(jk+1)*stepm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         if(jl <= -ju)            lli= log(survp); 
           dh[mi][i]=jk;          } 
         else  
           dh[mi][i]=jk+1;          else if  (s2==-5) { 
         if(dh[mi][i]==0)            for (j=1,survp=0. ; j<=2; j++)  
           dh[mi][i]=1; /* At least one step */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
     }          } 
   }          
   jmean=sum/k;          else{
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            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 */
 /*********** Tricode ****************************/          } 
 void tricode(int *Tvar, int **nbcode, int imx)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
   int Ndum[20],ij=1, k, j, i;          /*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); */
   int cptcode=0;          ipmx +=1;
   cptcoveff=0;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (k=0; k<19; k++) Ndum[k]=0;        } /* end of wave */
   for (k=1; k<=7; k++) ncodemax[k]=0;      } /* end of individual */
     }  else if(mle==2){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       ij=(int)(covar[Tvar[j]][i]);        for(mi=1; mi<= wav[i]-1; mi++){
       Ndum[ij]++;          for (ii=1;ii<=nlstate+ndeath;ii++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            for (j=1;j<=nlstate+ndeath;j++){
       if (ij > cptcode) cptcode=ij;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for (i=0; i<=cptcode; i++) {          for(d=0; d<=dh[mi][i]; d++){
       if(Ndum[i]!=0) ncodemax[j]++;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     ij=1;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
     for (i=1; i<=ncodemax[j]; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=0; k<=19; k++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (Ndum[k] != 0) {            savm=oldm;
           nbcode[Tvar[j]][ij]=k;            oldm=newm;
           ij++;          } /* end mult */
         }        
         if (ij > ncodemax[j]) break;          s1=s[mw[mi][i]][i];
       }            s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
   }            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
  for (k=0; k<19; k++) Ndum[k]=0;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  for (i=1; i<=ncovmodel-2; i++) {        } /* end of wave */
       ij=Tvar[i];      } /* end of individual */
       Ndum[ij]++;    }  else if(mle==3){  /* exponential inter-extrapolation */
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  ij=1;        for(mi=1; mi<= wav[i]-1; mi++){
  for (i=1; i<=10; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
    if((Ndum[i]!=0) && (i<=ncov)){            for (j=1;j<=nlstate+ndeath;j++){
      Tvaraff[ij]=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      ij++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    }            }
  }          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
     cptcoveff=ij-1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /*********** Health Expectancies ****************/            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   /* Health expectancies */            oldm=newm;
   int i, j, nhstepm, hstepm, h;          } /* end mult */
   double age, agelim,hf;        
   double ***p3mat;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   fprintf(ficreseij,"# Health expectancies\n");          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficreseij,"# 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 */
   for(i=1; i<=nlstate;i++)          ipmx +=1;
     for(j=1; j<=nlstate;j++)          sw += weight[i];
       fprintf(ficreseij," %1d-%1d",i,j);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficreseij,"\n");        } /* end of wave */
       } /* end of individual */
   hstepm=1*YEARM; /*  Every j years of age (in month) */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   agelim=AGESUP;        for(mi=1; mi<= wav[i]-1; mi++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for (ii=1;ii<=nlstate+ndeath;ii++)
     /* nhstepm age range expressed in number of stepm */            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Typically if 20 years = 20*12/6=40 stepm */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          for(d=0; d<dh[mi][i]; d++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            newm=savm;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            for (kk=1; kk<=cptcovage;kk++) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
           
     for(i=1; i<=nlstate;i++)            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, eij[i][j][(int)age]=0; h<=nhstepm; h++){            savm=oldm;
           eij[i][j][(int)age] +=p3mat[i][j][h];            oldm=newm;
         }          } /* end mult */
            
     hf=1;          s1=s[mw[mi][i]][i];
     if (stepm >= YEARM) hf=stepm/YEARM;          s2=s[mw[mi+1][i]][i];
     fprintf(ficreseij,"%.0f",age );          if( s2 > nlstate){ 
     for(i=1; i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<=nlstate;j++){          }else{
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
     fprintf(ficreseij,"\n");          ipmx +=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sw += weight[i];
   }          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]); */
         } /* end of wave */
 /************ Variance ******************/      } /* end of individual */
 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)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Variance of health expectancies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for(mi=1; mi<= wav[i]-1; mi++){
   double **newm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **dnewm,**doldm;            for (j=1;j<=nlstate+ndeath;j++){
   int i, j, nhstepm, hstepm, h;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k, cptcode;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *xp;            }
   double **gp, **gm;          for(d=0; d<dh[mi][i]; d++){
   double ***gradg, ***trgradg;            newm=savm;
   double ***p3mat;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double age,agelim;            for (kk=1; kk<=cptcovage;kk++) {
   int theta;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
    fprintf(ficresvij,"# Covariances of life expectancies\n");          
   fprintf(ficresvij,"# Age");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(j=1; j<=nlstate;j++)            savm=oldm;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            oldm=newm;
   fprintf(ficresvij,"\n");          } /* end mult */
         
   xp=vector(1,npar);          s1=s[mw[mi][i]][i];
   dnewm=matrix(1,nlstate,1,npar);          s2=s[mw[mi+1][i]][i];
   doldm=matrix(1,nlstate,1,nlstate);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            ipmx +=1;
   hstepm=1*YEARM; /* Every year of age */          sw += weight[i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   agelim = AGESUP;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        } /* end of wave */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* end of individual */
     if (stepm >= YEARM) hstepm=1;    } /* End of if */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     gp=matrix(0,nhstepm,1,nlstate);    return -l;
     gm=matrix(0,nhstepm,1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /*************** log-likelihood *************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  double funcone( double *x)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    /* Same as likeli but slower because of a lot of printf and if */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, ii, j, k, mi, d, kk;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
       if (popbased==1) {    double lli; /* Individual log likelihood */
         for(i=1; i<=nlstate;i++)    double llt;
           prlim[i][i]=probs[(int)age][i][ij];    int s1, s2;
       }    double bbh, survp;
          /*extern weight */
       for(j=1; j<= nlstate; j++){    /* We are differentiating ll according to initial status */
         for(h=0; h<=nhstepm; h++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    /*for(i=1;i<imx;i++) 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      printf(" %d\n",s[4][i]);
         }    */
       }    cov[1]=1.;
      
       for(i=1; i<=npar; i++) /* Computes gradient */    for(k=1; k<=nlstate; k++) ll[k]=0.;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
       if (popbased==1) {        for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=1; i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
           prlim[i][i]=probs[(int)age][i][ij];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
       for(j=1; j<= nlstate; j++){        for(d=0; d<dh[mi][i]; d++){
         for(h=0; h<=nhstepm; h++){          newm=savm;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          for (kk=1; kk<=cptcovage;kk++) {
         }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }          }
           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;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          oldm=newm;
         }        } /* end mult */
     } /* End theta */        
         s1=s[mw[mi][i]][i];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
     for(h=0; h<=nhstepm; h++)        /* bias is positive if real duration
       for(j=1; j<=nlstate;j++)         * is higher than the multiple of stepm and negative otherwise.
         for(theta=1; theta <=npar; theta++)         */
           trgradg[h][j][theta]=gradg[h][theta][j];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
     for(i=1;i<=nlstate;i++)        } else if  (s2==-2) {
       for(j=1;j<=nlstate;j++)          for (j=1,survp=0. ; j<=nlstate; j++) 
         vareij[i][j][(int)age] =0.;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(h=0;h<=nhstepm;h++){          lli= log(survp);
       for(k=0;k<=nhstepm;k++){        }else if (mle==1){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        } else if(mle==2){
         for(i=1;i<=nlstate;i++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           for(j=1;j<=nlstate;j++)        } else if(mle==3){  /* exponential inter-extrapolation */
             vareij[i][j][(int)age] += doldm[i][j];          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 */
       }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     }          lli=log(out[s1][s2]); /* Original formula */
     h=1;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     if (stepm >= YEARM) h=stepm/YEARM;          lli=log(out[s1][s2]); /* Original formula */
     fprintf(ficresvij,"%.0f ",age );        } /* End of if */
     for(i=1; i<=nlstate;i++)        ipmx +=1;
       for(j=1; j<=nlstate;j++){        sw += weight[i];
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        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]); */
     fprintf(ficresvij,"\n");        if(globpr){
     free_matrix(gp,0,nhstepm,1,nlstate);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     free_matrix(gm,0,nhstepm,1,nlstate);   %11.6f %11.6f %11.6f ", \
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   } /* End age */            llt +=ll[k]*gipmx/gsw;
              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   free_vector(xp,1,npar);          }
   free_matrix(doldm,1,nlstate,1,npar);          fprintf(ficresilk," %10.6f\n", -llt);
   free_matrix(dnewm,1,nlstate,1,nlstate);        }
       } /* end of wave */
 }    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 /************ Variance of prevlim ******************/    /* printf("l1=%f l2=%f ",ll[1],ll[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)    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 */
   /* Variance of prevalence limit */      gipmx=ipmx;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      gsw=sw;
   double **newm;    }
   double **dnewm,**doldm;    return -l;
   int i, j, nhstepm, hstepm;  }
   int k, cptcode;  
   double *xp;  
   double *gp, *gm;  /*************** function likelione ***********/
   double **gradg, **trgradg;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double age,agelim;  {
   int theta;    /* This routine should help understanding what is done with 
           the selection of individuals/waves and
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");       to check the exact contribution to the likelihood.
   fprintf(ficresvpl,"# Age");       Plotting could be done.
   for(i=1; i<=nlstate;i++)     */
       fprintf(ficresvpl," %1d-%1d",i,i);    int k;
   fprintf(ficresvpl,"\n");  
     if(*globpri !=0){ /* Just counts and sums, no printings */
   xp=vector(1,npar);      strcpy(fileresilk,"ilk"); 
   dnewm=matrix(1,nlstate,1,npar);      strcat(fileresilk,fileres);
   doldm=matrix(1,nlstate,1,nlstate);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresilk);
   hstepm=1*YEARM; /* Every year of age */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      }
   agelim = AGESUP;      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");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     if (stepm >= YEARM) hstepm=1;      for(k=1; k<=nlstate; k++) 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     gradg=matrix(1,npar,1,nlstate);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     gp=vector(1,nlstate);    }
     gm=vector(1,nlstate);  
     *fretone=(*funcone)(p);
     for(theta=1; theta <=npar; theta++){    if(*globpri !=0){
       for(i=1; i<=npar; i++){ /* Computes gradient */      fclose(ficresilk);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       }      fflush(fichtm); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } 
       for(i=1;i<=nlstate;i++)    return;
         gp[i] = prlim[i][i];  }
      
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*********** Maximum Likelihood Estimation ***************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         gm[i] = prlim[i][i];  {
     int i,j, iter;
       for(i=1;i<=nlstate;i++)    double **xi;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double fret;
     } /* End theta */    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
     trgradg =matrix(1,nlstate,1,npar);    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
     for(j=1; j<=nlstate;j++)      for (j=1;j<=npar;j++)
       for(theta=1; theta <=npar; theta++)        xi[i][j]=(i==j ? 1.0 : 0.0);
         trgradg[j][theta]=gradg[theta][j];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     for(i=1;i<=nlstate;i++)    strcat(filerespow,fileres);
       varpl[i][(int)age] =0.;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      printf("Problem with resultfile: %s\n", filerespow);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
     fprintf(ficresvpl,"%.0f ",age );      for(j=1;j<=nlstate+ndeath;j++)
     for(i=1; i<=nlstate;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    fprintf(ficrespow,"\n");
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);    powell(p,xi,npar,ftol,&iter,&fret,func);
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);    free_matrix(xi,1,npar,1,npar);
     free_matrix(trgradg,1,nlstate,1,npar);    fclose(ficrespow);
   } /* End age */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_vector(xp,1,npar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  }
   
 }  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 /************ Variance of one-step probabilities  ******************/  {
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double  **a,**y,*x,pd;
 {    double **hess;
   int i, j;    int i, j,jk;
   int k=0, cptcode;    int *indx;
   double **dnewm,**doldm;  
   double *xp;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double *gp, *gm;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   double **gradg, **trgradg;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double age,agelim, cov[NCOVMAX];    void ludcmp(double **a, int npar, int *indx, double *d) ;
   int theta;    double gompertz(double p[]);
   char fileresprob[FILENAMELENGTH];    hess=matrix(1,npar,1,npar);
   
   strcpy(fileresprob,"prob");    printf("\nCalculation of the hessian matrix. Wait...\n");
   strcat(fileresprob,fileres);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    for (i=1;i<=npar;i++){
     printf("Problem with resultfile: %s\n", fileresprob);      printf("%d",i);fflush(stdout);
   }      fprintf(ficlog,"%d",i);fflush(ficlog);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);     
         hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
   xp=vector(1,npar);      /*  printf(" %f ",p[i]);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    }
      
   cov[1]=1;    for (i=1;i<=npar;i++) {
   for (age=bage; age<=fage; age ++){      for (j=1;j<=npar;j++)  {
     cov[2]=age;        if (j>i) { 
     gradg=matrix(1,npar,1,9);          printf(".%d%d",i,j);fflush(stdout);
     trgradg=matrix(1,9,1,npar);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          hess[i][j]=hessij(p,delti,i,j,func,npar);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          
              hess[j][i]=hess[i][j];    
     for(theta=1; theta <=npar; theta++){          /*printf(" %lf ",hess[i][j]);*/
       for(i=1; i<=npar; i++)        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
          }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("\n");
        fprintf(ficlog,"\n");
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
            k=k+1;    
           gp[k]=pmmij[i][j];    a=matrix(1,npar,1,npar);
         }    y=matrix(1,npar,1,npar);
       }    x=vector(1,npar);
     indx=ivector(1,npar);
       for(i=1; i<=npar; i++)    for (i=1;i<=npar;i++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
        ludcmp(a,npar,indx,&pd);
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    for (j=1;j<=npar;j++) {
       k=0;      for (i=1;i<=npar;i++) x[i]=0;
       for(i=1; i<=(nlstate+ndeath); i++){      x[j]=1;
         for(j=1; j<=(nlstate+ndeath);j++){      lubksb(a,npar,indx,x);
           k=k+1;      for (i=1;i<=npar;i++){ 
           gm[k]=pmmij[i][j];        matcov[i][j]=x[i];
         }      }
       }    }
        
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    printf("\n#Hessian matrix#\n");
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      fprintf(ficlog,"\n#Hessian matrix#\n");
     }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        printf("%.3e ",hess[i][j]);
       for(theta=1; theta <=npar; theta++)        fprintf(ficlog,"%.3e ",hess[i][j]);
       trgradg[j][theta]=gradg[theta][j];      }
        printf("\n");
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      fprintf(ficlog,"\n");
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    }
   
      pmij(pmmij,cov,ncovmodel,x,nlstate);    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
      k=0;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      for(i=1; i<=(nlstate+ndeath); i++){    ludcmp(a,npar,indx,&pd);
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;    /*  printf("\n#Hessian matrix recomputed#\n");
          gm[k]=pmmij[i][j];  
         }    for (j=1;j<=npar;j++) {
      }      for (i=1;i<=npar;i++) x[i]=0;
            x[j]=1;
      /*printf("\n%d ",(int)age);      lubksb(a,npar,indx,x);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for (i=1;i<=npar;i++){ 
                y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        fprintf(ficlog,"%.3e ",y[i][j]);
      }*/      }
       printf("\n");
   fprintf(ficresprob,"\n%d ",(int)age);      fprintf(ficlog,"\n");
     }
   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]);    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    free_ivector(indx,1,npar);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    free_matrix(hess,1,npar,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
 }  }
  free_vector(xp,1,npar);  
 fclose(ficresprob);  /*************** hessian matrix ****************/
  exit(0);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 }  {
     int i;
 /******************* Printing html file ***********/    int l=1, lmax=20;
 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[] ){    double k1,k2;
   int jj1, k1, i1, cpt;    double p2[NPARMAX+1];
   FILE *fichtm;    double res;
   /*char optionfilehtm[FILENAMELENGTH];*/    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
   strcpy(optionfilehtm,optionfile);    int k=0,kmax=10;
   strcat(optionfilehtm,".htm");    double l1;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    fx=func(x);
   }    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">      l1=pow(10,l);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
 Total number of observations=%d <br>        delt = delta*(l1*k);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        p2[theta]=x[theta] +delt;
 <hr  size=\"2\" color=\"#EC5E5E\">        k1=func(p2)-fx;
 <li>Outputs files<br><br>\n        p2[theta]=x[theta]-delt;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        k2=func(p2)-fx;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        /*res= (k1-2.0*fx+k2)/delt/delt; */
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  #ifdef DEBUG
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        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);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><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);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  #endif
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         <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);          k=kmax;
          }
 fprintf(fichtm," <li>Graphs</li><p>");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
  m=cptcoveff;        }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
  jj1=0;        }
  for(k1=1; k1<=m;k1++){      }
    for(i1=1; i1<=ncodemax[k1];i1++){    }
        jj1++;    delti[theta]=delts;
        if (cptcovn > 0) {    return res; 
          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\">");  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
        }  {
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    int i;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        int l=1, l1, lmax=20;
        for(cpt=1; cpt<nlstate;cpt++){    double k1,k2,k3,k4,res,fx;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    double p2[NPARMAX+1];
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    int k;
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {    fx=func(x);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    for (k=1; k<=2; k++) {
 interval) in state (%d): v%s%d%d.gif <br>      for (i=1;i<=npar;i++) p2[i]=x[i];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        p2[thetai]=x[thetai]+delti[thetai]/k;
      }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      for(cpt=1; cpt<=nlstate;cpt++) {      k1=func(p2)-fx;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      p2[thetai]=x[thetai]+delti[thetai]/k;
      }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      k2=func(p2)-fx;
 health expectancies in states (1) and (2): e%s%d.gif<br>    
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      p2[thetai]=x[thetai]-delti[thetai]/k;
 fprintf(fichtm,"\n</body>");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
    }      k3=func(p2)-fx;
    }    
 fclose(fichtm);      p2[thetai]=x[thetai]-delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
 /******************* Gnuplot file **************/      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){  #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);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
   strcpy(optionfilegnuplot,optionfilefiname);    }
   strcat(optionfilegnuplot,".plt");    return res;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  }
     printf("Problem with file %s",optionfilegnuplot);  
   }  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
 #ifdef windows  { 
     fprintf(ficgp,"cd \"%s\" \n",pathc);    int i,imax,j,k; 
 #endif    double big,dum,sum,temp; 
 m=pow(2,cptcoveff);    double *vv; 
     
  /* 1eme*/    vv=vector(1,n); 
   for (cpt=1; cpt<= nlstate ; cpt ++) {    *d=1.0; 
    for (k1=1; k1<= m ; k1 ++) {    for (i=1;i<=n;i++) { 
       big=0.0; 
 #ifdef windows      for (j=1;j<=n;j++) 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        if ((temp=fabs(a[i][j])) > big) big=temp; 
 #endif      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 #ifdef unix      vv[i]=1.0/big; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    } 
 #endif    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
 for (i=1; i<= nlstate ; i ++) {        sum=a[i][j]; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        a[i][j]=sum; 
 }      } 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      big=0.0; 
     for (i=1; i<= nlstate ; i ++) {      for (i=j;i<=n;i++) { 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        sum=a[i][j]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (k=1;k<j;k++) 
 }          sum -= a[i][k]*a[k][j]; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        a[i][j]=sum; 
      for (i=1; i<= nlstate ; i ++) {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          big=dum; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          imax=i; 
 }          } 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      } 
 #ifdef unix      if (j != imax) { 
 fprintf(ficgp,"\nset ter gif small size 400,300");        for (k=1;k<=n;k++) { 
 #endif          dum=a[imax][k]; 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          a[imax][k]=a[j][k]; 
    }          a[j][k]=dum; 
   }        } 
   /*2 eme*/        *d = -(*d); 
         vv[imax]=vv[j]; 
   for (k1=1; k1<= m ; k1 ++) {      } 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      indx[j]=imax; 
          if (a[j][j] == 0.0) a[j][j]=TINY; 
     for (i=1; i<= nlstate+1 ; i ++) {      if (j != n) { 
       k=2*i;        dum=1.0/(a[j][j]); 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       for (j=1; j<= nlstate+1 ; j ++) {      } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_vector(vv,1,n);  /* Doesn't work */
 }    ;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  } 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  void lubksb(double **a, int n, int *indx, double b[]) 
       for (j=1; j<= nlstate+1 ; j ++) {  { 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int i,ii=0,ip,j; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double sum; 
 }     
       fprintf(ficgp,"\" t\"\" w l 0,");    for (i=1;i<=n;i++) { 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      ip=indx[i]; 
       for (j=1; j<= nlstate+1 ; j ++) {      sum=b[ip]; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      b[ip]=b[i]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (ii) 
 }          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      else if (sum) ii=i; 
       else fprintf(ficgp,"\" t\"\" w l 0,");      b[i]=sum; 
     }    } 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    for (i=n;i>=1;i--) { 
   }      sum=b[i]; 
        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   /*3eme*/      b[i]=sum/a[i][i]; 
     } 
   for (k1=1; k1<= m ; k1 ++) {  } 
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(cpt-1);  void pstamp(FILE *fichier)
       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);  {
       for (i=1; i< nlstate ; i ++) {    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  }
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  /************ 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 */
      
   /* CV preval stat */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     for (k1=1; k1<= m ; k1 ++) {    int first;
     for (cpt=1; cpt<nlstate ; cpt ++) {    double ***freq; /* Frequencies */
       k=3;    double *pp, **prop;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
       for (i=1; i< nlstate ; i ++)    
         fprintf(ficgp,"+$%d",k+i+1);    pp=vector(1,nlstate);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    prop=matrix(1,nlstate,iagemin,iagemax+3);
          strcpy(fileresp,"p");
       l=3+(nlstate+ndeath)*cpt;    strcat(fileresp,fileres);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       for (i=1; i< nlstate ; i ++) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
         l=3+(nlstate+ndeath)*cpt;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         fprintf(ficgp,"+$%d",l+i+1);      exit(0);
       }    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    j1=0;
     }    
   }      j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){    first=1;
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    for(k1=1; k1<=j;k1++){
         for(j=1; j <=ncovmodel; j++){      for(i1=1; i1<=ncodemax[k1];i1++){
                j1++;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           jk++;          scanf("%d", i);*/
           fprintf(ficgp,"\n");        for (i=-5; i<=nlstate+ndeath; i++)  
         }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       }            for(m=iagemin; m <= iagemax+3; m++)
     }              freq[i][jk][m]=0;
     }  
       for (i=1; i<=nlstate; i++)  
     for(jk=1; jk <=m; jk++) {        for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          prop[i][m]=0;
    i=1;        
    for(k2=1; k2<=nlstate; k2++) {        dateintsum=0;
      k3=i;        k2cpt=0;
      for(k=1; k<=(nlstate+ndeath); k++) {        for (i=1; i<=imx; i++) {
        if (k != k2){          bool=1;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          if  (cptcovn>0) {
 ij=1;            for (z1=1; z1<=cptcoveff; z1++) 
         for(j=3; j <=ncovmodel; j++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                bool=0;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          }
             ij++;          if (bool==1){
           }            for(m=firstpass; m<=lastpass; m++){
           else              k2=anint[m][i]+(mint[m][i]/12.);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           fprintf(ficgp,")/(1");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                        if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         for(k1=1; k1 <=nlstate; k1++){                  if (m<lastpass) {
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 ij=1;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           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]]]);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
             ij++;                  dateintsum=dateintsum+k2;
           }                  k2cpt++;
           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,",");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         i=i+ncovmodel;        pstamp(ficresp);
        }        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]]);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          fprintf(ficresp, "**********\n#");
    }        }
            for(i=1; i<=nlstate;i++) 
   fclose(ficgp);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 }  /* end gnuplot */        fprintf(ficresp, "\n");
         
         for(i=iagemin; i <= iagemax+3; i++){
 /*************** Moving average **************/          if(i==iagemax+3){
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){            fprintf(ficlog,"Total");
           }else{
   int i, cpt, cptcod;            if(first==1){
     for (agedeb=agemin; agedeb<=fage; agedeb++)              first=0;
       for (i=1; i<=nlstate;i++)              printf("See log file for details...\n");
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            }
           mobaverage[(int)agedeb][i][cptcod]=0.;            fprintf(ficlog,"Age %d", i);
              }
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){          for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i<=nlstate;i++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              pp[jk] += freq[jk][m][i]; 
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for(jk=1; jk <=nlstate ; jk++){
           }            for(m=-1, pos=0; m <=0 ; m++)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              pos += freq[jk][m][i];
         }            if(pp[jk]>=1.e-10){
       }              if(first==1){
     }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
 }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
 /***********************************************/              if(first==1)
 /**************** Main Program *****************/                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /***********************************************/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 int main(int argc, char *argv[])          }
 {  
           for(jk=1; jk <=nlstate ; jk++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double agedeb, agefin,hf;              pp[jk] += freq[jk][m][i];
   double agemin=1.e20, agemax=-1.e20;          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double fret;            pos += pp[jk];
   double **xi,tmp,delta;            posprop += prop[jk][i];
           }
   double dum; /* Dummy variable */          for(jk=1; jk <=nlstate ; jk++){
   double ***p3mat;            if(pos>=1.e-5){
   int *indx;              if(first==1)
   char line[MAXLINE], linepar[MAXLINE];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char title[MAXLINE];              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];            }else{
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   char filerest[FILENAMELENGTH];            if( i <= iagemax){
   char fileregp[FILENAMELENGTH];              if(pos>=1.e-5){
   char popfile[FILENAMELENGTH];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                /*probs[i][jk][j1]= pp[jk]/pos;*/
   int firstobs=1, lastobs=10;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int sdeb, sfin; /* Status at beginning and end */              }
   int c,  h , cpt,l;              else
   int ju,jl, mi;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          }
   int mobilav=0,popforecast=0;          
   int hstepm, nhstepm;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int *popage;/*boolprev=0 if date and zero if wave*/            for(m=-1; m <=nlstate+ndeath; m++)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   double bage, fage, age, agelim, agebase;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double ftolpl=FTOL;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double **prlim;              }
   double *severity;          if(i <= iagemax)
   double ***param; /* Matrix of parameters */            fprintf(ficresp,"\n");
   double  *p;          if(first==1)
   double **matcov; /* Matrix of covariance */            printf("Others in log...\n");
   double ***delti3; /* Scale */          fprintf(ficlog,"\n");
   double *delti; /* Scale */        }
   double ***eij, ***vareij;      }
   double **varpl; /* Variances of prevalence limits by age */    }
   double *epj, vepp;    dateintmean=dateintsum/k2cpt; 
   double kk1, kk2;   
   double *popeffectif,*popcount;    fclose(ficresp);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   double yp,yp1,yp2;    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    /* End of Freq */
   char *alph[]={"a","a","b","c","d","e"}, str[4];  }
   
   /************ Prevalence ********************/
   char z[1]="c", occ;  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)
 #include <sys/time.h>  {  
 #include <time.h>    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   /* long total_usecs;    */
   struct timeval start_time, end_time;   
      int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double ***freq; /* Frequencies */
     double *pp, **prop;
     double pos,posprop; 
   printf("\n%s",version);    double  y2; /* in fractional years */
   if(argc <=1){    int iagemin, iagemax;
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    iagemin= (int) agemin;
   }    iagemax= (int) agemax;
   else{    /*pp=vector(1,nlstate);*/
     strcpy(pathtot,argv[1]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    j1=0;
   /*cygwin_split_path(pathtot,path,optionfile);    
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    j=cptcoveff;
   /* cutv(path,optionfile,pathtot,'\\');*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    for(k1=1; k1<=j;k1++){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      for(i1=1; i1<=ncodemax[k1];i1++){
   chdir(path);        j1++;
   replace(pathc,path);        
         for (i=1; i<=nlstate; i++)  
 /*-------- arguments in the command line --------*/          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
   strcpy(fileres,"r");       
   strcat(fileres, optionfilefiname);        for (i=1; i<=imx; i++) { /* Each individual */
   strcat(fileres,".txt");    /* Other files have txt extension */          bool=1;
           if  (cptcovn>0) {
   /*---------arguments file --------*/            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                bool=0;
     printf("Problem with optionfile %s\n",optionfile);          } 
     goto end;          if (bool==1) { 
   }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   strcpy(filereso,"o");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   strcat(filereso,fileres);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   if((ficparo=fopen(filereso,"w"))==NULL) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*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]]);*/
   /* Reads comments: lines beginning with '#' */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   while((c=getc(ficpar))=='#' && c!= EOF){                  prop[s[m][i]][iagemax+3] += weight[i]; 
     ungetc(c,ficpar);                } 
     fgets(line, MAXLINE, ficpar);              }
     puts(line);            } /* end selection of waves */
     fputs(line,ficparo);          }
   }        }
   ungetc(c,ficpar);        for(i=iagemin; i <= iagemax+3; i++){  
           
   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(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   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);            posprop += prop[jk][i]; 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          } 
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){     
     fgets(line, MAXLINE, ficpar);            if( i <=  iagemax){ 
     puts(line);              if(posprop>=1.e-5){ 
     fputs(line,ficparo);                probs[i][jk][j1]= prop[jk][i]/posprop;
   }              } else
   ungetc(c,ficpar);                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
              } 
              }/* end jk */ 
   covar=matrix(0,NCOVMAX,1,n);        }/* end i */ 
   cptcovn=0;      } /* end i1 */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    } /* end k1 */
     
   ncovmodel=2+cptcovn;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   /* Read guess parameters */  }  /* End of prevalence */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /************* Waves Concatenation ***************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, 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)
     puts(line);  {
     fputs(line,ficparo);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   }       Death is a valid wave (if date is known).
   ungetc(c,ficpar);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       and mw[mi+1][i]. dh depends on stepm.
     for(i=1; i <=nlstate; i++)       */
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int i, mi, m;
       fprintf(ficparo,"%1d%1d",i1,j1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       printf("%1d%1d",i,j);       double sum=0., jmean=0.;*/
       for(k=1; k<=ncovmodel;k++){    int first;
         fscanf(ficpar," %lf",&param[i][j][k]);    int j, k=0,jk, ju, jl;
         printf(" %lf",param[i][j][k]);    double sum=0.;
         fprintf(ficparo," %lf",param[i][j][k]);    first=0;
       }    jmin=1e+5;
       fscanf(ficpar,"\n");    jmax=-1;
       printf("\n");    jmean=0.;
       fprintf(ficparo,"\n");    for(i=1; i<=imx; i++){
     }      mi=0;
        m=firstpass;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   p=param[1][1];          mw[++mi][i]=m;
          if(m >=lastpass)
   /* Reads comments: lines beginning with '#' */          break;
   while((c=getc(ficpar))=='#' && c!= EOF){        else
     ungetc(c,ficpar);          m++;
     fgets(line, MAXLINE, ficpar);      }/* end while */
     puts(line);      if (s[m][i] > nlstate){
     fputs(line,ficparo);        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
   ungetc(c,ficpar);           /* Only death is a correct wave */
         mw[mi][i]=m;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){      wav[i]=mi;
     for(j=1; j <=nlstate+ndeath-1; j++){      if(mi==0){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        nbwarn++;
       printf("%1d%1d",i,j);        if(first==0){
       fprintf(ficparo,"%1d%1d",i1,j1);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       for(k=1; k<=ncovmodel;k++){          first=1;
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);        if(first==1){
         fprintf(ficparo," %le",delti3[i][j][k]);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
       fscanf(ficpar,"\n");      } /* end mi==0 */
       printf("\n");    } /* End individuals */
       fprintf(ficparo,"\n");  
     }    for(i=1; i<=imx; i++){
   }      for(mi=1; mi<wav[i];mi++){
   delti=delti3[1][1];        if (stepm <=0)
            dh[mi][i]=1;
   /* Reads comments: lines beginning with '#' */        else{
   while((c=getc(ficpar))=='#' && c!= EOF){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     ungetc(c,ficpar);            if (agedc[i] < 2*AGESUP) {
     fgets(line, MAXLINE, ficpar);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     puts(line);              if(j==0) j=1;  /* Survives at least one month after exam */
     fputs(line,ficparo);              else if(j<0){
   }                nberr++;
   ungetc(c,ficpar);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  j=1; /* Temporary Dangerous patch */
   matcov=matrix(1,npar,1,npar);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   for(i=1; i <=npar; i++){                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]);
     fscanf(ficpar,"%s",&str);                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);
     printf("%s",str);              }
     fprintf(ficparo,"%s",str);              k=k+1;
     for(j=1; j <=i; j++){              if (j >= jmax){
       fscanf(ficpar," %le",&matcov[i][j]);                jmax=j;
       printf(" %.5le",matcov[i][j]);                ijmax=i;
       fprintf(ficparo," %.5le",matcov[i][j]);              }
     }              if (j <= jmin){
     fscanf(ficpar,"\n");                jmin=j;
     printf("\n");                ijmin=i;
     fprintf(ficparo,"\n");              }
   }              sum=sum+j;
   for(i=1; i <=npar; i++)              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     for(j=i+1;j<=npar;j++)              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       matcov[i][j]=matcov[j][i];            }
              }
   printf("\n");          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     /*-------- data file ----------*/  
     if((ficres =fopen(fileres,"w"))==NULL) {            k=k+1;
       printf("Problem with resultfile: %s\n", fileres);goto end;            if (j >= jmax) {
     }              jmax=j;
     fprintf(ficres,"#%s\n",version);              ijmax=i;
                }
     if((fic=fopen(datafile,"r"))==NULL)    {            else if (j <= jmin){
       printf("Problem with datafile: %s\n", datafile);goto end;              jmin=j;
     }              ijmin=i;
             }
     n= lastobs;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     severity = vector(1,maxwav);            /*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]);*/
     outcome=imatrix(1,maxwav+1,1,n);            if(j<0){
     num=ivector(1,n);              nberr++;
     moisnais=vector(1,n);              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]);
     annais=vector(1,n);              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]);
     moisdc=vector(1,n);            }
     andc=vector(1,n);            sum=sum+j;
     agedc=vector(1,n);          }
     cod=ivector(1,n);          jk= j/stepm;
     weight=vector(1,n);          jl= j -jk*stepm;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          ju= j -(jk+1)*stepm;
     mint=matrix(1,maxwav,1,n);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     anint=matrix(1,maxwav,1,n);            if(jl==0){
     s=imatrix(1,maxwav+1,1,n);              dh[mi][i]=jk;
     adl=imatrix(1,maxwav+1,1,n);                  bh[mi][i]=0;
     tab=ivector(1,NCOVMAX);            }else{ /* We want a negative bias in order to only have interpolation ie
     ncodemax=ivector(1,8);                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
     i=1;              bh[mi][i]=ju;
     while (fgets(line, MAXLINE, fic) != NULL)    {            }
       if ((i >= firstobs) && (i <=lastobs)) {          }else{
                    if(jl <= -ju){
         for (j=maxwav;j>=1;j--){              dh[mi][i]=jk;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              bh[mi][i]=jl;       /* bias is positive if real duration
           strcpy(line,stra);                                   * is higher than the multiple of stepm and negative otherwise.
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                                   */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }
         }            else{
                      dh[mi][i]=jk+1;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            }
             if(dh[mi][i]==0){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              dh[mi][i]=1; /* At least one step */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         for (j=ncov;j>=1;j--){          } /* end if mle */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
         }      } /* end wave */
         num[i]=atol(stra);    }
            jmean=sum/k;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    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);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
    }
         i=i+1;  
       }  /*********** Tricode ****************************/
     }  void tricode(int *Tvar, int **nbcode, int imx)
     /* printf("ii=%d", ij);  {
        scanf("%d",i);*/    
   imx=i-1; /* Number of individuals */    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
   /* for (i=1; i<=imx; i++){    cptcoveff=0; 
     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;    for (k=0; k<maxncov; k++) Ndum[k]=0;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    for (k=1; k<=7; k++) ncodemax[k]=0;
     }  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for (i=1; i<=imx; i++)      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     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]));*/                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   /* Calculation of the number of parameter from char model*/        Ndum[ij]++; /*store the modality */
   Tvar=ivector(1,15);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   Tprod=ivector(1,15);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   Tvaraff=ivector(1,15);                                         Tvar[j]. If V=sex and male is 0 and 
   Tvard=imatrix(1,15,1,2);                                         female is 1, then  cptcode=1.*/
   Tage=ivector(1,15);            }
      
   if (strlen(model) >1){      for (i=0; i<=cptcode; i++) {
     j=0, j1=0, k1=1, k2=1;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
     j=nbocc(model,'+');      }
     j1=nbocc(model,'*');  
     cptcovn=j+1;      ij=1; 
     cptcovprod=j1;      for (i=1; i<=ncodemax[j]; i++) {
            for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
     strcpy(modelsav,model);            nbcode[Tvar[j]][ij]=k; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            /* store the modality in an array. 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; */
       printf("Error. Non available option model=%s ",model);            
       goto end;            ij++;
     }          }
              if (ij > ncodemax[j]) break; 
     for(i=(j+1); i>=1;i--){        }  
       cutv(stra,strb,modelsav,'+');      } 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    }  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/   for (k=0; k< maxncov; k++) Ndum[k]=0;
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');   for (i=1; i<=ncovmodel-2; i++) { 
         if (strcmp(strc,"age")==0) {     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           cptcovprod--;     ij=Tvar[i];
           cutv(strb,stre,strd,'V');     Ndum[ij]++;
           Tvar[i]=atoi(stre);   }
           cptcovage++;  
             Tage[cptcovage]=i;   ij=1;
             /*printf("stre=%s ", stre);*/   for (i=1; i<= maxncov; i++) {
         }     if((Ndum[i]!=0) && (i<=ncovcol)){
         else if (strcmp(strd,"age")==0) {       Tvaraff[ij]=i; /*For printing */
           cptcovprod--;       ij++;
           cutv(strb,stre,strc,'V');     }
           Tvar[i]=atoi(stre);   }
           cptcovage++;   
           Tage[cptcovage]=i;   cptcoveff=ij-1; /*Number of simple covariates*/
         }  }
         else {  
           cutv(strb,stre,strc,'V');  /*********** Health Expectancies ****************/
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);  {
           Tvard[k1][2]=atoi(stre);    /* Health expectancies, no variances */
           Tvar[cptcovn+k2]=Tvard[k1][1];    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int nhstepma, nstepma; /* Decreasing with age */
           for (k=1; k<=lastobs;k++)    double age, agelim, hf;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    double ***p3mat;
           k1++;    double eip;
           k2=k2+2;  
         }    pstamp(ficreseij);
       }    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");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    for(i=1; i<=nlstate;i++){
        /*  scanf("%d",i);*/      for(j=1; j<=nlstate;j++){
       cutv(strd,strc,strb,'V');        fprintf(ficreseij," e%1d%1d ",i,j);
       Tvar[i]=atoi(strc);      }
       }      fprintf(ficreseij," e%1d. ",i);
       strcpy(modelsav,stra);      }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    fprintf(ficreseij,"\n");
         scanf("%d",i);*/  
     }    
 }    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    }
   printf("cptcovprod=%d ", cptcovprod);    else  hstepm=estepm;   
   scanf("%d ",i);*/    /* We compute the life expectancy from trapezoids spaced every estepm months
     fclose(fic);     * 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
     /*  if(mle==1){*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
     if (weightopt != 1) { /* Maximisation without weights*/     * progression in between and thus overestimating or underestimating according
       for(i=1;i<=n;i++) weight[i]=1.0;     * to the curvature of the survival function. If, for the same date, we 
     }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     /*-calculation of age at interview from date of interview and age at death -*/     * to compare the new estimate of Life expectancy with the same linear 
     agev=matrix(1,maxwav,1,imx);     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
    for (i=1; i<=imx; i++)  
      for(m=2; (m<= maxwav); m++)    /* For example we decided to compute the life expectancy with the smallest unit */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
          anint[m][i]=9999;       nhstepm is the number of hstepm from age to agelim 
          s[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 */
     for (i=1; i<=imx; i++)  {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[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] >0){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           if (s[m][i] == nlstate+1) {       results. So we changed our mind and took the option of the best precision.
             if(agedc[i]>0)    */
               if(moisdc[i]!=99 && andc[i]!=9999)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               agev[m][i]=agedc[i];  
             else {    agelim=AGESUP;
               if (andc[i]!=9999){    /* If stepm=6 months */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
               agev[m][i]=-1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
               }      
             }  /* nhstepm age range expressed in number of stepm */
           }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           else if(s[m][i] !=9){ /* Should no more exist */    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /* if (stepm >= YEARM) hstepm=1;*/
             if(mint[m][i]==99 || anint[m][i]==9999)    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               agev[m][i]=1;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    for (age=bage; age<=fage; age ++){ 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             else if(agev[m][i] >agemax){      /* if (stepm >= YEARM) hstepm=1;*/
               agemax=agev[m][i];      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }      /* If stepm=6 months */
             /*agev[m][i]=anint[m][i]-annais[i];*/      /* Computed by stepm unit matrices, product of hstepma matrices, stored
             /*   agev[m][i] = age[i]+2*m;*/         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           }      
           else { /* =9 */      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
             agev[m][i]=1;      
             s[m][i]=-1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           }      
         }      printf("%d|",(int)age);fflush(stdout);
         else /*= 0 Unknown */      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           agev[m][i]=1;      
       }      /* Computing expectancies */
          for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++)
     for (i=1; i<=imx; i++)  {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for(m=1; (m<= maxwav); m++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         if (s[m][i] > (nlstate+ndeath)) {            
           printf("Error: Wrong value in nlstate or ndeath\n");              /* 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]);*/
           goto end;  
         }          }
       }  
     }      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        eip=0;
         for(j=1; j<=nlstate;j++){
     free_vector(severity,1,maxwav);          eip +=eij[i][j][(int)age];
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     free_vector(moisnais,1,n);        }
     free_vector(annais,1,n);        fprintf(ficreseij,"%9.4f", eip );
     /* free_matrix(mint,1,maxwav,1,n);      }
        free_matrix(anint,1,maxwav,1,n);*/      fprintf(ficreseij,"\n");
     free_vector(moisdc,1,n);      
     free_vector(andc,1,n);    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        printf("\n");
     wav=ivector(1,imx);    fprintf(ficlog,"\n");
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  }
      
     /* Concatenates waves */  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[] )
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
   {
     /* Covariances of health expectancies eij and of total life expectancies according
       Tcode=ivector(1,100);     to initial status i, ei. .
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    */
       ncodemax[1]=1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    int nhstepma, nstepma; /* Decreasing with age */
          double age, agelim, hf;
    codtab=imatrix(1,100,1,10);    double ***p3matp, ***p3matm, ***varhe;
    h=0;    double **dnewm,**doldm;
    m=pow(2,cptcoveff);    double *xp, *xm;
      double **gp, **gm;
    for(k=1;k<=cptcoveff; k++){    double ***gradg, ***trgradg;
      for(i=1; i <=(m/pow(2,k));i++){    int theta;
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    double eip, vip;
            h++;  
            if (h>m) h=1;codtab[h][k]=j;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
          }    xp=vector(1,npar);
        }    xm=vector(1,npar);
      }    dnewm=matrix(1,nlstate*nlstate,1,npar);
    }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
    /*for(i=1; i <=m ;i++){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
      for(k=1; k <=cptcovn; k++){    fprintf(ficresstdeij,"# Age");
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    for(i=1; i<=nlstate;i++){
      }      for(j=1; j<=nlstate;j++)
      printf("\n");        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
    }      fprintf(ficresstdeij," e%1d. ",i);
    scanf("%d",i);*/    }
        fprintf(ficresstdeij,"\n");
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */    pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
        fprintf(ficrescveij,"# Age");
        for(i=1; i<=nlstate;i++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(j=1; j<=nlstate;j++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        cptj= (j-1)*nlstate+i;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i2=1; i2<=nlstate;i2++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(j2=1; j2<=nlstate;j2++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            cptj2= (j2-1)*nlstate+i2;
                  if(cptj2 <= cptj)
     /* For Powell, parameters are in a vector p[] starting at p[1]              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
        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) */      }
     fprintf(ficrescveij,"\n");
     if(mle==1){    
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
        }
     /*--------- results files --------------*/    else  hstepm=estepm;   
     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);    /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
    jk=1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
    fprintf(ficres,"# Parameters\n");     * progression in between and thus overestimating or underestimating according
    printf("# Parameters\n");     * to the curvature of the survival function. If, for the same date, we 
    for(i=1,jk=1; i <=nlstate; i++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      for(k=1; k <=(nlstate+ndeath); k++){     * to compare the new estimate of Life expectancy with the same linear 
        if (k != i)     * hypothesis. A more precise result, taking into account a more precise
          {     * curvature will be obtained if estepm is as small as stepm. */
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    /* For example we decided to compute the life expectancy with the smallest unit */
            for(j=1; j <=ncovmodel; j++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
              printf("%f ",p[jk]);       nhstepm is the number of hstepm from age to agelim 
              fprintf(ficres,"%f ",p[jk]);       nstepm is the number of stepm from age to agelin. 
              jk++;       Look at hpijx to understand the reason of that which relies in memory size
            }       and note for a fixed period like estepm months */
            printf("\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
            fprintf(ficres,"\n");       survival function given by stepm (the optimization length). Unfortunately it
          }       means that if the survival funtion is printed only each two years of age and if
      }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    }       results. So we changed our mind and took the option of the best precision.
  if(mle==1){    */
     /* Computing hessian and covariance matrix */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);    /* If stepm=6 months */
  }    /* nhstepm age range expressed in number of stepm */
     fprintf(ficres,"# Scales\n");    agelim=AGESUP;
     printf("# Scales\n");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
      for(i=1,jk=1; i <=nlstate; i++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(j=1; j <=nlstate+ndeath; j++){    /* if (stepm >= YEARM) hstepm=1;*/
         if (j!=i) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           fprintf(ficres,"%1d%1d",i,j);    
           printf("%1d%1d",i,j);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(k=1; k<=ncovmodel;k++){    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             printf(" %.5e",delti[jk]);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
             fprintf(ficres," %.5e",delti[jk]);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
             jk++;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
           }    gm=matrix(0,nhstepm,1,nlstate*nlstate);
           printf("\n");  
           fprintf(ficres,"\n");    for (age=bage; age<=fage; age ++){ 
         }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      }      /* if (stepm >= YEARM) hstepm=1;*/
          nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     k=1;  
     fprintf(ficres,"# Covariance\n");      /* If stepm=6 months */
     printf("# Covariance\n");      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     for(i=1;i<=npar;i++){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       /*  if (k>nlstate) k=1;      
       i1=(i-1)/(ncovmodel*nlstate)+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/      /* Computing  Variances of health expectancies */
       fprintf(ficres,"%3d",i);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       printf("%3d",i);         decrease memory allocation */
       for(j=1; j<=i;j++){      for(theta=1; theta <=npar; theta++){
         fprintf(ficres," %.5e",matcov[i][j]);        for(i=1; i<=npar; i++){ 
         printf(" %.5e",matcov[i][j]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficres,"\n");        }
       printf("\n");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       k++;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     }    
            for(j=1; j<= nlstate; j++){
     while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1; i<=nlstate; i++){
       ungetc(c,ficpar);            for(h=0; h<=nhstepm-1; h++){
       fgets(line, MAXLINE, ficpar);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
       puts(line);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       fputs(line,ficparo);            }
     }          }
     ungetc(c,ficpar);        }
         
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        for(ij=1; ij<= nlstate*nlstate; ij++)
              for(h=0; h<=nhstepm-1; h++){
     if (fage <= 2) {            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       bage = agemin;          }
       fage = agemax;      }/* End theta */
     }      
          
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for(h=0; h<=nhstepm-1; h++)
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        for(j=1; j<=nlstate*nlstate;j++)
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
     while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);       for(ij=1;ij<=nlstate*nlstate;ij++)
     puts(line);        for(ji=1;ji<=nlstate*nlstate;ji++)
     fputs(line,ficparo);          varhe[ij][ji][(int)age] =0.;
   }  
   ungetc(c,ficpar);       printf("%d|",(int)age);fflush(stdout);
         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);       for(h=0;h<=nhstepm-1;h++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(k=0;k<=nhstepm-1;k++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
                matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   while((c=getc(ficpar))=='#' && c!= EOF){          for(ij=1;ij<=nlstate*nlstate;ij++)
     ungetc(c,ficpar);            for(ji=1;ji<=nlstate*nlstate;ji++)
     fgets(line, MAXLINE, ficpar);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     puts(line);        }
     fputs(line,ficparo);      }
   }  
   ungetc(c,ficpar);      /* Computing expectancies */
        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        for(j=1; j<=nlstate;j++)
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          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;
   fscanf(ficpar,"pop_based=%d\n",&popbased);            
    fprintf(ficparo,"pop_based=%d\n",popbased);              /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
    fprintf(ficres,"pop_based=%d\n",popbased);    
           }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(ficresstdeij,"%3.0f",age );
     fgets(line, MAXLINE, ficpar);      for(i=1; i<=nlstate;i++){
     puts(line);        eip=0.;
     fputs(line,ficparo);        vip=0.;
   }        for(j=1; j<=nlstate;j++){
   ungetc(c,ficpar);          eip += eij[i][j][(int)age];
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mob_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
 /*------------ gnuplot -------------*/      fprintf(ficresstdeij,"\n");
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);  
        fprintf(ficrescveij,"%3.0f",age );
 /*------------ free_vector  -------------*/      for(i=1; i<=nlstate;i++)
  chdir(path);        for(j=1; j<=nlstate;j++){
            cptj= (j-1)*nlstate+i;
  free_ivector(wav,1,imx);          for(i2=1; i2<=nlstate;i2++)
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            for(j2=1; j2<=nlstate;j2++){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                cptj2= (j2-1)*nlstate+i2;
  free_ivector(num,1,n);              if(cptj2 <= cptj)
  free_vector(agedc,1,n);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            }
  fclose(ficparo);        }
  fclose(ficres);      fprintf(ficrescveij,"\n");
       
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     ungetc(c,ficpar);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     fgets(line, MAXLINE, ficpar);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     puts(line);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     fputs(line,ficparo);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);    printf("\n");
      fprintf(ficlog,"\n");
   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);    free_vector(xm,1,npar);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    free_vector(xp,1,npar);
 /*--------- index.htm --------*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
    
   /*--------------- Prevalence limit --------------*/  /************ Variance ******************/
    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   strcpy(filerespl,"pl");  {
   strcat(filerespl,fileres);    /* Variance of health expectancies */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    /* double **newm;*/
   }    double **dnewm,**doldm;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double **dnewmp,**doldmp;
   fprintf(ficrespl,"#Prevalence limit\n");    int i, j, nhstepm, hstepm, h, nstepm ;
   fprintf(ficrespl,"#Age ");    int k, cptcode;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double *xp;
   fprintf(ficrespl,"\n");    double **gp, **gm;  /* for var eij */
      double ***gradg, ***trgradg; /*for var eij */
   prlim=matrix(1,nlstate,1,nlstate);    double **gradgp, **trgradgp; /* for var p point j */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *gpp, *gmp; /* for var p point j */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***p3mat;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double age,agelim, hf;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double ***mobaverage;
   k=0;    int theta;
   agebase=agemin;    char digit[4];
   agelim=agemax;    char digitp[25];
   ftolpl=1.e-10;  
   i1=cptcoveff;    char fileresprobmorprev[FILENAMELENGTH];
   if (cptcovn < 1){i1=1;}  
     if(popbased==1){
   for(cptcov=1;cptcov<=i1;cptcov++){      if(mobilav!=0)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        strcpy(digitp,"-populbased-mobilav-");
         k=k+1;      else strcpy(digitp,"-populbased-nomobil-");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    else 
         for(j=1;j<=cptcoveff;j++)      strcpy(digitp,"-stablbased-");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");    if (mobilav!=0) {
              mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for (age=agebase; age<=agelim; age++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficrespl,"%.0f",age );        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           for(i=1; i<=nlstate;i++)      }
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");  
         }    strcpy(fileresprobmorprev,"prmorprev"); 
       }    sprintf(digit,"%-d",ij);
     }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   fclose(ficrespl);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   /*------------- h Pij x at various ages ------------*/    strcat(fileresprobmorprev,fileres);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    }
   }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   printf("Computing pij: result on file '%s' \n", filerespij);   
      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    pstamp(ficresprobmorprev);
   /*if (stepm<=24) stepsize=2;*/    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);
   agelim=AGESUP;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   hstepm=stepsize*YEARM; /* Every year of age */      fprintf(ficresprobmorprev," p.%-d SE",j);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   k=0;    }  
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresprobmorprev,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\n# Routine varevsij");
       k=k+1;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         fprintf(ficrespij,"\n#****** ");    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");
         for(j=1;j<=cptcoveff;j++)    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   } */
         fprintf(ficrespij,"******\n");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            pstamp(ficresvij);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if(popbased==1)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    else
           oldm=oldms;savm=savms;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresvij,"# Age");
           fprintf(ficrespij,"# Age");    for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)      for(j=1; j<=nlstate;j++)
             for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficresvij,"\n");
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){    xp=vector(1,npar);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    dnewm=matrix(1,nlstate,1,npar);
             for(i=1; i<=nlstate;i++)    doldm=matrix(1,nlstate,1,nlstate);
               for(j=1; j<=nlstate+ndeath;j++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficrespij,"\n");  
           }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    gpp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficrespij,"\n");    gmp=vector(nlstate+1,nlstate+ndeath);
         }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     }    
   }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    }
     else  hstepm=estepm;   
   fclose(ficrespij);    /* 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. 
   if(stepm == 1) {       nhstepm is the number of hstepm from age to agelim 
   /*---------- Forecasting ------------------*/       nstepm is the number of stepm from age to agelin. 
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;       Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /*printf("calage= %f", calagedate);*/       survival function given by stepm (the optimization length). Unfortunately it
         means that if the survival funtion is printed every two years of age and if
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
   strcpy(fileresf,"f");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   strcat(fileresf,fileres);    agelim = AGESUP;
   if((ficresf=fopen(fileresf,"w"))==NULL) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   printf("Computing forecasting: result on file '%s' \n", fileresf);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   free_matrix(mint,1,maxwav,1,n);      gp=matrix(0,nhstepm,1,nlstate);
   free_matrix(anint,1,maxwav,1,n);      gm=matrix(0,nhstepm,1,nlstate);
   free_matrix(agev,1,maxwav,1,imx);  
   
   /* Mobile average */      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   if (mobilav==1) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }        if (popbased==1) {
           if(mobilav ==0){
   stepsize=(int) (stepm+YEARM-1)/YEARM;            for(i=1; i<=nlstate;i++)
   if (stepm<=12) stepsize=1;              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   agelim=AGESUP;            for(i=1; i<=nlstate;i++)
   /*hstepm=stepsize*YEARM; *//* Every year of age */              prlim[i][i]=mobaverage[(int)age][i][ij];
   hstepm=1;          }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        }
   yp1=modf(dateintmean,&yp);    
   anprojmean=yp;        for(j=1; j<= nlstate; j++){
   yp2=modf((yp1*12),&yp);          for(h=0; h<=nhstepm; h++){
   mprojmean=yp;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   yp1=modf((yp2*30.5),&yp);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   jprojmean=yp;          }
   if(jprojmean==0) jprojmean=1;        }
   if(mprojmean==0) jprojmean=1;        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);           as a weighted average of prlim.
         */
   if (popforecast==1) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     if((ficpop=fopen(popfile,"r"))==NULL)    {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       printf("Problem with population file : %s\n",popfile);goto end;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }        }    
     popage=ivector(0,AGESUP);        /* end probability of death */
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
     i=1;          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       {   
         i=i+1;        if (popbased==1) {
       }          if(mobilav ==0){
     imx=i;            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
       k=k+1;  
       fprintf(ficresf,"\n#******");        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
       for(j=1;j<=cptcoveff;j++) {          for(h=0; h<=nhstepm; h++){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficresf,"******\n");          }
       fprintf(ficresf,"# StartingAge FinalAge");        }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        /* This for computing probability of death (h=1 means
       if (popforecast==1)  fprintf(ficresf," [Population]");           computed over hstepm matrices product = hstepm*stepm months) 
                 as a weighted average of prlim.
      for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        */
         fprintf(ficresf,"\n");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        }    
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        /* end probability of death */
         nhstepm = nhstepm/hstepm;  
                for(j=1; j<= nlstate; j++) /* vareij */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(h=0; h<=nhstepm; h++){
         oldm=oldms;savm=savms;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
          
         for (h=0; h<=nhstepm; h++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           if (h==(int) (calagedate+YEARM*cpt)) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        }
           }  
           for(j=1; j<=nlstate+ndeath;j++) {      } /* End theta */
             kk1=0.;kk2=0;  
             for(i=1; i<=nlstate;i++) {              trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
               if (mobilav==1)  
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for(h=0; h<=nhstepm; h++) /* veij */
               else {        for(j=1; j<=nlstate;j++)
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for(theta=1; theta <=npar; theta++)
                            trgradg[h][j][theta]=gradg[h][theta][j];
               }  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];        for(theta=1; theta <=npar; theta++)
             }          trgradgp[j][theta]=gradgp[theta][j];
              
             if (h==(int)(calagedate+12*cpt)){  
               fprintf(ficresf," %.3f", kk1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                    for(i=1;i<=nlstate;i++)
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);        for(j=1;j<=nlstate;j++)
             }          vareij[i][j][(int)age] =0.;
           }  
         }      for(h=0;h<=nhstepm;h++){
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(k=0;k<=nhstepm;k++){
         }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     }          for(i=1;i<=nlstate;i++)
   }            for(j=1;j<=nlstate;j++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   if (popforecast==1) {      }
     free_ivector(popage,0,AGESUP);    
     free_vector(popeffectif,0,AGESUP);      /* pptj */
     free_vector(popcount,0,AGESUP);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   free_imatrix(s,1,maxwav+1,1,n);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   free_vector(weight,1,n);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   fclose(ficresf);          varppt[j][i]=doldmp[j][i];
   }/* End forecasting */      /* end ppptj */
   else{      /*  x centered again */
     erreur=108;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     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);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
   }      if (popbased==1) {
         if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   /*---------- Health expectancies and variances ------------*/            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
   strcpy(filerest,"t");          for(i=1; i<=nlstate;i++)
   strcat(filerest,fileres);            prlim[i][i]=mobaverage[(int)age][i][ij];
   if((ficrest=fopen(filerest,"w"))==NULL) {        }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      }
   }               
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
   strcpy(filerese,"e");      */
   strcat(filerese,fileres);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if((ficreseij=fopen(filerese,"w"))==NULL) {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   }      }    
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      /* end probability of death */
   
  strcpy(fileresv,"v");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   strcat(fileresv,fileres);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        }
       } 
   k=0;      fprintf(ficresprobmorprev,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficresvij,"%.0f ",age );
       k=k+1;      for(i=1; i<=nlstate;i++)
       fprintf(ficrest,"\n#****** ");        for(j=1; j<=nlstate;j++){
       for(j=1;j<=cptcoveff;j++)          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       fprintf(ficrest,"******\n");      fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       fprintf(ficreseij,"\n#****** ");      free_matrix(gm,0,nhstepm,1,nlstate);
       for(j=1;j<=cptcoveff;j++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       fprintf(ficreseij,"******\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
       fprintf(ficresvij,"\n#****** ");    free_vector(gpp,nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++)    free_vector(gmp,nlstate+1,nlstate+ndeath);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       fprintf(ficresvij,"******\n");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       oldm=oldms;savm=savms;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       oldm=oldms;savm=savms;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
          fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",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(ficrest,"\n");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
            /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       hf=1;  */
       if (stepm >= YEARM) hf=stepm/YEARM;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       epj=vector(1,nlstate+1);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_vector(xp,1,npar);
         if (popbased==1) {    free_matrix(doldm,1,nlstate,1,nlstate);
           for(i=1; i<=nlstate;i++)    free_matrix(dnewm,1,nlstate,1,npar);
             prlim[i][i]=probs[(int)age][i][k];    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
            free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrest," %.0f",age);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fclose(ficresprobmorprev);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    fflush(ficgp);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    fflush(fichtm); 
           }  }  /* end varevsij */
           epj[nlstate+1] +=epj[j];  
         }  /************ Variance of prevlim ******************/
         for(i=1, vepp=0.;i <=nlstate;i++)  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[])
           for(j=1;j <=nlstate;j++)  {
             vepp += vareij[i][j][(int)age];    /* Variance of prevalence limit */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         for(j=1;j <=nlstate;j++){    double **newm;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
         fprintf(ficrest,"\n");    int k, cptcode;
       }    double *xp;
     }    double *gp, *gm;
   }    double **gradg, **trgradg;
            double age,agelim;
            int theta;
     
     pstamp(ficresvpl);
  fclose(ficreseij);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
  fclose(ficresvij);    fprintf(ficresvpl,"# Age");
   fclose(ficrest);    for(i=1; i<=nlstate;i++)
   fclose(ficpar);        fprintf(ficresvpl," %1d-%1d",i,i);
   free_vector(epj,1,nlstate+1);    fprintf(ficresvpl,"\n");
   /*  scanf("%d ",i); */  
     xp=vector(1,npar);
   /*------- Variance limit prevalence------*/      dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
 strcpy(fileresvpl,"vpl");    
   strcat(fileresvpl,fileres);    hstepm=1*YEARM; /* Every year of age */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    agelim = AGESUP;
     exit(0);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
  k=0;      gradg=matrix(1,npar,1,nlstate);
  for(cptcov=1;cptcov<=i1;cptcov++){      gp=vector(1,nlstate);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      gm=vector(1,nlstate);
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");      for(theta=1; theta <=npar; theta++){
      for(j=1;j<=cptcoveff;j++)        for(i=1; i<=npar; i++){ /* Computes gradient */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      fprintf(ficresvpl,"******\n");        }
              prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        for(i=1;i<=nlstate;i++)
      oldm=oldms;savm=savms;          gp[i] = prlim[i][i];
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      
    }        for(i=1; i<=npar; i++) /* Computes gradient */
  }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   fclose(ficresvpl);        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        for(i=1;i<=nlstate;i++)
            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      } /* End theta */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
        trgradg =matrix(1,nlstate,1,npar);
    
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      for(j=1; j<=nlstate;j++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(theta=1; theta <=npar; theta++)
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          trgradg[j][theta]=gradg[theta][j];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
        for(i=1;i<=nlstate;i++)
   free_matrix(matcov,1,npar,1,npar);        varpl[i][(int)age] =0.;
   free_vector(delti,1,npar);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   if(erreur >0)  
     printf("End of Imach with error %d\n",erreur);      fprintf(ficresvpl,"%.0f ",age );
   else   printf("End of Imach\n");      for(i=1; i<=nlstate;i++)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        fprintf(ficresvpl,"\n");
   /* 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);*/      free_vector(gp,1,nlstate);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      free_vector(gm,1,nlstate);
   /*------ End -----------*/      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
  end:  
 #ifdef windows    free_vector(xp,1,npar);
   /* chdir(pathcd);*/    free_matrix(doldm,1,nlstate,1,npar);
 #endif    free_matrix(dnewm,1,nlstate,1,nlstate);
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/  }
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  /************ Variance of one-step probabilities  ******************/
  strcpy(plotcmd,GNUPLOTPROGRAM);  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[])
  strcat(plotcmd," ");  {
  strcat(plotcmd,optionfilegnuplot);    int i, j=0,  i1, k1, l1, t, tj;
  system(plotcmd);    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
 #ifdef windows    int first=1, first1;
   while (z[0] != 'q') {    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     chdir(path);    double **dnewm,**doldm;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    double *xp;
     scanf("%s",z);    double *gp, *gm;
     if (z[0] == 'c') system("./imach");    double **gradg, **trgradg;
     else if (z[0] == 'e') {    double **mu;
       chdir(path);    double age,agelim, cov[NCOVMAX];
       system(optionfilehtm);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     }    int theta;
     else if (z[0] == 'q') exit(0);    char fileresprob[FILENAMELENGTH];
   }    char fileresprobcov[FILENAMELENGTH];
 #endif    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,"\nset noparametric;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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   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 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;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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++){
         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);
     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;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         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 '%d' at line number %d %s 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);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     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(1,15); /* 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; 
       cptcovprod=j1; /*Number of products */
       
       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);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         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 */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*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 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             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);  
         /*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 */
   
     Tcode=ivector(1,100);
     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++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             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 \n",h, k,j,codtab[h][k],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 */
     
       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;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           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 */
     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_ivector(Tcode,1,100);
   
       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.1.25  
changed lines
  Added in v.1.128


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